%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
%% Created for Spencer Smith at 2023-03-23 10:22:24 -0400
%% Saved with string encoding Unicode (UTF-8)
@article{UsmanEtAl2017,
author = {Usman, Muhammad and Iqbal, Muhammad Zohaib and Khan, Muhammad Uzair},
date-added = {2023-03-23 10:22:22 -0400},
date-modified = {2023-03-23 10:22:22 -0400},
doi = {10.1016/j.jss.2016.09.049},
journal = {Journal of Systems and Software},
month = {01},
pages = {1-32},
title = {A Product-line Model-driven Engineering Approach for Generating Feature-based Mobile Applications},
volume = {123},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1016/j.jss.2016.09.049}}
@inproceedings{Robillard2021,
abstract = {When contributors to a software project leave, the knowledge they hold may become lost, thus impacting code quality and team productivity. Although well-known strategies can be used to mitigate knowledge loss, these strategies have to be tailored to their target context to be effective. To help software development organizations mitigate turnover-induced knowledge loss, we sought to better understand the different contexts in which developers experience this knowledge loss, and the resulting implications. We conducted qualitative interviews with 27 professional developers and managers from three different companies that provide software products and services. Leveraging the experience of these practitioners, we contribute a framework for characterizing turnover-induced knowledge loss and descriptions of the implications of knowledge loss, synthesized into 20 observations. These observations about knowledge loss in practice are organized into four themes, validated by the participants, and discussed within the context of the research literature in software engineering.},
address = {New York, NY, USA},
author = {Robillard, Martin P.},
booktitle = {Proceedings of the 29th ACM Joint Meeting on European Software Engineering Conference and Symposium on the Foundations of Software Engineering},
doi = {10.1145/3468264.3473923},
isbn = {9781450385626},
keywords = {documentation, Knowledge loss, knowledge management, knowledge sharing},
location = {Athens, Greece},
numpages = {11},
pages = {1292--1302},
publisher = {Association for Computing Machinery},
series = {ESEC/FSE 2021},
title = {Turnover-Induced Knowledge Loss in Practice},
url = {https://doi.org/10.1145/3468264.3473923},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1145/3468264.3473923}}
@inproceedings{CaretteEtAl2022-Eelco,
address = {Delft},
author = {Jacques Carette and Spencer Smith and Jason Balaci},
booktitle = {Eelco Visser Commemorative Symposium},
date-added = {2022-10-31 09:04:21 -0400},
date-modified = {2022-10-31 14:02:17 -0400},
pages = {1--8},
title = {Generating Software for Well-Understood Domains},
year = {Submitted 2022},
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@inproceedings{CaretteEtAl2022,
author = {Jacques Carette and Spencer Smith and Jason Balaci},
booktitle = {Proceedings of Eelco Visser Commemorative Symposium},
date-added = {2022-10-21 15:00:39 -0400},
date-modified = {2022-10-21 15:04:42 -0400},
month = {October},
pages = {1--8},
title = {When Capturing Knowledge Improves Productivity},
year = {Submitted 2022}}
@article{SmithEtAl2022_MISOP,
author = {Spencer Smith and Ao Dong and Jacques Carette and Michael Noseworthy},
date-added = {2022-10-21 14:27:54 -0400},
date-modified = {2022-10-21 14:36:30 -0400},
journal = {Archives of Computational Methods in Engineering},
pages = {1--44},
title = {State of the Practice for Medical Imaging Software},
year = {Submitted 2022},
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@manual{Ward2000,
author = {B. Douglas Ward},
date-added = {2022-10-17 14:46:39 -0400},
date-modified = {2022-10-17 14:46:39 -0400},
month = {April},
organization = {Biophysics Research Institute, Medical College of Wisconsin},
title = {Program 3dfim+},
url = {https://afni.nimh.nih.gov/afni/doc/manual/3dfim+.pdf},
year = {2000},
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bdsk-url-1 = {https://afni.nimh.nih.gov/afni/doc/manual/3dfim+.pdf}}
@article{Fagan1976,
author = {Fagan, M. E.},
date-added = {2022-10-17 11:10:33 -0400},
date-modified = {2022-10-17 11:12:59 -0400},
doi = {10.1147/sj.153.0182},
journal = {IBM Systems Journal},
number = {3},
pages = {182-211},
title = {Design and code inspections to reduce errors in program development},
volume = {15},
year = {1976},
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bdsk-url-1 = {https://doi.org/10.1147/sj.153.0182}}
@inproceedings{RigbyAndBird2013,
abstract = {Software peer review is practiced on a diverse set of software projects that have drastically different settings, cultures, incentive systems, and time pressures. In an effort to characterize and understand these differences we examine two Google-led projects, Android and Chromium OS, three Microsoft projects, Bing, Office, and MS SQL, and projects internal to AMD. We contrast our findings with data taken from traditional software inspection conducted on a Lucent project and from open source software peer review on six projects, including Apache, Linux, and KDE. Our measures of interest include the review interval, the number of developers involved in review, and proxy measures for the number of defects found during review. We find that despite differences among projects, many of the characteristics of the review process have independently converged to similar values which we think indicate general principles of code review practice. We also introduce a measure of the degree to which knowledge is shared during review. This is an aspect of review practice that has traditionally only had experiential support. Our knowledge sharing measure shows that conducting peer review increases the number of distinct files a developer knows about by 66% to 150% depending on the project. This paper is one of the first studies of contemporary review in software firms and the most diverse study of peer review to date.},
address = {New York, NY, USA},
author = {Rigby, Peter C. and Bird, Christian},
booktitle = {Proceedings of the 2013 9th Joint Meeting on Foundations of Software Engineering},
date-added = {2022-10-17 11:07:51 -0400},
date-modified = {2022-10-17 11:08:21 -0400},
doi = {10.1145/2491411.2491444},
isbn = {9781450322379},
keywords = {Inspection, Empirical Software Engineering, Open source software, Software firms, Peer code review},
location = {Saint Petersburg, Russia},
numpages = {11},
pages = {202--212},
publisher = {Association for Computing Machinery},
series = {ESEC/FSE 2013},
title = {Convergent Contemporary Software Peer Review Practices},
url = {https://doi.org/10.1145/2491411.2491444},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1145/2491411.2491444},
bdsk-url-2 = {https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/rigby2013convergent.pdf}}
@article{MacLeodEtAl2018,
author = {MacLeod, Laura and Greiler, Michaela and Storey, Margaret-Anne and Bird, Christian and Czerwonka, Jacek},
date-added = {2022-10-16 12:33:14 -0400},
date-modified = {2022-10-16 12:33:34 -0400},
doi = {10.1109/MS.2017.265100500},
journal = {IEEE Software},
number = {4},
pages = {34-42},
title = {Code Reviewing in the Trenches: Challenges and Best Practices},
volume = {35},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1109/MS.2017.265100500},
bdsk-url-2 = {http://chisel.cs.uvic.ca/pubs/macleod-IEEESoftware2017.pdf}}
@inproceedings{BirdAndBacchelli2013,
abstract = {Code review is a common software engineering practice employed both in open source and industrial contexts. Review today is less formal and more "lightweight" than the code inspections performed and studied in the 70s and 80s. We empirically explore the motivations, challenges, and outcomes of tool-based code reviews. We observed, interviewed, and surveyed developers and managers and manually classified hundreds of review comments across diverse teams at Microsoft. Our study reveals that while finding defects remains the main motivation for review, reviews are less about defects than expected and instead provide additional benefits such as knowledge transfer, increased team awareness, and creation of alternative solutions to problems. Moreover, we find that code and change understanding is the key aspect of code reviewing and that developers employ a wide range of mechanisms to meet their understanding needs, most of which are not met by current tools. We provide recommendations for practitioners and researchers.},
author = {Bird, Christian and Bacchelli, Alberto},
booktitle = {Proceedings of the International Conference on Software Engineering},
date-added = {2022-10-16 12:31:53 -0400},
date-modified = {2022-10-16 12:32:07 -0400},
edition = {Proceedings of the International Conference on Software Engineering},
month = {May},
publisher = {IEEE},
title = {Expectations, Outcomes, and Challenges of Modern Code Review},
url = {https://www.microsoft.com/en-us/research/publication/expectations-outcomes-and-challenges-of-modern-code-review/},
year = {2013},
bdsk-url-1 = {https://www.microsoft.com/en-us/research/publication/expectations-outcomes-and-challenges-of-modern-code-review/},
bdsk-url-2 = {https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/ICSE202013-codereview.pdf}}
@inproceedings{SadowskiEtAl2018,
author = {Sadowski, Caitlin and S{\"o}derberg, Emma and Church, Luke and Sipko, Michal and Bacchelli, Alberto},
booktitle = {Proceedings of the 40th International Conference on Software Engineering: Software Engineering in Practice},
date-added = {2022-10-16 12:30:33 -0400},
date-modified = {2022-10-16 12:31:00 -0400},
pages = {181--190},
title = {Modern code review: a case study at google},
year = {2018},
bdsk-url-1 = {https://dl.acm.org/doi/pdf/10.1145/3183519.3183525}}
@misc{LestangEtAl2022,
author = {Thibault Lestang and Dominik Krzeminski and Valerio Maggio},
date-added = {2022-10-16 12:18:52 -0400},
date-modified = {2022-10-16 12:20:01 -0400},
howpublished = {\url{https://www.exascaleproject.org/wp-content/uploads/2022/08/webinar-codereview-221012.pdf}},
month = {October},
title = {Investing in Code Reviews for Better Research Software},
year = {2022},
bdsk-url-1 = {https://www.exascaleproject.org/wp-content/uploads/2022/08/webinar-codereview-221012.pdf},
bdsk-url-2 = {https://www.exascaleproject.org/event/codereview/}}
@misc{KhalilAndZacchiroli2022,
author = {Zeinab Abou Khalil and Stefano Zacchiroli},
date-added = {2022-08-18 11:38:07 -0400},
date-modified = {2022-08-18 11:39:37 -0400},
howpublished = {\url{https://arxiv.org/abs/2207.08436}},
month = {July},
title = {Software Artifact Mining in Software Engineering Conferences: A Meta-Analysis},
year = {2022},
bdsk-url-1 = {https://arxiv.org/abs/2207.08436}}
@book{JanickiEtAl2022,
author = {Ryszard Janicki and Ketty Kleijn and Miciej Kotny and Lukasz Mikulski},
date-added = {2022-07-21 09:35:53 -0400},
date-modified = {2022-07-21 09:38:07 -0400},
publisher = {Springer},
series = {Studies in Computational Intelligence},
title = {Paradigms of Concurrency: Observations, Behaviours, and Systems -- a Petri Net View},
volume = {1020},
year = {2022},
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@inproceedings{SmithAndCarette2022_Grenoble,
address = {Hamilton, Ontario, Canada},
author = {Spencer Smith and Jacques Carette},
booktitle = {Universit\'e Grenoble Alpes -- McMaster University Joint Workshop},
date-added = {2022-07-19 16:34:19 -0400},
date-modified = {2022-07-19 16:37:53 -0400},
title = {Combining Literate Programming and Code Generation to Improve the Reproducibility and Sustainability of Scientific Computing Software},
year = {June 2022},
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@inproceedings{SmithAndCarette2022_CRSC,
address = {Montr\'eal},
author = {Spencer Smith and Jacques Carette},
booktitle = {Canadian Research Software Conference},
date-added = {2022-07-19 16:26:55 -0400},
date-modified = {2022-07-19 16:37:53 -0400},
title = {A Holistic Approach to Pain Relief for Research Software Developers},
year = {May 2022},
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@article{SmithEtAl2022,
author = {Spencer Smith and Peter Michalski and Jacques Carette and Zahra Keshavarz-Motamed},
date-added = {2022-07-18 14:27:28 -0400},
date-modified = {2022-10-21 14:36:37 -0400},
journal = {Archives of Computational Methods in Engineering},
pages = {1--46},
title = {State of the Practice for {L}attice {B}oltzmann {M}ethod Software},
year = {Submitted 2022},
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@article{FarisAndShuren2017,
annote = {``In the future, computer-based modeling may change the way we think about device validation in other ways, allowing for much smaller clinical trials, or may change the way we think about running trials, in that some ``clinical'' information may be derived from simulations. Device manufacturers are increasingly developing stochastic engineering models that may have the capability to simulate clinical outcomes for ``virtual patients'' by modeling a relationship between bench outcomes and clinical end points. If it can be shown that these virtual patients are similar, in a precisely defined way, to real patients, future trials may be able to rely partially on virtual-patient information, thus lessening the burden of enrolling additional real patients.'' },
author = {Faris, Owen and Shuren, Jeffrey},
date-added = {2022-07-15 20:30:29 -0400},
date-modified = {2022-07-15 20:31:04 -0400},
doi = {10.1056/NEJMra1512592},
eprint = {https://doi.org/10.1056/NEJMra1512592},
journal = {New England Journal of Medicine},
note = {PMID: 28379790},
number = {14},
pages = {1350-1357},
title = {An FDA Viewpoint on Unique Considerations for Medical-Device Clinical Trials},
url = {https://doi.org/10.1056/NEJMra1512592},
volume = {376},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1056/NEJMra1512592}}
@misc{GreilerEtAl2022,
author = {Greiler, Michaela and Storey, Margaret-Anne and Noda, Abi},
copyright = {arXiv.org perpetual, non-exclusive license},
date-added = {2022-07-15 17:25:46 -0400},
date-modified = {2022-07-15 17:26:01 -0400},
doi = {10.48550/ARXIV.2205.06352},
keywords = {Software Engineering (cs.SE), FOS: Computer and information sciences, FOS: Computer and information sciences},
publisher = {arXiv},
title = {An Actionable Framework for Understanding and Improving Developer Experience},
url = {https://arxiv.org/abs/2205.06352},
year = {2022},
bdsk-url-1 = {https://arxiv.org/abs/2205.06352},
bdsk-url-2 = {https://doi.org/10.48550/ARXIV.2205.06352}}
@inproceedings{StoreyEtAl2022,
author = {Storey, Margaret-Anne and Houck, Brian and Zimmermann, Thomas},
booktitle = {2022 IEEE/ACM 15th International Workshop on Cooperative and Human Aspects of Software Engineering (CHASE)},
date-added = {2022-07-12 18:42:47 -0400},
date-modified = {2022-07-12 18:43:09 -0400},
organization = {IEEE},
pages = {26--35},
title = {How Developers and Managers Define and Trade Productivity for Quality},
year = {2022},
bdsk-url-1 = {https://arxiv.org/abs/2111.04302},
bdsk-url-2 = {https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=9796208&casa_token=VNHCLYslSRgAAAAA:b-WyECroDISeSiZz2h2nu8XfYMukzRWcuY6hHICZmB2XOg9Q6-Yu99qh8peFA4ZldavTfGiutQ&tag=1}}
@misc{DaponteAndFalquet2021,
author = {Daponte, Vincenzo and Falquet, Gilles},
copyright = {Creative Commons Attribution 4.0 International},
date-added = {2022-07-11 23:19:52 -0400},
date-modified = {2022-07-11 23:20:12 -0400},
doi = {10.48550/ARXIV.2107.04347},
keywords = {Artificial Intelligence (cs.AI), Digital Libraries (cs.DL), Logic in Computer Science (cs.LO), FOS: Computer and information sciences, FOS: Computer and information sciences},
publisher = {arXiv},
title = {An ontology for the formalization and visualization of scientific knowledge},
url = {https://arxiv.org/abs/2107.04347},
year = {2021},
bdsk-url-1 = {https://arxiv.org/abs/2107.04347},
bdsk-url-2 = {https://doi.org/10.48550/ARXIV.2107.04347}}
@inproceedings{PimentelEtAl2019,
abstract = {Jupyter Notebooks have been widely adopted by many different communities, both in science and industry. They support the creation of literate programming documents that combine code, text, and execution results with visualizations and all sorts of rich media. The self-documenting aspects and the ability to reproduce results have been touted as significant benefits of notebooks. At the same time, there has been growing criticism that the way notebooks are being used leads to unexpected behavior, encourage poor coding practices, and that their results can be hard to reproduce. To understand good and bad practices used in the development of real notebooks, we studied 1.4 million notebooks from GitHub. We present a detailed analysis of their characteristics that impact reproducibility. We also propose a set of best practices that can improve the rate of reproducibility and discuss open challenges that require further research and development.},
author = {Pimentel, Jo\~{a}o Felipe and Murta, Leonardo and Braganholo, Vanessa and Freire, Juliana},
booktitle = {Proceedings of the 16th International Conference on Mining Software Repositories},
date-added = {2022-06-24 16:54:59 -0400},
date-modified = {2022-06-24 16:55:24 -0400},
doi = {10.1109/MSR.2019.00077},
keywords = {reproducibility, jupyter notebook, github},
location = {Montreal, Quebec, Canada},
numpages = {11},
pages = {507--517},
publisher = {IEEE Press},
series = {MSR '19},
title = {A Large-Scale Study about Quality and Reproducibility of Jupyter Notebooks},
url = {https://doi.org/10.1109/MSR.2019.00077},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1109/MSR.2019.00077},
bdsk-url-2 = {https://dl.acm.org/doi/10.1109/MSR.2019.00077},
bdsk-url-3 = {http://www2.ic.uff.br/~leomurta/papers/pimentel2019a.pdf}}
@inproceedings{Kohlhase2021,
author = {Michael Kohlhase},
booktitle = {Proceedings of Conference on Intelligent Computer Mathematics (CICM 2021)},
date-added = {2022-06-14 22:35:11 -0400},
date-modified = {2022-06-14 22:39:10 -0400},
title = {Referential Semantics: Briding Between Representations of Mathematical/Technical Documents and Knowledge},
year = {2021},
bdsk-file-1 = {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}}
@misc{BernholdtEtAl2022,
annote = {- notes on the draft brochure for the SSSDU workshop summary, to help with adding my notes to the PRDs (Priority Research Directions) and Theme documents.
- investment in software is an investment in science
- concerns are growing about the productivity of the developers and users of scientific software, its sustainability, and our ability to trust the results that it produces.
- Software has become an essential part of modern science, impacting not only new discovery, but also policy and technological development; in order to have full confidence in science delivered via software, we must improve the processes and tools that help us create and use it, requiring deep understanding of the diverse individuals and teams doing the work.
PRD1: Develop methodologies and tools to comprehensively improve team-based scientific software development and use
Key question: What practices, processes, and tools can help improve the development, sustainment, evolution, and use of scientific software by teams?
PRD2: Develop next-generation tools to enhance developer productivity and software sustainability
Key questions: How can we create and adapt tools to improve developer effectiveness and efficiency, software sustainability, and support for the continuous evolution of software? How can we support and encourage the adoption of such tools by developers?
We anticipate future software-generating environments that translate scientific programmer intent into source code fragments that can be tuned and refined. We also expect advances in tools that assist in generating software tests, documentation, clean and readable source code, and more.
PRD3: Develop methodologies, tools, and infrastructure for trustworthy software-intensive science
Key questions: How can we facilitate and encourage effective and efficient reuse of data and software from third parties while ensuring the integrity of our software and the resulting science? How can we provide flexible environments that ``bake in'' the tracking of software, provenance, and experiment management required to support peer review and reproducibility?
We need to easily detect and correct perturbations in state and execution, and we need to be able to preserve provenance down to the finest details for the purposes of assessment and audit.
Theme 1: We need to consider both human and technical elements to better understand how to improve the development and use of scientific software.
Theme 2: We need to address urgent challenges in workforce recruitment and retention in the computing sciences with growth through expanded diversity, stable career paths, and the creation of a community and culture that attract and retain new generations of scientists.
{to do that need documentation!} {need code of conduct}
Theme 3: Scientific software has become essential to all areas of science and technology, creating opportunities for expanded partnerships, collaboration, and impact.},
author = {David Bernholdt and others},
date-added = {2022-04-28 15:49:20 -0400},
date-modified = {2022-04-28 16:30:20 -0400},
howpublished = {\url{https://drive.google.com/drive/folders/1KxhAo2gtWAWkQ8vSh5fqWv0tfGtPGhGm}},
title = {Science of Scientific Software Development and Use (SSSDU) (Brochure)},
year = {2022},
bdsk-url-1 = {https://drive.google.com/drive/folders/1KxhAo2gtWAWkQ8vSh5fqWv0tfGtPGhGm}}
@article{Smart2018,
author = {Ashley Smart},
date-added = {2022-04-28 10:44:32 -0400},
date-modified = {2022-04-28 10:47:04 -0400},
doi = {10.1063/PT.6.1.20180822a},
journal = {Physics Today},
month = {Aug},
title = {The war over supercooled water},
url = {https://physicstoday.scitation.org/do/10.1063/PT.6.1.20180822a/full/},
year = {2018},
bdsk-url-1 = {https://physicstoday.scitation.org/do/10.1063/PT.6.1.20180822a/full/},
bdsk-url-2 = {https://doi.org/10.1063/PT.6.1.20180822a}}
@article{AmpatzoglouEtAl2019,
author = {Ampatzoglou, Apostolos and Bibi, Stamatia and Avgeriou, Paris and Verbeek, Marijn and Chatzigeorgiou, Alexander},
date-added = {2022-04-20 11:51:29 -0400},
date-modified = {2022-04-20 11:51:29 -0400},
doi = {10.1016/j.infsof.2018.10.006},
journal = {Information and Software Technology},
month = {02},
title = {Identifying, Categorizing and Mitigating Threats to Validity in Software Engineering Secondary Studies},
volume = {106},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1016/j.infsof.2018.10.006}}
@article{SlaughterEtAl2021,
author = {Slaughter, Andrew and Permann, Cody and Miller, Jason and Alger, Brian and Novascone, Stephen},
date-added = {2022-04-18 18:11:02 -0400},
date-modified = {2022-04-18 18:11:02 -0400},
doi = {10.1080/00295450.2020.1826804},
journal = {Nuclear Technology},
month = {01},
pages = {1-8},
title = {Continuous Integration, In-Code Documentation, and Automation for Nuclear Quality Assurance Conformance},
volume = {207},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1080/00295450.2020.1826804}}
@article{FitzgeraldAndStol2017,
abstract = {Throughout its short history, software development has been characterized by harmful disconnects between important activities such as planning, development and implementation. The problem is further exacerbated by the episodic and infrequent performance of activities such as planning, testing, integration and releases. Several emerging phenomena reflect attempts to address these problems. For example, Continuous Integration is a practice which has emerged to eliminate discontinuities between development and deployment. In a similar vein, the recent emphasis on DevOps recognizes that the integration between software development and its operational deployment needs to be a continuous one. We argue a similar continuity is required between business strategy and development, BizDev being the term we coin for this. These disconnects are even more problematic given the need for reliability and resilience in the complex and data-intensive systems being developed today. We identify a number of continuous activities which together we label as `Continuous *' (i.e. Continuous Star) which we present as part of an overall roadmap for Continuous Software engineering. We argue for a continuous (but not necessarily rapid) software engineering delivery pipeline. We conclude the paper with a research agenda.},
author = {Brian Fitzgerald and Klaas-Jan Stol},
date-added = {2022-04-18 11:50:28 -0400},
date-modified = {2022-04-18 11:50:28 -0400},
doi = {https://doi.org/10.1016/j.jss.2015.06.063},
issn = {0164-1212},
journal = {Journal of Systems and Software},
keywords = {Continuous software engineering, Lean software development, DevOps},
pages = {176-189},
title = {Continuous software engineering: A roadmap and agenda},
url = {https://www.sciencedirect.com/science/article/pii/S0164121215001430},
volume = {123},
year = {2017},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0164121215001430},
bdsk-url-2 = {https://doi.org/10.1016/j.jss.2015.06.063}}
@book{HumbleAndFarley2010,
abstract = {Getting software released to users is often a painful, risky, and time-consuming process. This groundbreaking new book sets out the principles and technical practices that enable rapid, incremental delivery of high quality, valuable new functionality to users. Through automation of the build, deployment, and testing process, and improved collaboration between developers, testers, and operations, delivery teams can get changes released in a matter of hours---sometimes even minutes---no matter what the size of a project or the complexity of its code base. Jez Humble and David Farley begin by presenting the foundations of a rapid, reliable, low-risk delivery process. Next, they introduce the deployment pipeline, an automated process for managing all changes, from check-in to release. Finally, they discuss the 'ecosystem' needed to support continuous delivery, from infrastructure, data and configuration management to governance. The authors introduce state-of-the-art techniques, including automated infrastructure management and data migration, and the use of virtualization. For each, they review key issues, identify best practices, and demonstrate how to mitigate risks.},
added-at = {2017-05-27T20:32:20.000+0200},
address = {Upper Saddle River, NJ},
author = {Humble, Jez and Farley, David G.},
biburl = {https://www.bibsonomy.org/bibtex/27c9faebd9b029323654c5289b8ae09e2/flint63},
date-added = {2022-04-18 10:40:08 -0400},
date-modified = {2022-04-18 10:40:22 -0400},
file = {eBook:2010/HumbleFarley10.pdf:PDF;InformIT Product page:http\://www.informit.com/title/0321601912:URL;Amazon Search inside:http\://www.amazon.de/gp/reader/0321601912/:URL},
groups = {public},
interhash = {0eff27916272b940e52c92bb719ccef8},
intrahash = {7c9faebd9b029323654c5289b8ae09e2},
isbn = {978-0-321-60191-9},
keywords = {01841 105 safari book software development build process},
publisher = {Addison-Wesley},
timestamp = {2018-04-16T11:55:45.000+0200},
title = {Continuous Delivery: Reliable Software Releases through Build, Test, and Deployment Automation},
url = {http://my.safaribooksonline.com/9780321601919},
username = {flint63},
year = 2010,
bdsk-file-1 = {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},
bdsk-url-1 = {http://my.safaribooksonline.com/9780321601919}}
@inproceedings{HiltonEtAl2016,
author = {Hilton, Michael and Tunnell, Timothy and Huang, Kai and Marinov, Darko and Dig, Danny},
booktitle = {2016 31st IEEE/ACM International Conference on Automated Software Engineering (ASE)},
date-added = {2022-04-13 15:55:31 -0400},
date-modified = {2022-04-13 15:55:31 -0400},
pages = {426--437},
title = {Usage, costs, and benefits of continuous integration in open-source projects},
year = {2016},
bdsk-url-1 = {https://ieeexplore.ieee.org/abstract/document/7582778},
bdsk-url-2 = {https://dl.acm.org/doi/pdf/10.1145/2970276.2970358}}
@article{ShahinEtAl2017,
abstract = {Continuous practices, i.e., continuous integration, delivery, and deployment, are the software
development industry practices that enable organizations to frequently and reliably release new features
and products. With the increasing interest in the literature on continuous practices, it is important to
systematically review and synthesize the approaches, tools, challenges, and practices reported for adopting
and implementing continuous practices. This paper aimed at systematically reviewing the state of the art of
continuous practices to classify approaches and tools, identify challenges and practices in this regard, and
identify the gaps for future research. We used the systematic literature review method for reviewing the peer
reviewed papers on continuous practices published between 2004 and June 1, 2016. We applied the thematic
analysis method for analyzing the data extracted from reviewing 69 papers selected using predefined criteria.
We have identified 30 approaches and associated tools, which facilitate the implementation of continuous
practices in the following ways: 1) reducing build and test time in continuous integration (CI); 2) increasing
visibility and awareness on build and test results in CI; 3) supporting (semi-) automated continuous testing;
4) detecting violations, flaws, and faults in CI; 5) addressing security and scalability issues in deployment
pipeline; and 6) improving dependability and reliability of deployment process. We have also determined
a list of critical factors, such as testing (effort and time), team awareness and transparency, good design
principles, customer, highly skilled and motivated team, application domain, and appropriate infrastructure
that should be carefully considered when introducing continuous practices in a given organization. The
majority of the reviewed papers were validation (34.7%) and evaluation (36.2%) research types. This paper
also reveals that continuous practices have been successfully applied to both greenfield and maintenance
projects. Continuous practices have become an important area of software engineering research and practice.
While the reported approaches, tools, and practices are addressing a wide range of challenges, there are
several challenges and gaps, which require future research work for improving the capturing and reporting
of contextual information in the studies reporting different aspects of continuous practices; gaining a deep
understanding of how software-intensive systems should be (re-) architected to support continuous practices;
and addressing the lack of knowledge and tools for engineering processes of designing and running secure
deployment pipelines.},
author = {Shahin, Mojtaba and Ali Babar, Muhammad and Zhu, Liming},
date-added = {2022-04-13 15:54:41 -0400},
date-modified = {2022-04-18 10:24:26 -0400},
doi = {10.1109/ACCESS.2017.2685629},
journal = {IEEE Access},
pages = {3909-3943},
title = {Continuous Integration, Delivery and Deployment: A Systematic Review on Approaches, Tools, Challenges and Practices},
volume = {5},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1109/ACCESS.2017.2685629},
bdsk-url-2 = {https://ieeexplore.ieee.org/abstract/document/7884954},
bdsk-url-3 = {https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7884954}}
@misc{Fowler2006,
author = {Martin Fowler},
date-added = {2022-04-13 15:52:52 -0400},
date-modified = {2022-04-13 15:53:33 -0400},
howpublished = {\url{https://martinfowler.com/articles/continuousIntegration.html}},
month = {May},
title = {Continuous Integration},
year = {2006},
bdsk-url-1 = {https://martinfowler.com/articles/continuousIntegration.html}}
@article{MengEtAl2018,
abstract = { The success of an application programming interface (API) crucially depends on how well its documentation meets the information needs of software developers. Previous research suggests that these information needs have not been sufficiently understood. This article presents the results of a series of semistructured interviews and a follow-up questionnaire conducted to explore the learning goals and learning strategies of software developers, the information resources they turn to and the quality criteria they apply to API documentation. Our results show that developers initially try to form a global understanding regarding the overall purpose and main features of an API, but then adopt either a concepts-oriented or a code-oriented learning strategy that API documentation both needs to address. Our results also show that general quality criteria such as completeness and clarity are relevant to API documentation as well. Developing and maintaining API documentation therefore need to involve the expertise of communication professionals. },
author = {Michael Meng and Stephanie Steinhardt and Andreas Schubert},
date-added = {2022-04-13 14:06:28 -0400},
date-modified = {2022-04-13 14:06:28 -0400},
doi = {10.1177/0047281617721853},
eprint = {https://doi.org/10.1177/0047281617721853},
journal = {Journal of Technical Writing and Communication},
number = {3},
pages = {295-330},
title = {Application Programming Interface Documentation: What Do Software Developers Want?},
url = {https://doi.org/10.1177/0047281617721853},
volume = {48},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1177/0047281617721853}}
@misc{Carty2020,
author = {David Carty},
date-added = {2022-04-12 16:21:29 -0400},
date-modified = {2022-04-12 16:22:24 -0400},
howpublished = {\url{https://www.techtarget.com/searchsoftwarequality/feature/Follow-Googles-lead-with-programming-style-guides}},
month = {July},
title = {Follow Google's lead with programming style guides},
year = {2020},
bdsk-url-1 = {https://www.techtarget.com/searchsoftwarequality/feature/Follow-Googles-lead-with-programming-style-guides}}
@misc{PEO2021,
author = {{Professional Engineers Act}},
date-added = {2022-04-12 14:40:35 -0400},
date-modified = {2022-04-12 14:45:02 -0400},
howpublished = {\url{https://canlii.ca/t/5568z}},
month = {Dec},
title = {Professional Engineers Act, RSO 1990, c P. 28},
year = {2021},
bdsk-url-1 = {https://canlii.ca/t/5568z},
bdsk-url-2 = {https://www.ontario.ca/laws/regulation/900941}}
@misc{IEEE1999,
author = {{IEEE-CS/ACM}, Joint Task Force on Software Engineering Ethics and Professional Practices},
date-added = {2022-04-12 14:31:23 -0400},
date-modified = {2022-04-12 14:34:40 -0400},
howpublished = {\url{https://www.computer.org/education/code-of-ethics}},
title = {Code of Ethics, {IEEE} Computer Society},
year = {1999},
bdsk-url-1 = {https://www.computer.org/education/code-of-ethics}}
@article{SinghEtAl2021,
abstract = {This paper focuses on codes of conduct (CoC) of Free and Open Source Software (F/OSS) and their role in improving women's participation in online communities of OSS. We investigated 355 F/OSS software package websites for the presence of codes of conduct and then analyzed these for diversity elements. Qualitative content analysis of the websites shows that less than 10{\%} (28) of the analyzed websites had some type of community rules such as CoC. In-depth analysis of the CoCs demonstrated many discrepancies in the terminology, length, enforcement, and adoption of codes of conduct. To investigate the usage of these CoCs, we investigate five women-focused OSS discussion forums. This analysis shows the value of creating/adopting a CoC and the impact CoC can have on the participation of women. We also present the challenges in the usage and enforcement of CoCs as discussed by women of these forums. We conclude with recommendations for better enforcement of CoC and reflection on the ethical underpinnings of CoC as a tool to improve diversity and inclusion in OSS.},
author = {Singh, Vandana and Bongiovanni, Brice and Brandon, William},
date = {2021/02/28},
date-added = {2022-04-12 14:18:23 -0400},
date-modified = {2022-04-12 14:18:47 -0400},
doi = {10.1007/s11219-020-09543-w},
id = {Singh2021},
isbn = {1573-1367},
journal = {Software Quality Journal},
title = {Codes of conduct in Open Source Software---for warm and fuzzy feelings or equality in community?},
url = {https://doi.org/10.1007/s11219-020-09543-w},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1007/s11219-020-09543-w}}
@inproceedings{TouraniEtAl2017,
author = {Tourani, Parastou and Adams, Bram and Serebrenik, Alexander},
booktitle = {2017 IEEE 24th International Conference on Software Analysis, Evolution and Reengineering (SANER)},
date-added = {2022-04-12 11:09:59 -0400},
date-modified = {2022-04-12 11:10:14 -0400},
doi = {10.1109/SANER.2017.7884606},
pages = {24-33},
title = {Code of conduct in open source projects},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1109/SANER.2017.7884606},
bdsk-url-2 = {https://www.researchgate.net/publication/315638638_Code_of_conduct_in_open_source_projects}}
@misc{Pichler2012,
author = {Roman Pichler},
date-added = {2022-04-12 10:38:46 -0400},
date-modified = {2022-04-12 10:39:52 -0400},
howpublished = {\url{https://www.romanpichler.com/blog/agile-product-roadmap/}},
month = {May},
title = {Working with an Agile Product Roadmap},
year = {2012},
bdsk-url-1 = {https://www.romanpichler.com/blog/agile-product-roadmap/}}
@inproceedings{VahaniittyEtAl2002,
address = {Helsinki, Finland},
author = {Jarno V{\"a}h{\"a}niitty and Casper Lassenius and Kristian Rautiainen},
date-added = {2022-04-12 10:14:42 -0400},
date-modified = {2022-04-12 10:14:42 -0400},
organization = {University of Technologie, Software Business and Engineering Institute},
title = {An Approach to Product Roadmapping in Small Software Product Businesses},
year = {2002},
bdsk-url-1 = {https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.100.7624&rep=rep1&type=pdf}}
@inproceedings{PhaalEtAl2005,
author = {Phaal, R. and Farrukh, C.J.P. and Probert, D.R.},
booktitle = {A Unifying Discipline for Melting the Boundaries Technology Management:},
date-added = {2022-04-12 10:08:50 -0400},
date-modified = {2022-04-12 10:09:03 -0400},
doi = {10.1109/PICMET.2005.1509680},
pages = {99-111},
title = {Developing a technology roadmapping system},
year = {2005},
bdsk-url-1 = {https://doi.org/10.1109/PICMET.2005.1509680}}
@inproceedings{MunchEtAl2019,
author = {M{\"u}nch, J{\"u}rgen and Trieflinger, Stefan and Lang, Dominic},
booktitle = {2019 IEEE International Conference on Engineering, Technology and Innovation (ICE/ITMC)},
date-added = {2022-04-12 10:06:09 -0400},
date-modified = {2022-04-12 10:06:53 -0400},
doi = {10.1109/ICE.2019.8792654},
pages = {1-8},
title = {Product Roadmap -- From Vision to Reality: A Systematic Literature Review},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1109/ICE.2019.8792654}}
@article{SoodEtAl2019,
author = {Kanika Sood and Anshu Dubey and boyana norris and Lois Curfman McInnes},
date-added = {2022-04-09 14:37:05 -0400},
date-modified = {2022-04-09 14:37:05 -0400},
doi = {10.6084/m9.figshare.7772894.v2},
month = {2},
title = {{Repository-Analysis of Open-source and Scientific Software Development Projects}},
url = {https://figshare.com/articles/presentation/Analyzing_Open-source_Scientific_Software_Projects/7772894},
year = {2019},
bdsk-url-1 = {https://figshare.com/articles/presentation/Analyzing_Open-source_Scientific_Software_Projects/7772894},
bdsk-url-2 = {https://doi.org/10.6084/m9.figshare.7772894.v2}}
@article{GrannanEtAl2020,
abstract = {Scientific discovery increasingly relies on computation through simulations, analytics, and machine and deep learning. Of these, simulations on high-performance computing (HPC) platforms have been the cornerstone of scientific computing for more than two decades. However, the development of simulation software has, in general, occurred through accretion, with a few exceptions. With an increase in scientific understanding, models have become more complex, rendering an accretion mode untenable to the point where software productivity and sustainability have become active concerns in scientific computing. In this survey paper, we examine a modest set of HPC scientific simulation applications that are already using cutting-edge HPC platforms. Several have been in existence for a decade or more. Our objective in this survey is twofold: first, to understand the landscape of scientific computing on HPC platforms in order to distill the currently scattered knowledge about software practices that have helped both developer and software productivity, and second, to understand the kind of tools and methodologies that need attention for continued productivity. },
author = {A Grannan and K Sood and B Norris and A Dubey},
date-added = {2022-04-09 14:09:11 -0400},
date-modified = {2022-04-09 14:09:39 -0400},
doi = {10.1177/1094342019899451},
eprint = {https://doi.org/10.1177/1094342019899451},
journal = {The International Journal of High Performance Computing Applications},
number = {4},
pages = {465-477},
title = {Understanding the landscape of scientific software used on high-performance computing platforms},
url = {https://doi.org/10.1177/1094342019899451},
volume = {34},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1177/1094342019899451}}
@misc{Kashyap2020,
author = {Neeraj Kashyap},
date-added = {2022-04-05 14:19:40 -0400},
date-modified = {2022-04-05 14:20:25 -0400},
howpublished = {\url{https://towardsdatascience.com/githubs-path-to-128m-public-repositories-f6f656ab56b1}},
month = {March},
title = {GitHub's Path to 128M Public Repositories},
year = {2020},
bdsk-url-1 = {https://towardsdatascience.com/githubs-path-to-128m-public-repositories-f6f656ab56b1}}
@inproceedings{SmithAndMichalski2022,
author = {Spencer Smith and Peter Michalski},
booktitle = {Proceedings of the International Conference on Computational Science, {ICCS}},
date-added = {2022-04-01 16:31:44 -0400},
date-modified = {2022-04-11 15:13:28 -0400},
month = {June},
pages = {1--14},
title = {Digging Deeper Into the State of the Practice for Domain Specific Research Software},
year = {2022},
bdsk-file-1 = {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},
bdsk-url-1 = {https://github.com/smiths/AIMSS/blob/master/StateOfPractice/Papers/ICCS-2022-SOP_MethodologyPlusExamples/DigDeep.pdf}}
@inproceedings{KumarEtAl2022,
abstract = {R is a package-based, multi-paradigm programming language for
scientific software. It provides an easy way to install third-party
code, datasets, tests, documentation and examples through CRAN
(Comprehensive R Archive Network). Prior works indicated
developers tend to code workarounds to bypass CRAN's automated
checks (performed when submitting a package) instead of fixing the
code--doing so reduces packages' quality. It may become a threat
to those analyses written in R that rely on miss-checked code. This
preliminary study card-sorted source code comments and analysed
StackOverflow (SO) conversations discussing CRAN checks to
understand developers' attitudes. We determined that about a
quarter of SO posts aim to bypass a check with a workaround;
the most affected are code-related problems, package dependencies,
installation and feasibility. We analyse these checks and outline
future steps to improve similar automated analyses},
author = {Pranjay Kumar and Davin Ie and Melina Vidoni},
booktitle = {IEEE/ACM 30th International Conference on Program Comprehension (ICPC)},
date-added = {2022-03-28 15:19:04 -0400},
date-modified = {2022-03-28 15:21:02 -0400},
pages = {1--5},
title = {On the Developers' Attitude Towards CRAN Checks},
year = {2022},
bdsk-url-1 = {https://melvidoni.rbind.io/publication/2022-cranchecks.pdf}}
@article{SadeghiEtAl2022b,
author = {Reza Sadeghi and Nadav Gasner and Seyedvahid Khodaei and Julio Garcia and Zahra Keshavarz-Motamed},
date-added = {2022-03-16 14:39:39 -0400},
date-modified = {2022-03-16 14:44:42 -0400},
doi = {https://doi.org/10.1016/j.ijmecsci.2021.107038},
journal = {International Journal of Mechanical Sciences},
keywords = {Coarctation, Mixed valvular disease, Aortic fluid dynamics, Hemodynamics, Lattice Boltzmann method, Patient-specific lumped parameter model, Abnormal hemodynamics},
title = {Impact of mixed valvular disease on coarctation hemodynamics using patient-specific lumped parameter and Lattice Boltzmann modeling},
url = {https://www.sciencedirect.com/science/article/pii/S0020740321007244},
volume = {217},
year = {2022},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0020740321007244},
bdsk-url-2 = {https://doi.org/10.1016/j.ijmecsci.2021.107038}}
@article{SadeghiEtAl2022,
author = {Sadeghi, R. and Tomka, B. and Khodaei, S. and Garcia, J. and Ganame, J. and Keshavarz‐Motamed, Z.},
date-added = {2022-03-16 14:33:28 -0400},
date-modified = {2022-03-16 14:38:48 -0400},
journal = {Journal of the American Heart Association},
month = {January},
number = {2},
pages = {26},
title = {Reducing Morbidity and Mortality in Patients With Coarctation Requires Systematic Differentiation of Impacts of Mixed Valvular Disease on Coarctation Hemodynamics},
volume = {11},
year = {2022},
bdsk-url-1 = {https://www.ahajournals.org/doi/epub/10.1161/JAHA.121.022664},
bdsk-url-2 = {https://www.ahajournals.org/doi/10.1161/JAHA.121.022664}}
@misc{Maric2022,
author = {Tomislav Maric},
date-added = {2022-03-09 14:33:50 -0500},
date-modified = {2022-03-09 14:36:21 -0500},
howpublished = {\url{https://www.exascaleproject.org/wp-content/uploads/2022/02/webinar-DesignPatterns-220309.pdf}},
month = {March},
title = {Software Design Patterns in Research Software with examples from {OpenFOAM}},
year = {2022},
bdsk-url-1 = {https://www.exascaleproject.org/wp-content/uploads/2022/02/webinar-DesignPatterns-220309.pdf}}
@article{MatkerimEtAl2013,
annote = {- starts with PDE - derivation is not documented
- emphasis is on parallel solver
- close to the implementation, close to code
- not as abstract as Drasil},
author = {Bazargul Matkerim and Darhan Akhmed-Zaki and Manuel Barata},
date-added = {2022-03-03 11:34:26 -0500},
date-modified = {2022-03-03 11:34:26 -0500},
journal = {Applied Mathematical Sciences},
number = {100},
pages = {4961--4974},
title = {Development High Performance Scientific Computing Application Using Model-Driven Architecture},
volume = {7},
year = {2013},
bdsk-url-1 = {http://www.m-hikari.com/ams/ams-2013/ams-97-100-2013/matkerimAMS97-100-2013.pdf},
bdsk-url-2 = {https://www.researchgate.net/publication/286976410_Development_high_performance_scientific_computing_application_using_model-driven_architecture}}
@software{CaretteEtAl2021-Drasil,
author = {Carette, Jacques and Smith, Spencer and Balaci, Jason and Hunt, Anthony and Wu, Ting-Yu and Crawford, Samuel and Chen, Dong and Szymczak, Dan and MacLachlan, Brooks and Scime, Dan and Niazi, Maryyam},
date-added = {2022-03-03 11:08:55 -0500},
date-modified = {2022-03-03 11:09:14 -0500},
license = {BSD-2-Clause},
month = {2},
title = {{Drasil}},
url = {https://github.com/JacquesCarette/Drasil/tree/v0.1-alpha},
version = {v0.1-alpha},
year = {2021},
bdsk-url-1 = {https://github.com/JacquesCarette/Drasil/tree/v0.1-alpha}}
@book{Kuchner2012,
address = {Washington, D.C.},
author = {Marc J. Kuchner},
date-added = {2022-03-02 13:40:40 -0500},
date-modified = {2022-03-02 13:42:46 -0500},
publisher = {Island Press},
title = {Marketing for Scientists: How to Shine in Tough Times},
year = {2012}}
@article{Wyld2012,
abstract = {{Marketing for Scientists: How to Shine in Tough Times. Marc J. Kuchner. Island Press, 2011. 248 pp., illus. \\$19.95 (ISBN 9781597269940 paper).Ever wonder why automotive engineers design car doors to produce a particularly solid-sounding thunk when you close them? It is all part of a marketing strategy that author Marc J. Kuchner believes can be applied to science and scientists as well. In his well-written book Marketing for Scientists: How to Shine in Tough Times, Kuchner offers scientists some career-building guidance using the principles of marketing that he learned from his experience as a country music songwriter. His insights into the marketing field have been retooled for the science community and applied to finding a position, seeking grants, and having an impact on the public's perception of science. Because learning the skills of personal marketing is not typically a part of the educational experience for PhD candidates, this book offers a unique perspective that scientists at all stages of their careers will find interesting and perhaps useful.}},
author = {Wyld, Jean A.},
date-added = {2022-03-01 19:36:59 -0500},
date-modified = {2022-03-01 19:37:11 -0500},
doi = {10.1525/bio.2012.62.11.13},
eprint = {https://academic.oup.com/bioscience/article-pdf/62/11/998/19405693/62-11-998.pdf},
issn = {0006-3568},
journal = {BioScience},
month = {11},
number = {11},
pages = {998-1000},
title = {{A Marketing Tool Kit for Scientists}},
url = {https://doi.org/10.1525/bio.2012.62.11.13},
volume = {62},
year = {2012},
bdsk-url-1 = {https://doi.org/10.1525/bio.2012.62.11.13}}
@misc{McQuaid2018,
author = {Mike McQuaid},
date-added = {2022-03-01 19:32:43 -0500},
date-modified = {2022-03-01 19:33:32 -0500},
howpublished = {\url{https://mikemcquaid.com/2018/08/14/the-open-source-contributor-funnel-why-people-dont-contribute-to-your-open-source-project/}},
lastchecked = {March 2022},
month = {August},
title = {The Open Source Contributor Funnel (or: Why People Don't Contribute To Your Open Source Project)},
year = {2018},
bdsk-url-1 = {https://mikemcquaid.com/2018/08/14/the-open-source-contributor-funnel-why-people-dont-contribute-to-your-open-source-project/}}
@misc{Garcia2016,
annote = {- project should clearly outline what it does, who it is for, why it's different and when and where it should be used
- contributing guidelines
- easy and well-defined initial contributions
- code quality and documentation
- foster initial contributions
- look further than online (conferences, local user meet ups)},
author = {Jeremy Garcia},
date-added = {2022-03-01 19:27:53 -0500},
date-modified = {2022-03-01 19:28:55 -0500},
howpublished = {\url{https://opensource.com/business/16/9/how-to-get-programmers}},
lastchecked = {March 2022},
month = {September},
title = {How do you get programmers to join your project?},
year = {2016},
bdsk-url-1 = {https://opensource.com/business/16/9/how-to-get-programmers}}
@misc{Proffitt2017,
annote = {- build good on-ramps: make it easy to contribute, contributions are not just code, can also be documentation, design and even issue reports
- provide a list of easy to get started with tasks conbed with personal invitations
- recognize newcomers for their individuality},
author = {Brian Proffitt},
date-added = {2022-03-01 19:21:50 -0500},
date-modified = {2022-03-01 19:23:34 -0500},
howpublished = {\url{https://www.redhat.com/en/blog/how-attract-new-contributors}},
lastchecked = {March 2022},
month = {February},
title = {How to Attract New Contributors},
year = {2017},
bdsk-url-1 = {https://www.redhat.com/en/blog/how-attract-new-contributors}}
@misc{Jalan2016,
author = {Shubhkesha Jalan},
date-added = {2022-03-01 16:09:53 -0500},
date-modified = {2022-03-01 16:10:30 -0500},
howpublished = {\url{https://www.freecodecamp.org/news/how-to-attract-new-contributors-to-your-open-source-project-46f8b791d787/}},
month = {November},
title = {How to attract new contributors to your open source project},
year = {2016},
bdsk-url-1 = {https://www.freecodecamp.org/news/how-to-attract-new-contributors-to-your-open-source-project-46f8b791d787/}}
@misc{Smith2021-CitationsOnGitHub,
author = {Arfon Smith},
date-added = {2022-03-01 15:57:07 -0500},
date-modified = {2022-03-01 15:58:31 -0500},
howpublished = {\url{https://github.blog/2021-08-19-enhanced-support-citations-github/}},
lastchecked = {March 2022},
month = {March},
title = {Enhanced support for citations on GitHub},
year = {2022},
bdsk-url-1 = {https://github.blog/2021-08-19-enhanced-support-citations-github/}}
@misc{ChueHongEtAl2019,
author = {Chue Hong, Neil P. and Allen, Alice and Gonzalez-Beltran and de Waard, Anita and Smith, Arfon M. and Robinson, Carly and Jones, Catherine and Bouquin, Daina and Katz, Daniel S. and Kennedy, David and Ryder, Gerry and Hausman, Jessica and Hwang, Lorraine and Jones, Matthew B. and Harrison, Melissa and Crosas, Merc{\`e} and Wu, Mingfang and L{\"o}we, Peter and Haines, Robert and Edmunds, Scott and Stall, Shelley and Swaminathan, Sowmya and Druskat, Stephan and Crick, Tom and Morrell, Tom and Pollard, Tom},
date-added = {2022-03-01 15:50:31 -0500},
date-modified = {2022-03-01 15:50:54 -0500},
doi = {10.5281/zenodo.3482769},
month = oct,
publisher = {Zenodo},
title = {Software Citation Checklist for Developers},
url = {https://doi.org/10.5281/zenodo.3482769},
version = {0.9.0},
year = 2019,
bdsk-url-1 = {https://doi.org/10.5281/zenodo.3482769}}
@article{Jones2008,
author = {Jones, Capers},
date-added = {2022-03-01 14:35:56 -0500},
date-modified = {2022-03-01 14:38:41 -0500},
journal = {Crosstalk, The Journal of Defense Software Engineering},
month = {June},
number = {6},
pages = {11--13},
title = {Measuring Defect Potentials and Defect Removal Efficiency},
volume = {21},
year = {2008},
bdsk-url-1 = {https://epmc2.monsite-orange.fr/file/f5b78d8982ff536e2d6bd0fa65bf7c18.pdf},
bdsk-url-2 = {https://web.archive.org/web/20120806092322/http://www.crosstalkonline.org/storage/issue-archives/2008/200806/200806-0-Issue.pdf}}
@misc{SourceLevel2022_Lint,
author = {SourceLevel},
date-added = {2022-03-01 14:02:16 -0500},
date-modified = {2022-03-01 14:02:16 -0500},
howpublished = {\url{https://sourcelevel.io/blog/what-is-a-linter-and-why-your-team-should-use-it}},
lastchecked = {March, 2022},
month = {March},
title = {What is a linter and why your team should use it?},
year = {2022},
bdsk-url-1 = {https://sourcelevel.io/blog/what-is-a-linter-and-why-your-team-should-use-it}}
@misc{Wikipedia2022_Lint,
author = {Wikipedia},
date-added = {2022-03-01 13:58:20 -0500},
date-modified = {2022-03-01 13:59:45 -0500},
howpublished = {\url{https://en.wikipedia.org/wiki/Lint_(software)}},
lastchecked = {March, 2022},
month = {March},
title = {Lint (software)},
year = {2022},
bdsk-url-1 = {https://en.wikipedia.org/wiki/Lint_(software)}}
@article{Wilson2022,
annote = {The tips are:
Tip 1: Design after the fact.
Tip 2: Design for people's cognitive capacity.
Tip 3: Design in coherent levels.
Tip 4: Design for evolution.
Tip 5: Group related information together.
Tip 6: Use common patterns.
Tip 7: Design for delivery.
Tip 8: Design for testability.
Tip 9: Design as if code was data.
Tip 10: Design graphically.
Tip 11: Design with everyone in mind.
Tip 12: Design for contribution.
{Good advice, although the definition of informaiton hiding isn't quite right.}},
author = {Greg Wilson},
date-added = {2022-02-25 16:49:17 -0500},
date-modified = {2022-02-25 16:53:44 -0500},
doi = {10.1371/journal.pcbi.1009809},
journal = {{PLoS} Computational Biology},
month = {February},
number = {2},
pages = {1--12},
publisher = {Public Library of Science},
title = {Twelve quick tips for software design},
url = {https://doi.org/10.1371/journal.pcbi.1009809},
volume = {18},
year = {2022},
bdsk-url-1 = {https://journals.plos.org/ploscompbiol/article/comments?id=10.1371/journal.pcbi.1009809},
bdsk-url-2 = {https://doi.org/10.1371/journal.pcbi.1009809}}
@misc{Smith2022,
author = {Spencer Smith},
date-added = {2022-02-18 13:08:38 -0500},
date-modified = {2022-02-18 13:10:18 -0500},
doi = {10.17632/5dym63wn6z.1},
howpublished = {\url{https://data.mendeley.com/datasets/5dym63wn6z/1}},
month = {February},
title = {Software Quality Grades for Lattice Boltzmann Solvers},
year = {2022},
bdsk-url-1 = {https://data.mendeley.com/datasets/5dym63wn6z/1},
bdsk-url-2 = {https://doi.org/10.17632/5dym63wn6z.1}}
@misc{Szulik2017,
author = {Keenan Szulik},
date-added = {2022-02-17 20:40:18 -0500},
date-modified = {2022-02-17 20:40:59 -0500},
howpublished = {\url{https://blog.tidelift.com/dont-judge-a-project-by-its-github-stars-alone}},
month = {December},
title = {Don't judge a project by its GitHub stars alone},
year = {2017},
bdsk-url-1 = {https://blog.tidelift.com/dont-judge-a-project-by-its-github-stars-alone}}
@article{kaagstrom1998gemm,
author = {K{\aa}gstr{\"o}m, Bo and Ling, Per and Van Loan, Charles},
date-added = {2022-02-17 18:52:14 -0500},
date-modified = {2022-02-17 18:52:14 -0500},
journal = {ACM Transactions on Mathematical Software (TOMS)},
number = {3},
pages = {268--302},
publisher = {ACM New York, NY, USA},
title = {GEMM-based level 3 BLAS: High-performance model implementations and performance evaluation benchmark},
volume = {24},
year = {1998}}
@article{KatzEtAl2021,
author = {Katz, DS and Chue Hong, NP and Clark, T and Muench, A and Stall, S and Bouquin, D and Cannon, M and Edmunds, S and Faez, T and Feeney, P and Fenner, M and Friedman, M and Grenier, G and Harrison, M and Heber, J and Leary, A and MacCallum, C and Murray, H and Pastrana, E and Perry, K and Schuster, D and Stockhause, M and Yeston, J},
date-added = {2022-02-14 17:02:08 -0500},
date-modified = {2022-02-14 17:02:17 -0500},
doi = {10.12688/f1000research.26932.2},
journal = {F1000Research},
number = {1257},
title = {Recognizing the value of software: a software citation guide [version 2; peer review: 2 approved]},
volume = {9},
year = {2021},
bdsk-url-1 = {https://doi.org/10.12688/f1000research.26932.2}}
@misc{KaterbowAndFeulner2018,
author = {Katerbow, Matthias and Feulner, Georg},
date-added = {2022-02-14 13:28:37 -0500},
date-modified = {2022-02-14 13:28:55 -0500},
doi = {10.5281/zenodo.1172988},
month = mar,
publisher = {Zenodo},
title = {{Recommendations on the development, use and provision of Research Software}},
url = {https://doi.org/10.5281/zenodo.1172988},
year = 2018,
bdsk-url-1 = {https://doi.org/10.5281/zenodo.1172988}}
@article{Goble2014,
author = {Goble, Carole},
date-added = {2022-02-14 13:26:42 -0500},
date-modified = {2022-02-14 13:26:59 -0500},
doi = {10.1109/MIC.2014.88},
journal = {IEEE Internet Computing},
number = {5},
pages = {4-8},
title = {Better Software, Better Research},
volume = {18},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1109/MIC.2014.88},
bdsk-url-2 = {https://ieeexplore.ieee.org/document/6886129}}
@article{SmithEtAl2016-softcite,
abstract = {
Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.
},
author = {Smith, Arfon M and Katz, Daniel S and Niemeyer, Kyle E and FORCE11 Software Citation Working Group},
date-added = {2022-02-12 12:37:06 -0500},
date-modified = {2022-02-12 12:37:39 -0500},
doi = {10.7287/peerj.preprints.2169v4},
issn = {2167-9843},
journal = {PeerJ Preprints},
keywords = {Software citation, Software credit, Attribution},
month = aug,
pages = {e2169v4},
title = {Software Citation Principles},
url = {https://doi.org/10.7287/peerj.preprints.2169v4},
volume = 4,
year = 2016,
bdsk-url-1 = {https://doi.org/10.7287/peerj.preprints.2169v4}}
@article{SmithEtAl2018-joss,
abstract = {This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI).},
added-at = {2018-06-18T21:23:34.000+0200},
author = {Smith, Arfon M. and Niemeyer, Kyle E. and Katz, Daniel S. and Barba, Lorena A. and Githinji, George and Gymrek, Melissa and Huff, Kathryn D. and Madan, Christopher R. and Cabunoc Mayes, Abigail and Moerman, Kevin M. and Prins, Pjotr and Ram, Karthik and Rokem, Ariel and Teal, Tracy K. and Valls Guimera, Roman and Vanderplas, Jacob T.},
biburl = {https://www.bibsonomy.org/bibtex/2238e38acbe70ba5b4486a4257a7af754/pbett},
citeulike-article-id = {14538275},
citeulike-linkout-0 = {http://dx.doi.org/10.7717/peerj-cs.147},
date-added = {2022-02-12 12:32:29 -0500},
date-modified = {2022-02-12 12:32:47 -0500},
day = 12,
doi = {10.7717/peerj-cs.147},
interhash = {62038dc1e4723687b4d872a3513ff998},
intrahash = {238e38acbe70ba5b4486a4257a7af754},
issn = {2376-5992},
journal = {PeerJ Computer Science},
keywords = {software citations publishing},
month = feb,
pages = {e147+},
posted-at = {2018-02-20 10:50:05},
priority = {2},
timestamp = {2018-06-22T18:39:21.000+0200},
title = {Journal of Open Source Software (JOSS): design and first-year review},
url = {http://dx.doi.org/10.7717/peerj-cs.147},
volume = 4,
year = 2018,
bdsk-url-1 = {http://dx.doi.org/10.7717/peerj-cs.147}}
@article{HowisonAndBullard2016,
abstract = {Software is increasingly crucial to scholarship, yet the visibility and usefulness of software in the scientific record are in question. Just as with data, the visibility of software in publications is related to incentives to share software in reusable ways, and so promote efficient science. In this article, we examine software in publications through content analysis of a random sample of 90 biology articles. We develop a coding scheme to identify software "mentions" and classify them according to their characteristics and ability to realize the functions of citations. Overall, we find diverse and problematic practices: Only between 31% and 43% of mentions involve formal citations; informal mentions are very common, even in high impact factor journals and across different kinds of software. Software is frequently inaccessible 15%-29% of packages in any form; between 90% and 98% of specific versions; only between 24%-40% provide source code. Cites to publications are particularly poor at providing version information, whereas informal mentions are particularly poor at providing crediting information. We provide recommendations to improve the practice of software citation, highlighting recent nascent efforts. Software plays an increasingly great role in scientific practice; it deserves a clear and useful place in scholarly communication.},
address = {USA},
author = {Howison, James and Bullard, Julia},
date-added = {2022-02-12 12:30:48 -0500},
date-modified = {2022-02-12 12:31:00 -0500},
doi = {10.1002/asi.23538},
issn = {2330-1635},
issue_date = {September 2016},
journal = {J. Assoc. Inf. Sci. Technol.},
keywords = {bibliographic citations, journals, biology},
month = {sep},
number = {9},
numpages = {19},
pages = {2137--2155},
publisher = {John Wiley & Sons, Inc.},
title = {Software in the Scientific Literature: Problems with Seeing, Finding, and Using Software Mentioned in the Biology Literature},
url = {https://doi.org/10.1002/asi.23538},
volume = {67},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1002/asi.23538}}
@misc{VenigallaAndChimalakonda2021,
archiveprefix = {arXiv},
author = {Akhila Sri Manasa Venigalla and Sridhar Chimalakonda},
date-added = {2022-02-12 00:37:57 -0500},
date-modified = {2022-02-12 00:38:34 -0500},
eprint = {2102.12727},
primaryclass = {cs.SE},
title = {What's in a GitHub Repository? -- A Software Documentation Perspective},
year = {2021},
bdsk-url-1 = {https://arxiv.org/abs/2102.12727},
bdsk-url-2 = {https://arxiv.org/pdf/2102.12727.pdf}}
@book{Fogel2005,
abstract = {The corporate market is now embracing free, "open source" software like never before, as evidenced by the recent success of the technologies underlying LAMP (Linux, Apache, MySQL, and PHP). Each is the result of a publicly collaborative process among numerous developers who volunteer their time and energy to create better software. The truth is, however, that the overwhelming majority of free software projects fail. To help you beat the odds, O'Reilly has put together Producing Open Source Software, a guide that recommends tried and true steps to help free software developers work together toward a common goal. Not just for developers who are considering starting their own free software project, this book will also help those who want to participate in the process at any level. The book tackles this very complex topic by distilling it down into easily understandable parts. Starting with the basics of project management, it details specific tools used in free software projects, including version control, IRC, bug tracking, and Wikis. Author Karl Fogel, known for his work on CVS and Subversion, offers practical advice on how to set up and use a range of tools in combination with open mailing lists and archives. He also provides several chapters on the essentials of recruiting and motivating developers, as well as how to gain much-needed publicity for your project. While managing a team of enthusiastic developers -- most of whom you've never even met -- can be challenging, it can also be fun. Producing Open Source Software takes this into account, too, as it speaks of the sheer pleasure to be had from working with a motivated team of free software developers.},
author = {Fogel, Karl},
date-added = {2022-02-10 12:06:03 -0500},
date-modified = {2022-02-10 12:06:17 -0500},
isbn = {0596007590},
publisher = {O'Reilly Media, Inc.},
title = {Producing Open Source Software: How to Run a Successful Free Software Project},
year = {2005},
bdsk-url-1 = {https://producingoss.com/},
bdsk-url-2 = {https://producingoss.com/en/index.html}}
@misc{Genota2018,
author = {Lauraine Genota},
date-added = {2022-02-07 10:29:59 -0500},
date-modified = {2022-02-07 10:31:57 -0500},
howpublished = {Education Week, \url{https://www.edweek.org/teaching-learning/why-generation-z-learners-prefer-youtube-lessons-over-printed-books/2018/09}},
month = {Sept},
title = {Why Generation Z Learners Prefer YouTube Lessons Over Printed Books},
year = {2018},
bdsk-url-1 = {https://www.edweek.org/teaching-learning/why-generation-z-learners-prefer-youtube-lessons-over-printed-books/2018/09#:~:text=The%20visual%20aspect%20of%20videos,what%20they're%20writing.%E2%80%9D}}
@article{JungEtAl2022,
author = {Jung, Reiner and Gundlach, Sven and Hasselbring, Wilhelm},
date-added = {2022-02-03 11:47:37 -0500},
date-modified = {2022-03-17 12:18:59 -0400},
doi = {10.1016/j.envsoft.2022.105323},
issn = {1364-8152},
journal = {Environmental Modelling \& Software},
month = {Jan},
pages = {105323},
publisher = {Elsevier BV},
title = {Thematic Domain Analysis for Ocean Modeling},
url = {http://dx.doi.org/10.1016/j.envsoft.2022.105323},
year = {2022},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.envsoft.2022.105323},
bdsk-url-2 = {https://arxiv.org/pdf/2202.00747.pdf}}
@other{OrvizEtAl2017,
abstract = {The purpose of this document is to define a set of quality standards, procedures and best practices to conform a Software Quality Assurance plan to serve as a reference within the European research ecosystem related projects for the adequate development and timely delivery of software products.},
author = {Pablo Orviz and {\'A}lvaro L{\'o}pez Garc{\'\i}a and Doina Cristina Duma and Giacinto Donvito and Mario David and Jorge Gomes},
date-added = {2022-02-01 16:30:31 -0500},
date-modified = {2022-02-01 16:30:42 -0500},
doi = {10.20350/digitalCSIC/12543},
organization = {The INDIGO-DataCloud, DEEP-Hybrid-DataCloud and eXtreme-DataCloud projects have received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement number 653549, 777435 and 777367 respectively},
title = {A set of common software quality assurance baseline criteria for research projects},
year = {2017},
bdsk-url-1 = {https://doi.org/10.20350/digitalCSIC/12543}}
@misc{Zadka2018,
author = {Moshe Zadka},
date-added = {2022-02-01 14:26:16 -0500},
date-modified = {2022-02-01 14:26:55 -0500},
howpublished = {\url{https://opensource.com/article/18/12/tips-open-sourcing-python-libraries}},
month = {Dec},
title = {How to open source your Python library},
year = {2018},
bdsk-url-1 = {https://opensource.com/article/18/12/tips-open-sourcing-python-libraries}}
@misc{FLOSS2022,
author = {Free/Libre and Open Source Software},
date-added = {2022-02-01 14:24:14 -0500},
date-modified = {2022-02-01 14:25:10 -0500},
howpublished = {\url{https://bestpractices.coreinfrastructure.org/en/criteria/0}},
title = {{FLOSS} Best Practices Criteria (Passing Badge)},
year = {2022},
bdsk-url-1 = {https://bestpractices.coreinfrastructure.org/en/criteria/0}}
@misc{SSI2022,
author = {Software Sustainability Institute},
date-added = {2022-02-01 14:11:47 -0500},
date-modified = {2022-02-01 14:12:45 -0500},
howpublished = {\url{https://www.software.ac.uk/resources/online-sustainability-evaluation}},
title = {Online sustainability evaluation},
year = {2022},
bdsk-url-1 = {https://www.software.ac.uk/resources/online-sustainability-evaluation}}
@misc{Aragon2021,
author = {Selina Aragon},
date-added = {2022-02-01 14:04:53 -0500},
date-modified = {2022-02-01 14:05:43 -0500},
howpublished = {\url{https://www.software.ac.uk/blog/2021-11-30-improving-open-source-software-through-ssi-online-sustainability-evaluation}},
month = {November},
title = {Improving open source software through the {SSI} online sustainability evaluation},
year = {2021},
bdsk-url-1 = {https://www.software.ac.uk/blog/2021-11-30-improving-open-source-software-through-ssi-online-sustainability-evaluation},
bdsk-url-2 = {https://www.software.ac.uk/resources/online-sustainability-evaluation}}
@misc{ThielEtAl2020,
author = {Carsten Thiel},
date-added = {2022-02-01 13:53:46 -0500},
date-modified = {2022-02-01 14:00:13 -0500},
howpublished = {\url{https://technical-reference.readthedocs.io/en/latest/}},
title = {{EURISE} Network Technical Reference},
year = {2020},
bdsk-url-1 = {https://technical-reference.readthedocs.io/en/latest/}}
@misc{UofE2020,
author = {{Unniversity of Edinburgh}},
date-added = {2022-02-01 13:42:36 -0500},
date-modified = {2022-02-01 13:44:22 -0500},
howpublished = {\url{https://www.ed.ac.uk/files/atoms/files/quick_guide_8_-_fair_software_v1.2_0.pdf}},
month = {November},
title = {Research Data Support: Quick Guide 8, `{FAIR}' Software},
year = {2020},
bdsk-url-1 = {https://www.ed.ac.uk/files/atoms/files/quick_guide_8_-_fair_software_v1.2_0.pdf}}
@misc{Givler2020,
author = {Ray Givler},
date-added = {2022-02-01 13:40:17 -0500},
date-modified = {2022-02-01 13:41:02 -0500},
howpublished = {\url{https://www.linkedin.com/pulse/checklist-basic-software-engineering-practices-data-analysts-givler/?articleId=6681691007303630849}},
month = {June},
title = {A Checklist of Basic Software Engineering Practices for Data Analysts and Data Scientists},
year = {2020},
bdsk-url-1 = {https://www.linkedin.com/pulse/checklist-basic-software-engineering-practices-data-analysts-givler/?articleId=6681691007303630849}}
@article{Gomez-DiazAndRecio2019,
abstract = {Background: Evaluation of the quality of research software is a challenging and relevant issue, still not sufficiently addressed by the scientific community. Methods: Our contribution begins by defining, precisely but widely enough, the notions of research software and of its authors followed by a study of the evaluation issues, as the basis for the proposition of a sound assessment protocol: the CDUR procedure. Results: CDUR comprises four steps introduced as follows: Citation, to deal with correct RS identification, Dissemination, to measure good dissemination practices, Use, devoted to the evaluation of usability aspects, and Research, to assess the impact of the scientific work. Conclusions: Some conclusions and recommendations are finally included. The evaluation of research is the keystone to boost the evolution of the Open Science policies and practices. It is as well our belief that research software evaluation is a fundamental step to induce better research software practices and, thus, a step towards more efficient science.},
an = {31814965},
author = {Gomez-Diaz, Teresa and Recio, Tomas},
date = {2019/08/05},
date-added = {2022-02-01 13:34:48 -0500},
date-modified = {2022-02-01 13:35:22 -0500},
db = {PubMed},
doi = {10.12688/f1000research.19994.2},
isbn = {2046-1402},
j2 = {F1000Res},
journal = {F1000Research},
keywords = {*Open Science; *Research Software; *Research Software Citation; *Research Software Evaluation; *Research evaluation; *Scientific Software; Research; *Software},
l2 = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883399/},
la = {eng},
month = {08},
pages = {1353--1353},
publisher = {F1000 Research Limited},
title = {On the evaluation of research software: the CDUR procedure},
u1 = {31814965{$[$}pmid{$]$}},
u2 = {PMC6883399{$[$}pmcid{$]$}},
url = {https://pubmed.ncbi.nlm.nih.gov/31814965},
volume = {8},
year = {2019},
bdsk-url-1 = {https://pubmed.ncbi.nlm.nih.gov/31814965},
bdsk-url-2 = {https://doi.org/10.12688/f1000research.19994.2}}
@misc{HerouxEtAl2008,
author = {Michael A. Heroux and James M. Bieman and Robert T. Heaphy},
date-added = {2022-02-01 13:32:38 -0500},
date-modified = {2022-02-01 13:34:01 -0500},
howpublished = {\url{https://faculty.csbsju.edu/mheroux/fall2012_csci330/TrilinosDevGuide2.pdf}},
month = {April},
title = {Trilinos Developers Guide Part {II}: {ASC} Softwar Quality Engineering Practices Version 2.0},
year = {2008},
bdsk-url-1 = {https://faculty.csbsju.edu/mheroux/fall2012_csci330/TrilinosDevGuide2.pdf}}
@misc{SmithAndRoscoe2018,
abstractnote = {We are working toward the development of an Extreme-scale Scientific Software Development Kit (xSDK)---a collection of related and complementary software elements that provide the building blocks, tools, models, processes, and related artifacts for rapid and efficient development of high-quality applications. As an initial step in creating the xSDK, we have written a set of xSDK community package policies that a software package must satisfy in order to be xSDK compatible. The designation of a package being xSDK compatible informs potential users that the package can be easily used with other xSDK libraries and components and thus helps to address issues in long-term sustainability and interoperability among packages.},
author = {Smith, Barry and Bartlett, Roscoe and Developers, xSDK},
date-added = {2022-02-01 13:30:58 -0500},
date-modified = {2022-02-01 13:31:43 -0500},
doi = {10.6084/m9.figshare.4495136.v6},
month = {Dec},
publisher = {figshare},
title = {xSDK Community Package Policies},
url = {https://figshare.com/articles/journal_contribution/xSDK_Community_Package_Policies/4495136/6},
year = {2018},
bdsk-url-1 = {https://figshare.com/articles/journal_contribution/xSDK_Community_Package_Policies/4495136/6},
bdsk-url-2 = {https://doi.org/10.6084/m9.figshare.4495136.v6}}
@misc{HerouxAndBernholdt2018,
author = {Michael A. Heroux and David E. Bernholdt},
date-added = {2022-02-01 13:28:53 -0500},
date-modified = {2022-02-01 14:35:10 -0500},
doi = {https://figshare.com/articles/journal_contribution/ATPESC_Software_Productivity_03_Better_Small_Scientific_Software_Teams/6941438},
howpublished = {\url{https://press3.mcs.anl.gov//atpesc/files/2018/08/ATPESC_2018_Track-6_3_8-8_1030am_Bernholdt-Better_Scientific_Software_Teams.pdf}},
title = {Better (Small) Scientific Software Teams, tutorial in {A}rgonne Training Program on Extreme-Scale Computing ({ATPESC})},
year = {2018},
bdsk-url-1 = {https://press3.mcs.anl.gov//atpesc/files/2018/08/ATPESC_2018_Track-6_3_8-8_1030am_Bernholdt-Better_Scientific_Software_Teams.pdf},
bdsk-url-2 = {https://figshare.com/articles/journal_contribution/ATPESC_Software_Productivity_03_Better_Small_Scientific_Software_Teams/6941438}}
@misc{Brown2015,
author = {Titus Brown},
date-added = {2022-02-01 11:42:23 -0500},
date-modified = {2022-02-01 11:44:09 -0500},
howpublished = {\url{http://ivory.idyll.org/blog/2015-growing-sustainable-software-development-process.html}},
month = {June},
title = {Notes from``How to grow a sustainable software development process (for scientific software)''},
year = {2015},
bdsk-url-1 = {http://ivory.idyll.org/blog/2015-growing-sustainable-software-development-process.html}}
@misc{TobiasEtAl2018,
author = {Schlauch, Tobias and Meinel, Michael and Haupt, Carina},
date-added = {2022-01-31 18:31:14 -0500},
date-modified = {2022-02-01 11:24:43 -0500},
doi = {10.5281/zenodo.1344612},
month = aug,
publisher = {Zenodo},
title = {DLR Software Engineering Guidelines},
url = {https://doi.org/10.5281/zenodo.1344612},
version = {1.0.0},
year = 2018,
bdsk-url-1 = {https://doi.org/10.5281/zenodo.1344612}}
@misc{USGS2019,
author = {{USGS}},
date-added = {2022-01-31 18:21:31 -0500},
date-modified = {2022-03-30 17:08:24 -0400},
howpublished = {\url{https://www.usgs.gov/media/files/usgs-software-planning-checklist}},
month = {December},
title = {{USGS} (United States Geological Survey) Software Plannning Checklist},
year = {2019},
bdsk-url-1 = {https://www.usgs.gov/media/files/usgs-software-planning-checklist}}
@misc{Yo2021,
author = {Yehudi, Yo},
date-added = {2022-01-31 18:12:15 -0500},
date-modified = {2022-01-31 18:12:32 -0500},
doi = {10.5281/zenodo.5655023},
month = nov,
publisher = {Zenodo},
title = {Open Source for Researchers - Lightning talk},
url = {https://doi.org/10.5281/zenodo.5655023},
year = 2021,
bdsk-url-1 = {https://doi.org/10.5281/zenodo.5655023}}
@article{Perkel2020,
author = {Jeffrey M. Perkel},
date-added = {2022-01-30 12:43:35 -0500},
date-modified = {2022-01-30 12:45:47 -0500},
doi = {doi: https://doi.org/10.1038/d41586-020-02462-7},
journal = {Nature Technology Features},
month = {Aug},
number = {584},
pages = {656--658},
title = {Challenge to scientists: does your ten-year-old code still run?},
year = {2020},
bdsk-url-1 = {https://www.nature.com/articles/d41586-020-02462-7},
bdsk-url-2 = {doi:%20https://doi.org/10.1038/d41586-020-02462-7}}
@article{GualaEtAl2022,
annote = {doi: 10.1016/j.jcmg.2021.09.023
- the required imaging seems extensive - does this make the technique less practical?
- they used Matlab to automatically extract thoracic aortic diameters
- they didn't use simulation; they used imaging
- used statistics},
author = {Guala Andrea and Dux-Santoy Lydia and Teixido-Tura Gisela and Ruiz-Mu{\~n}oz Aroa and Galian-Gay Laura and Servato Maria Luz and Valente Filipa and Guti{\'e}rrez Laura and Gonz{\'a}lez-Alujas Teresa and Johnson Kevin M. and Wieben Oliver and Casas-Masnou Guillem and Sao Avil{\'e}s Augusto and Fernandez-Galera Ruben and Ferreira-Gonzalez Ignacio and Evangelista Arturo and Rodr{\'\i}guez-Palomares Jose F.},
date = {2022/01/01},
date-added = {2022-01-22 12:35:18 -0500},
date-modified = {2022-01-22 12:44:50 -0500},
doi = {10.1016/j.jcmg.2021.09.023},
journal = {JACC: Cardiovascular Imaging},
journal1 = {JACC: Cardiovascular Imaging},
journal2 = {JACC: Cardiovascular Imaging},
month = {2022/01/22},
number = {1},
pages = {46--56},
publisher = {American College of Cardiology Foundation},
title = {Wall Shear Stress Predicts Aortic Dilation in Patients With Bicuspid Aortic Valve},
type = {doi: 10.1016/j.jcmg.2021.09.023},
url = {https://doi.org/10.1016/j.jcmg.2021.09.023},
volume = {15},
year = {2022},
year1 = {2022},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1016/j.jcmg.2021.09.023}}
@inproceedings{UditAndKatz2017,
author = {Nangia, Udit and Katz, Daniel S.},
date-added = {2022-01-18 11:07:34 -0500},
date-modified = {2022-02-12 11:53:58 -0500},
doi = {10.5281/zenodo.814220},
month = jun,
note = {{This paper was submitted to WSSSPE5.1 - http://wssspe.researchcomputing.org.uk/wssspe5-1/ The final accepted version is https://doi.org/10.6084/m9.figshare.5328442}},
pages = {1--6},
publisher = {Zenodo},
title = {{Track 1 Paper: Surveying the U.S. National Postdoctoral Association Regarding Software Use and Training in Research}},
url = {https://doi.org/10.5281/zenodo.814220},
year = 2017,
bdsk-url-1 = {https://doi.org/10.5281/zenodo.814220},
bdsk-url-2 = {https://danielskatz.org/papers/postdocsurveyfull_WSSSPE5.1.pdf}}
@article{LethbridgeEtAl2003,
author = {Lethbridge, T.C. and Singer, J. and Forward, A.},
date-added = {2022-01-12 18:20:24 -0500},
date-modified = {2022-01-12 18:22:51 -0500},
doi = {10.1109/MS.2003.1241364},
journal = {IEEE Software},
number = {6},
pages = {35-39},
title = {How software engineers use documentation: the state of the practice},
volume = {20},
year = {2003},
bdsk-url-1 = {https://doi.org/10.1109/MS.2003.1241364},
bdsk-url-2 = {https://www.researchgate.net/publication/3247967_How_Software_Engineers_Use_Documentation_The_State_of_the_Practice}}
@inproceedings{PintoEtAl2016,
author = {Pinto, Gustavo and Steinmacher, Igor and Gerosa, Marco Aur{\'e}lio},
booktitle = {2016 IEEE 23rd International Conference on Software Analysis, Evolution, and Reengineering (SANER)},
date-added = {2022-01-12 18:15:48 -0500},
date-modified = {2022-01-12 18:15:59 -0500},
doi = {10.1109/SANER.2016.68},
pages = {112-123},
title = {More Common Than You Think: An In-depth Study of Casual Contributors},
volume = {1},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1109/SANER.2016.68},
bdsk-url-2 = {https://www.researchgate.net/profile/Marco-Aurelio-Gerosa/publication/303513465_More_Common_Than_You_Think_An_In-depth_Study_of_Casual_Contributors/links/5b2fdba4a6fdcc8506cb80d2/More-Common-Than-You-Think-An-In-depth-Study-of-Casual-Contributors.pdf}}
@article{Carver2016,
author = {Carver, Jeffrey C.},
date-added = {2022-01-12 17:50:33 -0500},
date-modified = {2022-01-12 17:50:52 -0500},
doi = {10.1109/MCSE.2016.31},
isbn = {1521-9615},
journal = {Computing in Science \& Engineering},
keywords = {Software engineering; validation; testing; scientific computing},
l2 = {http://resolver.scholarsportal.info/resolve/15219615/v18i0002/4_sefs},
n2 = {AEIC Jeffrey C. Carver describes ways to improve software engineering for science, introduces the Software Engineering Track for CiSE magazine, and provides a link to a survey that can inform future progress.},
number = {2},
pages = {4--5},
publisher = {IEEE},
title = {Software Engineering for Science},
volume = {18},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1109/MCSE.2016.31}}
@misc{PranaEtAl2018,
abstract = {README files play an essential role in shaping a developer's first impression of a software repository and in documenting the software project that the repository hosts. Yet, we lack a systematic understanding of the content of a typical README file as well as tools that can process these files automatically. To close this gap, we conduct a qualitative study involving the manual annotation of 4,226 README file sections from 393 randomly sampled GitHub repositories and we design and evaluate a classifier and a set of features that can categorize these sections automatically. We find that information discussing the `What' and `How' of a repository is very common, while many README files lack information regarding the purpose and status of a repository. Our multi-label classifier which can predict eight different categories achieves an F1 score of 0.746. To evaluate the usefulness of the classification, we used the automatically determined classes to label sections in GitHub README files using badges and showed files with and without these badges to twenty software professionals. The majority of participants perceived the automated labeling of sections based on our classifier to ease information discovery. This work enables the owners of software repositories to improve the quality of their documentation and it has the potential to make it easier for the software development community to discover relevant information in GitHub README files.},
annote = {- categorizes the knowledge typically in README files
- shows a technique for verifying manual annotations by having two annotators and comparing their decisions},
archiveprefix = {arXiv},
author = {Gede Artha Azriadi Prana and Christoph Treude and Ferdian Thung and Thushari Atapattu and David Lo},
date-added = {2022-01-07 17:21:22 -0500},
date-modified = {2022-01-07 17:22:04 -0500},
eprint = {1802.06997},
primaryclass = {cs.SE},
title = {Categorizing the Content of GitHub README Files},
year = {2018},
bdsk-url-1 = {https://arxiv.org/abs/1802.06997},
bdsk-url-2 = {https://arxiv.org/pdf/1802.06997.pdf}}
@article{NassifEtAl2021,
abstract = {Software projects capture redundant information in various kinds of artifacts, as specifications from the source code are also tested and documented. Such redundancy provides an opportunity to reduce development effort by supporting the joint generation of different types of artifact. We introduce a tool-supported technique, called DScribe, that allows developers to combine unit tests and documentation templates, and to invoke those templates to generate documentation and unit tests. DScribe supports the detection and replacement of outdated documentation, and the use of templates can encourage extensive test suites with a consistent style. Our evaluation of 835 specifications revealed that 85% were not tested or correctly documented, and DScribe could be used to automatically generate 97% of the tests and documentation. An additional study revealed that tests generated by DScribe are more focused and readable than those written by human testers or generated by state-of-the-art automated techniques.},
annote = {``{\ldots}, the redundancy between
tests and documentation exacerbates the repetitiveness of the
testing and documentation effort. As a result, studies have
found recurrent issues in documentation [6] and unit tests [7],
[8], such as a lack of completeness and up-to-dateness.''},
author = {Nassif, Mathieu and Hernandez, Alexa and Sridharan, Ashvitha and Robillard, Martin P.},
date-added = {2022-01-07 16:59:25 -0500},
date-modified = {2022-01-07 17:00:11 -0500},
doi = {10.1109/TSE.2021.3087087},
issn = {1939-3520},
journal = {IEEE Transactions on Software Engineering},
pages = {1-1},
title = {Generating Unit Tests for Documentation},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1109/TSE.2021.3087087},
bdsk-url-2 = {https://www.cs.mcgill.ca/~martin/papers/tse2021a.pdf}}
@article{NassifAndRobillard2021,
abstract = {Context. The computational linguistics community has developed tools, called
wikifiers, to identify links to Wikipedia articles from free-form text. Software
engineering research can leverage wikifiers to add semantic information to
software artifacts. However, no empirically-grounded basis exists to choose an
effective wikifier and to configure it for the software domain, on which wikifiers
were not specifically trained.
Objective. We conducted a study to guide the selection of a wikifier and its
configuration for applications in the software domain, and to measure what
performance can be expected of wikifiers.
Method. We applied six wikifiers, with multiple configurations, to a sample of
500 Stack Overflow posts. We manually annotated the 41 124 articles identified
by the wikifiers as correct or not to compare their precision and recall.
Results. Each wikifier, in turn, achieved the highest precision, between 13%
and 82%, for different thresholds of recall, from 60% to 5%. However, filtering
the wikifiers' output with a whitelist can considerably improve the precision
above 79% for recall up to 30%, and above 47% for recall up to 60%.
Conclusions. Results reported in each wikifier's original article cannot be generalized to software-specific documents. Given that no wikifier performs universally better than all others, we provide empirically grounded insights to
select a wikifier for different scenarios, and suggest ways to further improve
their performance for the software domain.},
annote = {- difficult to do for software engineering articles, because of the natural language incorporates words and code together
{could likely process Drasil text to add links, if this was something we wanted to do}},
author = {Mathieu Nassif and Martin P. Robillard},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/journals/ese/NassifR21.bib},
date-added = {2022-01-07 16:44:17 -0500},
date-modified = {2022-01-07 16:46:11 -0500},
doi = {10.1007/s10664-020-09918-4},
journal = {Empir. Softw. Eng.},
keywords = {Wikipedia, Wikification, Comparative Evaluation, Stack Overflow, Knowledge-Driven Software Engineering},
number = {2},
pages = {31},
timestamp = {Tue, 23 Mar 2021 00:00:00 +0100},
title = {Wikifying software artifacts},
url = {https://doi.org/10.1007/s10664-020-09918-4},
volume = {26},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1007/s10664-020-09918-4},
bdsk-url-2 = {https://www.cs.mcgill.ca/~martin/papers/ese2021.pdf}}
@article{JimenezEtAl2017,
abstract = {Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
},
annote = {1. Make source code publicly accessible from day one
2. Make software easy to discover by providing software metadata via a popular community registry
3. Adopt a licence and comply with the licence of third-party dependencies
4. Define clear and transparent contribution, governance and communication processes
},
author = {Jim{\'e}nez RC, Kuzak M and Alhamdoosh M and et al.},
date-added = {2022-01-06 15:31:48 -0500},
date-modified = {2022-01-06 15:33:42 -0500},
doi = {10.12688/f1000research.11407.1},
journal = {F1000Research},
number = {876},
title = {Four simple recommendations to encourage best practices in research software [version 1; peer review: 3 approved]},
volume = {6},
year = {2017},
bdsk-url-1 = {https://doi.org/10.12688/f1000research.11407.1}}
@article{PiccoloAndFrampton2016,
abstract = {{When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced because of complexities in how software is packaged, installed, and executed---and because of limitations associated with how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges; here we describe seven such strategies. With a broad scientific audience in mind, we describe the strengths and limitations of each approach, as well as the circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.}},
annote = {- techniques listed/described for computational reproducibility:
- narrative descriptions
- custom scripts ad code for automation
- software frameworks (libraries with version numbers)
- literate programming (IPython, Jupyter, knitr_
- workflow management systems
- virtual machines
- software containers},
author = {Piccolo, Stephen R and Frampton, Michael B},
date-added = {2022-01-06 14:27:16 -0500},
date-modified = {2022-01-06 14:28:41 -0500},
doi = {10.1186/s13742-016-0135-4},
eprint = {https://academic.oup.com/gigascience/article-pdf/5/1/s13742-016-0135-4/25513324/13742\_2016\_article\_135.pdf},
issn = {2047-217X},
journal = {GigaScience},
month = {07},
note = {s13742-016-0135-4},
number = {1},
title = {{Tools and techniques for computational reproducibility}},
url = {https://doi.org/10.1186/s13742-016-0135-4},
volume = {5},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1186/s13742-016-0135-4}}
@article{EglenEtAl2017,
abstract = {Computational techniques are central in many areas of neuroscience and are relatively easy to share. This paper describes why computer programs underlying scientific publications should be shared and lists simple steps for sharing. Together with ongoing efforts in data sharing, this should aid reproducibility of research.},
annote = {Simple steps to help you share code
- Version control
- Persistent URLs
- License
- Etiquette (``When working with code written by others, observe Daniel Kahneman's 'reproducibility etiquette'24 and have a discussion with the authors of the code to give them a chance to fix bugs or respond to issues you have identified before you make any public statements.'')
- Documentation
- Tools (Org mode, IPython/Jupyter, Knitr (knitr is an engine for dynamic report generation with R. It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. The purpose of knitr is to allow reproducible research in R through the means of literate programming), Virtualization environments (VirtualBox, Docker))
- Case studies (follow existing successful examples - for instance Stanford Memory Lab publications are on GitHub with instructions on how to reproduce the figures (https://github.com/WagnerLabPapers))
- Data (should be released and made available)
- Standards (Use of (community) standards, where appropriate, should be encouraged, particularly use of nonproprietary formats to enable long-term accessibility.)
- Tests (``We recommend including test suites demonstrating that the code is producing the correct results''); ``Linking tests to continuous integration services (such as Travis CI, https://travis-ci.org) allows these tests to be automatically run each time a change is made to the code, ensuring that failing tests are immediately flagged and can be dealt with quickly.'')
- User support},
author = {Eglen, Stephen J and Marwick, Ben and Halchenko, Yaroslav O and Hanke, Michael and Sufi, Shoaib and Gleeson, Padraig and Silver, R Angus and Davison, Andrew P and Lanyon, Linda and Abrams, Mathew and Wachtler, Thomas and Willshaw, David J and Pouzat, Christophe and Poline, Jean-Baptiste},
date = {2017/06/01},
date-added = {2022-01-06 14:06:23 -0500},
date-modified = {2022-01-06 14:16:54 -0500},
doi = {10.1038/nn.4550},
id = {Eglen2017},
isbn = {1546-1726},
journal = {Nature Neuroscience},
number = {6},
pages = {770--773},
title = {Toward standard practices for sharing computer code and programs in neuroscience},
url = {https://doi.org/10.1038/nn.4550},
volume = {20},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1038/nn.4550}}
@article{AlNoamanyAndBorghi2018,
abstract = {Research software, which includes both source code and executables used as part of
the research process, presents a significant challenge for efforts aimed at ensuring
reproducibility. In order to inform such efforts, we conducted a survey to better
understand the characteristics of research software as well as how it is created, used,
and shared by researchers. Based on the responses of 215 participants, representing a
range of research disciplines, we found that researchers create, use, and share software
in a wide variety of forms for a wide variety of purposes, including data collection,
data analysis, data visualization, data cleaning and organization, and automation. More
participants indicated that they use open source software than commercial software.
While a relatively small number of programming languages (e.g., Python, R, JavaScript,
C++, MATLAB) are used by a large number, there is a long tail of languages used by
relatively few. Between-group comparisons revealed that significantly more participants
from computer science write source code and create executables than participants from
other disciplines. Differences between researchers from computer science and other
disciplines related to the knowledge of best practices of software creation and sharing
were not statistically significant. While many participants indicated that they draw
a distinction between the sharing and preservation of software, related practices and
perceptions were often not aligned with those of the broader scholarly communications
community.
- has a table showing the top ten languages, includes Python, R, SQL, Javascript, C++, Matlab, Java, C, PHP and PERL},
annote = {`` Software-related best practices have
been outlined for both individuals working in specific research disciplines (Eglen et al.,
2017; Marwick, 2017) and for the research community in general (e.g., Piccolo & Frampton,
2016; Sandve et al., 2013; Jimenez et al., 2017). In general, such best practice documents
focus on the importance of concepts such as proper documentation and version control
in ensuring that code is shared in a way that facilitates computational reproducibility. In
contrast, the focus of community organizations such as The Carpentries (Wilson, 2006;
Teal et al., 2015) and the Software Sustainability Institute (Crouch et al., 2013) is training
researchers to better develop, use, and maintain software tools. Bridging the perspectives of
stakeholders focused on encouraging best practices in sharing software and those focused
on educating researchers in its creation and use are organizations such as Force11, who
have published guidelines for describing and citing software in the scholarly literature
(Smith, Katz & Niemeyer, 2016).''
- found 81% use version control},
author = {Yasmin AlNoamany and John A. Borghi},
date-added = {2022-01-06 13:26:52 -0500},
date-modified = {2022-01-06 15:07:13 -0500},
journal = {PeerJ Computer Science},
month = {September},
number = {e163},
pages = {1--25},
title = {Towards computational reproducibility: researcher perspectives on the use and sharing of software},
volume = {4},
year = {2018},
bdsk-url-1 = {https://peerj.com/articles/cs-163/#}}
@misc{vanGompelEtAl2016,
author = {Maarten van Gompel and Jauco Noordzij and Reinier de Valk and Andrea Scharnhorst},
date-added = {2022-01-05 16:06:16 -0500},
date-modified = {2022-01-05 16:08:36 -0500},
howpublished = {\url{https://github.com/CLARIAH/software-quality-guidelines/blob/master/softwareguidelines.pdf}},
month = {September},
title = {Guidelines for Software Quality, {CLARIAH} Task Force 54.100},
year = {2016},
bdsk-url-1 = {https://github.com/CLARIAH/software-quality-guidelines/blob/master/softwareguidelines.pdf}}
@misc{BrettEtAl2021,
author = {Alys Brett and James Cook and Peter Fox and Ian Hinder and John Nonweiler and Richard Reeve and Robert Turner},
date-added = {2022-01-05 15:57:17 -0500},
date-modified = {2022-01-05 15:58:42 -0500},
howpublished = {\url{https://github.com/ScottishCovidResponse/modelling-software-checklist/blob/main/software-checklist.md}},
month = {August},
title = {Scottish Covid-19 Response Consortium},
year = {2021},
bdsk-url-1 = {https://github.com/ScottishCovidResponse/modelling-software-checklist/blob/main/software-checklist.md}}
@misc{SchlauchEtAl2018,
author = {T. Schlauch and M. Meinel and C. Haupt},
date-added = {2022-01-05 15:53:18 -0500},
date-modified = {2022-01-05 15:54:55 -0500},
howpublished = {\url{https://doi.org/10.5281/zenodo.1344612}},
month = {August},
title = {DLR Software Engineering Guidelines},
year = {2018},
bdsk-url-1 = {https://zenodo.org/record/1344612#.YdXihRPMJm8}}
@inproceedings{Smith2021,
author = {Spencer Smith},
booktitle = {Sponsored by the U.S. Department of Energy, Office of Advanced Scientific Computing Research},
date-added = {2022-01-03 14:46:11 -0500},
date-modified = {2022-01-03 14:51:32 -0500},
month = {Dec},
title = {Workshop on the Science of Scientific-Software Development and Use (Panel Discussion)},
year = {2021},
bdsk-url-1 = {https://web.cvent.com/event/1b7d7c3a-e9b4-409d-ae2b-284779cfe72f/websitePage:645d57e4-75eb-4769-b2c0-f201a0bfc6ce}}
@misc{SmithAndCarette2021,
archiveprefix = {arXiv},
author = {Spencer Smith and Jacques Carette},
date-added = {2022-01-03 14:33:05 -0500},
date-modified = {2022-11-04 16:21:55 -0400},
eprint = {2112.12580},
howpublished = {\url{https://arxiv.org/abs/2112.12580}},
month = {Dec},
note = {3 pp.},
primaryclass = {cs.SE},
title = {Long-Term Productivity Based on Science, not Preference},
year = {2021},
bdsk-url-1 = {https://arxiv.org/abs/2112.12580},
bdsk-url-2 = {https://arxiv.org/pdf/2112.12580.pdf}}
@article{DalpiazEtAl2018,
abstract = {As part of the growing interest in natural language processing for requirements engineering (RE), RE researchers, computational linguists, and industry practitioners met at the First Workshop on Natural Language Processing for Requirements Engineering (NLP4RE 18). This article summarizes the workshop and presents an overview of the discussion held on the field's future. This article is part of a theme issue on software engineering's 50th anniversary.},
annote = {Related to these on-line requirements repos:
- https://zenodo.org/record/1414117
- https://data.mendeley.com/datasets/7zbk8zsd8y/1
- https://zenodo.org/record/268542},
author = {Dalpiaz, Fabiano and Ferrari, Alessio and Franch, Xavier and Palomares, Cristina},
date-added = {2021-12-17 15:16:42 -0500},
date-modified = {2021-12-17 15:17:55 -0500},
doi = {10.1109/MS.2018.3571242},
journal = {IEEE Software},
number = {5},
pages = {115-119},
title = {Natural Language Processing for Requirements Engineering: The Best Is Yet to Come},
volume = {35},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1109/MS.2018.3571242},
bdsk-url-2 = {https://ieeexplore.ieee.org/document/8474507}}
@misc{HerouxEtAl2021,
annote = {- A variety of community reports have expressed the importance of increasing direct investment in scientific
software itself, not just as a byproduct of other research [1, 2, 3, 4, 5, 6, 7, 8]
- Even so, the scientific software community is a small part of the overall software
ecosystem and, from our observations, has received only modest attention from the
professional software community in comparison with other target domains.
- we believe there are unique opportunities for the scientific software
community to contribute to and benefit from R&D efforts in the science of research software
[15].
- {seems like they might have confused agile and waterfall, since say the problem for agile is that ``at the outset one may not know what to code, as
research is needed to determine appropriate algorithms, and then further research may be
needed to determine the most performant data structures and methods''}
- ``It is important for developers to realize that to a software user, the time to solution is the total
time, including startup time to learn the software, time to set up the problem within the software,
time to debug the setup, time to run, and time to analyze the data and/or visualize it. On the
other hand, it does not make sense to create an advanced and sophisticated graphical user
interface, which might require a team of multiple developers, to set up a run for some aspect of
computational software if that software has only a few users.''
{They mention AI multiple times. Could imagine using Drasil with AI to generate code and docs.}
- ``As a simple example, consider the challenges in applying the Scrum methodology to
settings where developers are often neither co-located nor dedicated to the project.''
- ``Scientific approaches to learning how to develop scientific software ultimately are of no use
without being taken up by the community. It is expected that there will be resistance to
changing methods, as there always is. So it is important that from the outset, those studying
how to improve methods have thoughts early on about how they would communicate their
effectiveness to a wider audience. Naturally, there will be a need for workshops and tutorials,
but these are greatly strengthened by showing the effectiveness of new methods in developing
non-trivial scientific applications.''},
author = {Michael A. Heroux and David Bernholdt and Lois Curfman Mcinnes and John Cary},
date-added = {2021-12-10 10:19:24 -0500},
date-modified = {2021-12-12 16:51:24 -0500},
howpublished = {\url{https://custom.cvent.com/DCBD4ADAAD004096B1E4AD96F3C8049E/files/event/1b7d7c3ae9b4409dae2b284779cfe72f/ed545ea9af834c1da1dfaf6e7570169f.pdf}},
month = {December},
title = {The Science of Scientific-Software Development and Use},
year = {2021},
bdsk-url-1 = {https://custom.cvent.com/DCBD4ADAAD004096B1E4AD96F3C8049E/files/event/1b7d7c3ae9b4409dae2b284779cfe72f/ed545ea9af834c1da1dfaf6e7570169f.pdf}}
@article{HasertEtAl2014,
abstract = {We present the open source Lattice Boltzmann solver Musubi. It is part of the parallel simulation framework APES, which utilizes octrees to represent sparse meshes and provides tools from automatic mesh generation to post-processing. The octree mesh representation enables the handling of arbitrarily complex simulation domains, even on massively parallel systems. Local grid refinement is implemented by several interpolation schemes in Musubi. Various kernels provide different physical models based on stream-collide algorithms. These models can be computed concurrently and can be coupled with each other. This paper explains our approach to provide a flexible yet scalable simulation environment and elaborates its design principles and implementation details. The efficiency of our approach is demonstrated with a performance evaluation on two supercomputers and a comparison to the widely used Lattice Boltzmann solver Palabos.},
author = {Manuel Hasert and Kannan Masilamani and Simon Zimny and Harald Klimach and Jiaxing Qi and J{\"o}rg Bernsdorf and Sabine Roller},
date-added = {2021-12-09 17:24:41 -0500},
date-modified = {2021-12-09 17:24:41 -0500},
doi = {https://doi.org/10.1016/j.jocs.2013.11.001},
issn = {1877-7503},
journal = {Journal of Computational Science},
keywords = {Octree, Parallel computing, Computational fluid dynamics, Lattice Boltzmann Method},
number = {5},
pages = {784-794},
title = {Complex fluid simulations with the parallel tree-based Lattice Boltzmann solver Musubi},
url = {https://www.sciencedirect.com/science/article/pii/S1877750313001270},
volume = {5},
year = {2014},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S1877750313001270},
bdsk-url-2 = {https://doi.org/10.1016/j.jocs.2013.11.001}}
@article{AnwarAndSukop2009,
abstract = {Lattice Boltzmann (LB) models can be used to simulate flow in porous media at scales much larger than pore size. LB-based models for such macroscopic scale porous media flow simulations are an extension of standard LB models. There are at least two alternative approaches for implementing such models. In the first approach the local velocity is altered during the collision step by incorporating an external force, F, equivalent to the damping effect of solid particles in porous media. The porous media can be permeable or impermeable depending upon the external forcing term. A sink term is introduced in the LB model to simulate a pumping well and this model is further applied to solve transient ground water well problems for confined aquifers. Directly solving the ground water flow equation with an LB model by exploiting its ability to solve the diffusion equation is another strategy. The second order transient ground water flow equation is analogous to the diffusion equation and mass diffusivity is analogous to hydraulic diffusivity. This diffusion model is used to solve transient ground water problems. Simulated results accurately match analytical solutions of the transient ground water flow equation.},
author = {Shadab Anwar and Michael C. Sukop},
date-added = {2021-12-09 14:33:29 -0500},
date-modified = {2021-12-09 15:17:12 -0500},
doi = {https://doi.org/10.1016/j.camwa.2009.02.025},
issn = {0898-1221},
journal = {Computers \& Mathematics with Applications},
keywords = {Porous media, Theis solution, Lattice Boltzmann, Ground water},
note = {Mesoscopic Methods in Engineering and Science},
number = {5},
pages = {1015-1023},
title = {Regional scale transient groundwater flow modeling using Lattice Boltzmann methods},
url = {https://www.sciencedirect.com/science/article/pii/S0898122109001060},
volume = {58},
year = {2009},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0898122109001060},
bdsk-url-2 = {https://doi.org/10.1016/j.camwa.2009.02.025}}
@article{ZhangEtAl2018,
abstract = {Polymer electrolyte membrane (PEM) fuel cells have higher efficiency and energy density and are capable of rapidly adjusting to power demands. Effective water management is one of the key issues for increasing the efficiency of PEMFC. In the current study, a three-dimensional (3D) lattice Boltzmann model is developed to simulate the water transport and oxygen diffusion in the gas diffusion layer (GDL) of PEM fuel cells with electrochemical reaction on the catalyst layer taken into account. In this paper, we demonstrate that this model is able to predict the liquid and gas flow fields within the 3D GDL structure and how they change with time. With the two-phase flow and electrochemical reaction coupled in the model, concentration of oxygen through the GDL and current density distribution can also be predicted. The model is then used to investigate the effect of microporous layer on the cell performance in 2D to reduce the computational cost. The results clearly show that the liquid water content can be reduced with the existence of microporous layer and thus the current density can be increased.},
author = {Duo Zhang and Qiong Cai and Sai Gu},
date-added = {2021-12-09 14:25:27 -0500},
date-modified = {2021-12-09 14:25:39 -0500},
doi = {https://doi.org/10.1016/j.electacta.2017.12.189},
issn = {0013-4686},
journal = {Electrochimica Acta},
keywords = {Polymer electrolyte membrane(PEM) fuel cells, Lattice Boltzmann method, Two-phase flow, Oxygen diffusion, Electrochemical reaction},
pages = {282-296},
title = {Three-dimensional lattice-Boltzmann model for liquid water transport and oxygen diffusion in cathode of polymer electrolyte membrane fuel cell with electrochemical reaction},
url = {https://www.sciencedirect.com/science/article/pii/S0013468617327639},
volume = {262},
year = {2018},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0013468617327639},
bdsk-url-2 = {https://doi.org/10.1016/j.electacta.2017.12.189}}
@article{CarverEtAl2022,
annote = {- nice reference on 90-95% of researchers relying on research software
- mention of Carpentries, IRIS-HEP (should look at) and MolSSI (should look at)
- difficult for researchers to find and use research software (Joppa et al, 2013)
- lack of standards and platforms for categorizing software for communities often leads to re-developing instead of reusing solutions (Howison et al, 2015)
- {should look at pain point papers - Pinto et al, 2018 and Wiese et al 2020}
- great review of the literature on studies of scientific software development
- maybe should point out the scientific software is the same thing as research software
- great information on the neglect (and importance) of requirements
- traceability between survey questions and RQs?
- were results different for different disciplines? they asked the respondents for this information
- future work should look at what the projects actually do, not just what they claim that they do - this is the work that Olu is currently doing
- excellent way to promote Drasil through the Tools support for development activities - less than 30% of respondents reported requirements, design, maintenance and documentation as well-supported
- use of CI can be contrated with the results from Ao's SOP paper
- do the respondents know what the terminology means - requirements, software carpentry, etc.?
- follow up interviews to fully explore, make sure understand?
- future work?
- threats to validity?
- Olu can compare her work to what the results of the surveys say - how many people actually write something that could be called a requirements document?
},
author = {Jeffrey C. Carver and Nicholas Weber and Karthik Ram and Sandra Gesing and Daniel S. Katz},
date-added = {2021-12-02 16:09:15 -0500},
date-modified = {2022-06-27 16:05:13 -0400},
doi = {https://doi.org/10.7717/peerj-cs.963},
journal = {PeerJ Computer Science},
number = {8:e963},
title = {A Survey of the State of the Practice for Research Software in the United States},
year = {2022},
bdsk-file-1 = {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},
bdsk-file-2 = {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},
bdsk-url-1 = {https://peerj.com/articles/cs-963/},
bdsk-url-2 = {https://doi.org/10.7717/peerj-cs.963}}
@misc{Dong2021-Data,
author = {Ao Dong},
date-added = {2021-11-24 10:14:13 -0500},
date-modified = {2021-11-24 10:17:14 -0500},
doi = {10.17632/k3pcdvdzj2.1},
howpublished = {Mendeley Data, V1, doi: 10.17632/k3pcdvdzj2.1},
month = {August},
title = {Software Quality Grades for MI Software},
year = {2021},
bdsk-url-1 = {https://data.mendeley.com/datasets/k3pcdvdzj2/1},
bdsk-url-2 = {https://doi.org/10.17632/k3pcdvdzj2.1}}
@article{KruchtenEtAl2012,
author = {Kruchten, Philippe and Nord, Robert L and Ozkaya, Ipek},
date-added = {2021-11-19 10:21:32 -0500},
date-modified = {2021-11-19 10:46:39 -0500},
journal = {IEEE Software},
number = {6},
pages = {18--21},
publisher = {IEEE},
title = {Technical debt: From metaphor to theory and practice},
volume = {29},
year = {2012},
bdsk-url-1 = {https://resources.sei.cmu.edu/asset_files/WhitePaper/2012_019_001_58818.pdf}}
@phdthesis{Deienbck2009,
author = {Florian Dei{\ss}enb{\"o}ck},
date-added = {2021-11-18 10:07:43 -0500},
date-modified = {2021-11-18 10:10:36 -0500},
school = {Technische Universit{\"a}t M{\"u}nchen},
title = {Continuous quality control of long lived software systems},
year = {2009},
bdsk-url-1 = {https://www.cqse.eu/fileadmin/content/news/publications/2009-continuous-quality-control-of-long-lived-software-systems.pdf},
bdsk-url-2 = {https://d-nb.info/998600407/34},
bdsk-url-3 = {https://www.semanticscholar.org/paper/Continuous-quality-control-of-long-lived-software-Dei%C3%9Fenb%C3%B6ck/b0f7cc4bd225f5bf3c159d85c5288d7a02ec6f6e}}
@article{DorianEtAl2021,
abstract = {The development of scientific software relies on the collaboration of various
stakeholders for the scientific computing and software engineering activities. Computer
languages have an impact on both activities and related concerns, as well as on the engineering
principles required to ensure the development of reliable scientific software. The more
general-purpose the language is ---with low-level, computing-related, system abstractions--- the
more flexibility it will provide, but also the more rigorous engineering principles and Validation &
Verification (V&V) activities it will require from the language user. In this paper, we investigate
the different levels of abstraction, linked to the diverse artifacts of the scientific software
development process, a software language can propose, and the V&V facilities associated to the
corresponding level of abstraction the language can provide to the user. We aim to raise
awareness among scientists, engineers and language providers on their shared responsibility in
developing reliable scientific software.},
annote = {- has examples of the importance of SC for Covid-19 and climate change
- link to: http://blog.khinsen.net/posts/2020/05/18/an-open-letter-to-software-engineers-criticizing-neil-ferguson-s-epidemics-simulation-code/
- they show a scientific V-model that subsumes the SE V-model, but this isn't really justified. The scientific V-model is really just a relabelling of the SE V-model, as shown in SmithEtAl 2007. :-) - in particular, they make it look like the numerical scheme provides the stakeholder requirements, but that isn't true. The mathematical model represents the stakeholder requirements!
- it is unclear whether they are describing what they think SC and SE should do, or what they think they are currently doing. The mention of use case diagrams for requirements jumps out as something that is unlikley to be done currently. - they seem to be imposing an OO mindset on the design that isn't always present.
- should look up what Galilean invariance testing entails
- the call at the bottom of page 7 to have a ``validity envelope'' is nice, but not particularly realistic - developers don't like artificial constraints (as experssed by John Luxat in a conversation we had). Moreover, the calculations needed to determine if inputs are realistic are often as much work as solving the problem. For instance, determining if a matrix is invertible, or whether a system of equations is positive definite, etc.
},
author = {Leroy, Dorian and Sallou, June and Bourcier, Johann and Combemale, Benoit},
date-added = {2021-11-17 17:54:24 -0500},
date-modified = {2021-11-18 17:34:35 -0500},
hal_id = {hal-03318348},
hal_version = {v2},
journal = {IEEE Computer},
pages = {1--11},
pdf = {https://hal.inria.fr/hal-03318348v2/file/IEEEComputer___When_Scientific_Software_Meets_Software_Engineering.pdf},
title = {When Scientific Software Meets Software Engineering},
url = {https://hal.inria.fr/hal-03318348},
year = {2021},
bdsk-url-1 = {https://hal.inria.fr/hal-03318348},
bdsk-url-2 = {https://hal.inria.fr/hal-03318348/document}}
@misc{SmithEtAl2021-QDef,
author = {Spencer Smith and Jacques Carette and Oluwaseun Owojaiye and Peter Michalski and Ao Dong},
date-added = {2021-11-17 14:42:36 -0500},
date-modified = {2021-11-17 14:44:21 -0500},
howpublished = {\url{https://github.com/smiths/AIMSS/blob/master/StateOfPractice/QDefOfQualities/QDefOfQualities.pdf}},
month = {Nov},
title = {Quality Definitions of Qualities},
year = {2021},
bdsk-url-1 = {https://github.com/smiths/AIMSS/blob/master/StateOfPractice/QDefOfQualities/QDefOfQualities.pdf}}
@article{WillcocksAndLester1996,
abstract = {Despite the massive investments in Information Technology in the developed economies, the IT impact on productivity and business performance continues to be questioned. The paper critically reviews this IT productivity paradox debate and finds that an important part, but by no means all, of the uncertainty about the IT payoff relates to weaknesses in measurement and evaluation practice. Based on extensive research by the authors and others, an integrated systems lifecycle approach is put forward as a long term way of improving evaluation practice in work organizations. The approach shows how to link business and IT/IS strategies with prioritizing investments in IT, and by setting up a set of interlinking measures, how IT costs and benefits may be evaluated and managed across the systems lifecycle, including consideration of potential uses of the external IT services market. An emphasis on a cultural change in evaluation from `control through numbers' to a focus on quality improvement offers one of the better routes out of the productivity paradox. Improved evaluation practice serves to demystify the paradox, but also links with and helps to stimulate improved planning for management and use of IT, thus also reducing the paradox in practical terms - through the creation of greater business value.},
author = {Leslie Willcocks and Stephanie Lester},
date-added = {2021-11-16 08:55:01 -0500},
date-modified = {2021-11-16 08:55:17 -0500},
doi = {https://doi.org/10.1016/0263-2373(96)00007-2},
issn = {0263-2373},
journal = {European Management Journal},
number = {3},
pages = {279-290},
title = {Beyond the IT productivity paradox},
url = {https://www.sciencedirect.com/science/article/pii/0263237396000072},
volume = {14},
year = {1996},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/0263237396000072},
bdsk-url-2 = {https://doi.org/10.1016/0263-2373(96)00007-2}}
@article{WillcocksAndLester1997,
abstract = { AbstractDespite the massive investments in Information Technology (IT) in the developed economies, the IT impact on productivity and business performance continues to be questioned. The paper critically reviews this `IT productivity paradox' debate. It suggests that important elements in the uncertainty about the IT payoff relate to deficiencies in measurement at the macroeconomic level, but also to weaknesses in organisational evaluation practice. The paper reports evidence from a 1996 UK survey pointing to such weaknesses. Focusing at the more meaningful organisational level, an integrated systems lifecycle approach is put forward as a long term way of strengthening evaluation practice. This incorporates a cultural change in evaluation from `control through numbers' to a focus on quality improvement. The approach is compared against 1995--96 research findings in a multinational insurance company, where senior managers in a newly created business division consciously sought related improvements in evaluation practice, and IT productivity. },
author = {L P Willcocks and S Lester},
date-added = {2021-11-16 08:52:29 -0500},
date-modified = {2021-11-16 08:52:42 -0500},
doi = {10.1057/palgrave.jors.2600463},
eprint = {https://doi.org/10.1057/palgrave.jors.2600463},
journal = {Journal of the Operational Research Society},
number = {11},
pages = {1082-1094},
publisher = {Taylor & Francis},
title = {In search of information technology productivity: Assessment issues},
url = {https://doi.org/10.1057/palgrave.jors.2600463},
volume = {48},
year = {1997},
bdsk-url-1 = {https://doi.org/10.1057/palgrave.jors.2600463},
bdsk-url-2 = {https://www.tandfonline.com/doi/abs/10.1057/palgrave.jors.2600463}}
@article{BrynjolfssonAndHitt1998,
author = {Brynjolfsson, Erik and Hitt, Lorin},
date-added = {2021-11-16 08:44:44 -0500},
date-modified = {2021-11-16 08:45:06 -0500},
doi = {10.1145/280324.280332},
journal = {Communications of the ACM},
month = {08},
pages = {49-55},
title = {Beyond the IT Productivity Paradox},
volume = {41},
year = {1998},
bdsk-url-1 = {https://doi.org/10.1145/280324.280332},
bdsk-url-2 = {https://www.researchgate.net/publication/262253744_Beyond_the_IT_Productivity_Paradox}}
@article{RajivEtAl1991,
abstract = { The cost of maintaining application software has been rapidly escalating, and is currently estimated to comprise from 50--80\% of corporate information systems department budgets. In this research we develop an estimable production frontier model of software maintenance, using a new methodology that allows the simultaneous estimation of both the production frontier and the effects of several productivity factors. Our model allows deviations on both sides of the estimated frontier to reflect the impact of both production inefficiencies and random effects such as measurement errors. The model is then estimated using an empirical dataset of 65 software maintenance projects from a large commercial bank. The insights obtained from the estimation results are found to be quite consistent for reasonable variations in the specification of the model. Estimates of the marginal impacts of all of the included productivity factors are obtained to aid managers in improving productivity in software maintenance. },
author = {Banker, Rajiv D. and Datar, Srikant M. and Kemerer, Chris F.},
date-added = {2021-11-16 08:34:22 -0500},
date-modified = {2021-11-16 08:34:34 -0500},
doi = {10.1287/mnsc.37.1.1},
eprint = {https://doi.org/10.1287/mnsc.37.1.1},
journal = {Management Science},
number = {1},
pages = {1-18},
title = {A Model to Evaluate Variables Impacting the Productivity of Software Maintenance Projects},
url = {https://doi.org/10.1287/mnsc.37.1.1},
volume = {37},
year = {1991},
bdsk-url-1 = {https://doi.org/10.1287/mnsc.37.1.1},
bdsk-url-2 = {https://www.researchgate.net/publication/227446230_A_Model_to_Evaluate_Variables_Impacting_the_Productivity_of_Software_Maintenance_Projects}}
@misc{StoreyEtAl2021,
archiveprefix = {arXiv},
author = {Margaret-Anne Storey and Brian Houck and Thomas Zimmermann},
date-added = {2021-11-09 09:55:39 -0500},
date-modified = {2021-11-09 09:55:54 -0500},
eprint = {2111.04302},
primaryclass = {cs.SE},
title = {How Developers and Managers Define and Trade Productivity for Quality},
year = {2021},
bdsk-url-1 = {https://arxiv.org/abs/2111.04302}}
@article{SadowskiAndZimmermann2019,
author = {Caitlin Sadowski and Thomas Zimmermann},
date-added = {2021-11-09 09:49:16 -0500},
date-modified = {2021-11-09 09:49:37 -0500},
journal = {Rethinking Productivity in Software Engineering},
title = {Rethinking Productivity in Software Engineering},
year = {2019},
bdsk-url-1 = {https://link.springer.com/book/10.1007/978-1-4842-4221-6},
bdsk-url-2 = {https://www.researchgate.net/publication/332921668_Rethinking_Productivity_in_Software_Engineering},
bdsk-url-3 = {https://www.goodreads.com/book/show/45995568-rethinking-productivity-in-software-engineering}}
@inproceedings{JhaEtAl2020,
abstract = {The functions of an autonomous system can generally be partitioned into those concerned with perception and those concerned with action. Perception builds and maintains an internal model of the world (i.e., the system's environment) that is used to plan and execute actions to accomplish a goal established by human supervisors.},
address = {Cham},
author = {Jha, Susmit and Rushby, John and Shankar, Natarajan},
booktitle = {Computer Safety, Reliability, and Security},
date-added = {2021-11-02 15:23:39 -0400},
date-modified = {2021-11-02 15:23:55 -0400},
editor = {Casimiro, Ant{\'o}nio and Ortmeier, Frank and Bitsch, Friedemann and Ferreira, Pedro},
isbn = {978-3-030-54549-9},
pages = {228--243},
publisher = {Springer International Publishing},
title = {Model-Centered Assurance for Autonomous Systems},
year = {2020},
bdsk-url-1 = {http://www.csl.sri.com/users/rushby/papers/safecomp20.pdf},
bdsk-url-2 = {https://link.springer.com/chapter/10.1007/978-3-030-54549-9_15#citeas},
bdsk-url-3 = {http://www.csl.sri.com/users/rushby/abstracts/safecomp20}}
@article{BrookeEtAl1995,
abstract = {Computational analysis has become an essential tool for the evaluation of designs for complex engineering products, and engineers are using more analysis applications to model a wider range of product behaviour than ever before. Existing technology is unable to offer effective solutions for the management and integration of either the applications themselves or the information they use and create. This is in part due to an inadequate understanding of the engineering analysis process.},
annote = {{} for comments, rather than summary
{fairly obvious steps in engineering analysis, but does provide a citation that we can use to show our process matches engineering practice}
- separates physical phenomena, physical models, mathematical model, method to solve mathematical model
- focuses on solid mechanics and thermal analysis
{- nothing deep on on what are assumptions, models, solution techniques, etc.}},
author = {Brooke, David M. and de Pennington, Alan and Susan Bloor, M.},
date = {1995/03/01},
date-added = {2021-10-28 16:09:58 -0400},
date-modified = {2021-10-28 16:13:56 -0400},
doi = {10.1007/BF01230443},
id = {Brooke1995},
isbn = {1435-5663},
journal = {Engineering with Computers},
number = {1},
pages = {36--45},
title = {An ontology for engineering analyses},
url = {https://doi.org/10.1007/BF01230443},
volume = {11},
year = {1995},
bdsk-url-1 = {https://doi.org/10.1007/BF01230443},
bdsk-url-2 = {https://www.academia.edu/14352754/An_ontology_for_engineering_analyses?email_work_card=view-paper}}
@inproceedings{AghajaniEtAl2019,
abstract = {(Good) Software documentation provides developers and users with a description of what a software system does, how it operates, and how it should be used. For example, technical documentation (e.g., an API reference guide) aids developers during evolution/maintenance activities, while a user manual explains how users are to interact with a system. Despite its intrinsic value, the creation and the maintenance of documentation is often neglected, negatively impacting its quality and usefulness, ultimately leading to a generally unfavorable take on documentation.
Previous studies investigating documentation issues have been based on surveying developers, which naturally leads to a somewhat biased view of problems affecting documentation. We present a large scale empirical study, where we mined, analyzed, and categorized 878 documentation-related artifacts stemming from four different sources, namely mailing lists, Stack Overflow discussions, issue repositories, and pull requests. The result is a detailed taxonomy of documentation issues from which we infer a series of actionable proposals both for researchers and practitioners.},
annote = {{} used for comments to myself, as opposed to statements in the original paper
- includes references that state the creation and maintenance of documentation is often neglected (references [3]-[7])
- previous work has looked at documentation by interviewing developers
- citations to papers on automatic documentation generation ([1] and [8]), but based on the titles of these papers they seem to be talking about automatically generating documentation from the code (and possibly also test cases)
- {generating documentation from the code is problematic because the detailed code is about ``how'' to do something, rather than ``what'' is required. The code also isn't likely to include the ``why''; that is, rationales are likely to be absent (except maybe in comments)}
- this paper looks at the documentation issues (potentially in an issue tracker) themselves, rather than interviewing developers
- this paper has a literature review on automatic document generation (code summarization) and a review on empirical studies of software documentation
- here is a good quote from Chen and Huang (2009): ``Most typical problems in software documentation quality for maintenance are that software documentation is untrustworthy, inadequate, incomplete or does not even exist, lacks traceability, does not include its changes, and lacks integrity and consistency.''
- {I haven't seen it explicitly mentioned in the paper to this point, but it seems that by documentation the authors (at least to this point), mean API documentation}
- RQ: What are the documentation issues faced by developers?
Results Discussion
- ``Figure 1 shows the hierarchical taxonomy of the 162 documentation issue types that we identified. They are grouped into four main categories: (i) problems related to the information content of the documentation describe issues arising from ``what'' is written in the documentation; (ii) issues classified under the information content (how) category focus on ``how'' the content is written and organized; (iii) the process-related category groups issues related to the documentation process; and (iv) tool-related matters originate from the usage of a documentation tool.``
- paper [4] (https://www.researchgate.net/publication/267215582_Cost_Benefits_and_Quality_of_Software_Development_Documentation_A_Systematic_Mapping) has definitions of qualities ({should consult these for the quality quality definitions document})
- paper [4] also has some meta-models of documentation development, usage and cost {the details don't resonate, but the big picture view that we should look at the cost, benefits and quality of documemtation resonates. We have argued elsewhere that it is by looking at the long-term benefits that justifies the cost of documentation}
``Our results highlight frequent issues related to the correctness, up-to-dateness and completeness of the information reported in the documentation. The documentation types most frequently affected by correctness issues are, not surprisingly, code examples.''
},
author = {Aghajani, Emad and Nagy, Csaba and Vega-M{\'a}rquez, Olga Lucero and Linares-V{\'a}squez, Mario and Moreno, Laura and Bavota, Gabriele and Lanza, Michele},
booktitle = {2019 IEEE/ACM 41st International Conference on Software Engineering (ICSE)},
date-added = {2021-10-27 16:14:38 -0400},
date-modified = {2021-10-27 23:21:10 -0400},
doi = {10.1109/ICSE.2019.00122},
pages = {1199-1210},
title = {Software Documentation Issues Unveiled},
year = {2019},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1109/ICSE.2019.00122}}
@misc{SmithEtAl2021,
author = {W. Spencer Smith and Jacques Carette and Peter Michalski and Ao Dong and Oluwaseun Owojaiye},
date-added = {2021-10-22 15:58:57 -0400},
date-modified = {2022-11-04 16:19:01 -0400},
howpublished = {\url{https://arxiv.org/ abs/2110.11575}},
month = {October},
note = {35 pp},
title = {Methodology for Assessing the State of the Practice for Domain {X}},
year = {2021},
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bdsk-url-1 = {https://arxiv.org/abs/2110.11575}}
@article{SadeghiEtAl2020,
abstract = {Coarctation of the aorta (COA) is a congenital narrowing of the proximal descending aorta. Although accurate and early diagnosis of COA hinges on blood flow quantification, proper diagnostic methods for COA are still lacking because fluid-dynamics methods that can be used for accurate flow quantification are not well developed yet. Most importantly, COA and the heart interact with each other and because the heart resides in a complex vascular network that imposes boundary conditions on its function, accurate diagnosis relies on quantifications of the global hemodynamics (heart-function metrics) as well as the local hemodynamics (detailed information of the blood flow dynamics in COA). In this study, to enable the development of new non-invasive methods that can quantify local and global hemodynamics for COA diagnosis, we developed an innovative fast computational-mechanics and imaging-based framework that uses Lattice Boltzmann method and lumped-parameter modeling that only need routine non-invasive clinical patient data. We used clinical data of patients with COA to validate the proposed framework and to demonstrate its abilities to provide new diagnostic analyses not possible with conventional diagnostic methods. We validated this framework against clinical cardiac catheterization data, calculations using the conventional finite-volume method and clinical Doppler echocardiographic measurements. The diagnostic information, that the framework can provide, is vitally needed to improve clinical outcomes, to assess patient risk and to plan treatment.},
author = {Sadeghi, Reza and Khodaei, Seyedvahid and Ganame, Javier and Keshavarz-Motamed, Zahra},
date = {2020/06/03},
date-added = {2021-10-22 14:53:15 -0400},
date-modified = {2021-10-22 14:53:27 -0400},
doi = {10.1038/s41598-020-65576-y},
id = {Sadeghi2020},
isbn = {2045-2322},
journal = {Scientific Reports},
number = {1},
pages = {9048},
title = {Towards non-invasive computational-mechanics and imaging-based diagnostic framework for personalized cardiology for coarctation},
url = {https://doi.org/10.1038/s41598-020-65576-y},
volume = {10},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1038/s41598-020-65576-y}}
@inproceedings{CaretteEtAl2021,
address = {Pittsburch, PA, United States},
author = {Jacques Carette and Spencer Smith and Jason Balaci},
booktitle = {Proceedings of New Ideas and Emerging Results (NIER) track of the International Conference on Software Engineering (ICSE)},
date-added = {2021-10-22 11:53:37 -0400},
date-modified = {2022-10-31 09:03:34 -0400},
keywords = {4 pp.},
organization = {In conjunction with ICSE 2022},
title = {When Capturing Knowledge Improves Productivity},
year = {Rejected 2021},
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@mastersthesis{Michalski2021,
address = {Hamilton, Ontario, Canada},
author = {Peter Michalski},
date-added = {2021-10-19 21:15:31 -0400},
date-modified = {2021-10-19 21:17:01 -0400},
month = {September},
school = {McMaster University},
title = {State of The Practice for Lattice Boltzmann Method Software},
year = {2021},
bdsk-file-1 = {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}}
@mastersthesis{Dong2021,
address = {Hamilton, ON, Canada},
author = {Ao Dong},
date-added = {2021-10-19 21:13:17 -0400},
date-modified = {2021-10-19 21:14:56 -0400},
month = {September},
school = {McMaster University},
title = {Assessing the State of the Practice for Medical Imaging Software},
year = {2021},
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@article{DouviEtAl2021,
abstract = {In this work, technologies related to the storage of solar energy, utilizing the latent heat content of phase change materials for the production of domestic hot water are reviewed. Many researchers have been involved in this field in order to accomplish the targets of environmentally friendly solutions and higher efficiency. For domestic use, materials with melting temperature between 40 and 80 $\,^{\circ}$C are commonly studied, with paraffins, fatty acids, salt hydrates and alcohols being the most popular. For harvesting the solar radiation, usually flat plate or evacuated tubes solar collectors are used, either commercial ones or modified. The storage unit may include only phase change material or it can have a hybrid form combined with water. The outcome of the most studies, is that the addition of phase change materials in comparison to systems without latent storage, increases the duration of heat release towards the domestic water at the end of the day and also increases the solar collector's efficiency because it does not experience large temperature fluctuations. However, difficulties emerge during the selection of the appropriate storage material as this must have a high melting temperature in order to provide hot enough domestic water, but not higher than the temperature that the solar collector can produce, in order to fully melt the material. Moreover, investigation is necessary for the selection of the optimum water flow rate that minimizes the charging duration and maximizes the system efficiency and hot water amount. Another challenge that researchers face is the low thermal conductivity of many phase change materials. For this purpose, methods for improving the performance of the systems have been examined and they are also reported.},
author = {Eleni Douvi and Christos Pagkalos and George Dogkas and Maria K. Koukou and Vassilis N. Stathopoulos and Yiannis Caouris and Michail Gr. Vrachopoulos},
date-added = {2021-10-14 16:26:42 -0400},
date-modified = {2021-10-14 16:26:42 -0400},
doi = {https://doi.org/10.1016/j.ijft.2021.100075},
issn = {2666-2027},
journal = {International Journal of Thermofluids},
keywords = {Latent heat storage, PCM, Domestic hot water, Review, Solar},
pages = {100075},
title = {Phase change materials in solar domestic hot water systems: A review},
url = {https://www.sciencedirect.com/science/article/pii/S2666202721000136},
volume = {10},
year = {2021},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S2666202721000136},
bdsk-url-2 = {https://doi.org/10.1016/j.ijft.2021.100075}}
@book{Dalkir2011,
abstract = {The ability to manage knowledge has become increasingly important in today's knowledge
economy. Knowledge is considered a valuable commodity, embedded in products and in
the tacit knowledge of highly mobile individual employees. Knowledge management (KM)
represents a deliberate and systematic approach to cultivating and sharing an organization's
knowledge base. It is a highly multidisciplinary field that encompasses both information
technology and intellectual capital. This textbook and professional reference offers
a comprehensive overview of the field of KM, providing both a substantive theoretical
grounding and a pragmatic approach to applying key concepts. Drawing on ideas, tools,
and techniques from such disciplines as sociology, cognitive science, organizational
behavior, and information science, the text describes KM theory and practice at the
individual, community, and organizational levels. It offers illuminating case studies
and vignettes from companies including IBM, Xerox, British Telecommunications, JP
Morgan Chase, and Nokia. This second edition has been updated and revised throughout.
New material has been added on the information and library science perspectives, taxonomies
and knowledge classification, the media richness of the knowledge-sharing channel,
e-learning, social networking in KM contexts, strategy tools, results-based outcome
assessments, knowledge continuity and organizational learning models, KM job descriptions,
copyleft and Creative Commons, and other topics. New case studies and vignettes have
been added; and the references and glossary have been updated and expanded. },
author = {Dalkir, Kimiz},
date-added = {2021-10-13 17:00:38 -0400},
date-modified = {2021-10-13 17:00:38 -0400},
editor = {3rd},
isbn = {0262015080},
publisher = {The MIT Press},
title = {Knowledge Management in Theory and Practice},
year = {2011},
bdsk-url-1 = {https://dl.acm.org/doi/book/10.5555/1995301}}
@inproceedings{Farmer2007,
abstract = {An axiomatic theory represents mathematical knowledge declaratively as a set of axioms. An algorithmic theory represents mathematical knowledge procedurally as a set of algorithms. A biform theory is simultaneously an axiomatic theory and an algorithmic theory. It represents mathematical knowledge both declaratively and procedurally. Since the algorithms of algorithmic theories manipulate the syntax of expressions, biform theories---as well as algorithmic theories---are difficult to formalize in a traditional logic without the means to reason about syntax. Chiron is a derivative of von-Neumann-Bernays-G{\"o}del (nbg) set theory that is intended to be a practical, general-purpose logic for mechanizing mathematics. It includes elements of type theory, a scheme for handling undefinedness, and a facility for reasoning about the syntax of expressions. It is an exceptionally well-suited logic for formalizing biform theories. This paper defines the notion of a biform theory, gives an overview of Chiron, and illustrates how biform theories can be formalized in Chiron.},
address = {Berlin, Heidelberg},
author = {Farmer, William M.},
booktitle = {Towards Mechanized Mathematical Assistants},
date-added = {2021-10-12 14:23:23 -0400},
date-modified = {2021-10-12 14:23:34 -0400},
editor = {Kauers, Manuel and Kerber, Manfred and Miner, Robert and Windsteiger, Wolfgang},
isbn = {978-3-540-73086-6},
pages = {66--79},
publisher = {Springer Berlin Heidelberg},
title = {Biform Theories in Chiron},
year = {2007}}
@inproceedings{ChueHong2018,
author = {Neil Chue Hong},
booktitle = {Best Practices for HPC Software Developers Webinar Series},
date-added = {2021-09-08 13:20:22 -0400},
date-modified = {2021-09-08 13:21:23 -0400},
title = {Software sustainability -- lessons learned from different disciplines},
year = {2018},
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@inbook{AbranAndAl-Qutaish2010,
abstract = {Summary This chapter contains sections titled: Introduction to ISO 9126 Analysis Models of ISO 9126: The (Quantitative) Models The Metrology-Related Part of ISO 9126: Base and Derived Measures Analysis of Derived Measures The Missing Links: From Metrology to Quantitative Analysis Outstanding Measurement Design Issues: Improvement Strategy Advanced Readings 1: Analysis of the Design of the Productivity Measure in ISO 9126 Advanced Readings 2: Attributes and Related Base Measures within ISO 9126},
author = {Alain Abran and Rafa E. Al-Qutaish},
booktitle = {Software Metrics and Software Metrology},
chapter = {10},
date-added = {2021-09-08 11:28:17 -0400},
date-modified = {2021-09-08 11:29:27 -0400},
doi = {https://doi.org/10.1002/9780470606834.ch10},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470606834.ch10},
isbn = {9780470606834},
keywords = {ISO 9126, analysis of quality models and measures, ISO 9126--1, structures of quality models - for software product quality, 3 Effectiveness-derived measures - task effectiveness, task completion and error frequency},
pages = {205-228},
publisher = {John Wiley & Sons, Ltd},
title = {ISO 9126: Analysis of Quality Models and Measures},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470606834.ch10},
year = {2010},
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bdsk-url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470606834.ch10},
bdsk-url-2 = {https://doi.org/10.1002/9780470606834.ch10}}
@book{BirdEtAl2002,
author = {Bird, R.B. and Lightfoot, E.N. and Stewart, W.E.},
date-added = {2021-09-08 11:17:48 -0400},
date-modified = {2021-09-08 11:17:58 -0400},
isbn = {9780471364740},
lccn = {2001023739},
publisher = {J. Wiley},
title = {Transport Phenomena},
url = {https://books.google.ca/books?id=wYnRQwAACAAJ},
year = {2002},
bdsk-file-1 = {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},
bdsk-url-1 = {https://books.google.ca/books?id=wYnRQwAACAAJ}}
@techreport{WeinstockAndGoodenough2009,
address = {Pittsburgh, PA},
author = {Charles Weinstock and John Goodenough},
date-added = {2021-09-08 10:35:31 -0400},
date-modified = {2021-09-08 10:36:09 -0400},
institution = {Software Engineering Institute, Carnegie Mellon University},
number = {CMU/SEI-2009-TN-018},
title = {Towards an Assurance Case Practice for Medical Devices},
url = {http://resources.sei.cmu.edu/library/asset-view.cfm?AssetID=8999},
year = {2009},
bdsk-file-1 = {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},
bdsk-url-1 = {http://resources.sei.cmu.edu/library/asset-view.cfm?AssetID=8999}}
@article{Schwer2007,
added-at = {2020-07-16T00:00:00.000+0200},
author = {Schwer, Leonard E.},
biburl = {https://www.bibsonomy.org/bibtex/215e20938db040fc73366d11ce6f024b6/dblp},
date-added = {2021-09-08 10:11:24 -0400},
date-modified = {2021-09-08 10:11:36 -0400},
ee = {https://doi.org/10.1007/s00366-007-0072-z},
interhash = {e51eb4e1e0c58be5822c20bbf796d587},
intrahash = {15e20938db040fc73366d11ce6f024b6},
journal = {Eng. Comput.},
keywords = {dblp},
number = 4,
pages = {245-252},
timestamp = {2020-07-24T00:17:30.000+0200},
title = {An overview of the PTC 60/V&V 10: guide for verification and validation in computational solid mechanics.},
url = {http://dblp.uni-trier.de/db/journals/ewc/ewc23.html#Schwer07},
volume = 23,
year = 2007,
bdsk-file-1 = {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},
bdsk-url-1 = {http://dblp.uni-trier.de/db/journals/ewc/ewc23.html#Schwer07}}
@inproceedings{ChowduryEtAl2017,
author = {Chowdhury, Thomas and Lin, Chung-Wei and Kim, BaekGyu and Lawford, Mark and Shiraishi, Shinichi and Wassyng, Alan},
booktitle = {2017 IEEE International Symposium on Software Reliability Engineering Workshops (ISSREW)},
date-added = {2021-08-31 11:58:13 -0400},
date-modified = {2021-08-31 11:58:31 -0400},
doi = {10.1109/ISSREW.2017.14},
pages = {69-72},
title = {Principles for Systematic Development of an Assurance Case Template from ISO 26262},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1109/ISSREW.2017.14}}
@article{ChenEtAl2020,
abstract = {Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound and major anatomical structures of interest (ventricles, atria, and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.},
author = {Chen, Chen and Qin, Chen and Qiu, Huaqi and Tarroni, Giacomo and Duan, Jinming and Bai, Wenjia and Rueckert, Daniel},
date-added = {2021-08-31 11:31:14 -0400},
date-modified = {2021-08-31 11:31:14 -0400},
doi = {10.3389/fcvm.2020.00025},
issn = {2297-055X},
journal = {Frontiers in Cardiovascular Medicine},
pages = {25},
title = {Deep Learning for Cardiac Image Segmentation: A Review},
url = {https://www.frontiersin.org/article/10.3389/fcvm.2020.00025},
volume = {7},
year = {2020},
bdsk-url-1 = {https://www.frontiersin.org/article/10.3389/fcvm.2020.00025},
bdsk-url-2 = {https://doi.org/10.3389/fcvm.2020.00025}}
@article{KongAndShadden2020,
author = {Fanwei Kong and S. Shadden},
date-added = {2021-08-31 11:29:20 -0400},
date-modified = {2021-08-31 11:29:20 -0400},
journal = {Journal of biomechanical engineering},
title = {Automating Model Generation for Imagebased Cardiac Flow Simulation.},
year = {2020},
bdsk-url-1 = {https://www.semanticscholar.org/paper/Automating-Model-Generation-for-Imagebased-Cardiac-Kong-Shadden/83046dcd5e394353f764c6701371ba0a60f83f20}}
@article{HeldtEtAl2010,
abstract = {CVSim is a lumped-parameter model of the human cardiovascular system that has been developed and used for research and for teaching quantitative physiology courses at MIT and Harvard Medical School since 1984. We present a brief historical background of lumped-parameter cardiovascular system models, followed by an overview of the development of the major versions of CVSim over a 25-year period in our laboratory. We describe the features and differences of four versions of CVSim that are freely available in open-source form via PhysioNet (http://physionet.org). These include a six-compartment cardiovascular model with an arterial baroreflex system, implemented in C for efficiency, with an X-based graphical user interface; a six-compartment model with a more extensive short-term regulatory system and incorporating resting physiologic perturbations, available as a stand-alone MATLAB application; and a pair of elaborated versions consisting of 6- and 21-compartment computational models implemented in C, with a separate and enhanced Java graphical user interface. We conclude with a discussion of the educational and research applications for which we have used CVSim.},
author = {Heldt, Thomas and Mukkamala, Ramakrishna and Moody, George B and Mark, Roger G},
date-added = {2021-08-31 11:22:15 -0400},
date-modified = {2021-08-31 11:22:56 -0400},
journal = {The open pacing, electrophysiology \& therapy journal},
pages = {45--54},
title = {CVSim: An Open-Source Cardiovascular Simulator for Teaching and Research},
url = {https://pubmed.ncbi.nlm.nih.gov/21949555},
volume = {3},
year = {2010},
bdsk-url-1 = {https://pubmed.ncbi.nlm.nih.gov/21949555}}
@article{MotamedEtAl2016,
abstract = {Objectives
This study sought to investigate the impact of transcatheter intervention on left ventricular function and aortic hemodynamics in patients with mild coarctation of the aorta (COA).
Background
The optimal method and timing of transcatheter intervention for COA remains unclear, especially when the severity of COA is mild (peak-to-peak transcoarctation pressure gradient <20 mm Hg). Debate rages regarding the risk/benefit ratio of intervention versus long-term effects of persistent minimal gradient in this heterogeneous population with differing blood pressures, ventricular function, and peripheral perfusion.
Methods
We developed a unique computational fluid dynamics and lumped parameter modeling framework based on patient-specific hemodynamic input parameters and validated it against patient-specific clinical outcomes (before and after intervention). We used clinically measured hemodynamic metrics and imaging of the aorta and the left ventricle in 34 patients with mild COA to make these correlations.
Results
Despite dramatic reduction in the transcoarctation pressure gradient (catheter and Doppler echocardiography pressure gradients reduced by 75% and 47.3%, respectively), there was only modest effect on aortic flow and no significant impact on aortic shear stress (the maximum time-averaged wall shear stress in descending aorta was reduced 5.1%). In no patient did transcatheter intervention improve left ventricular function (e.g., stroke work and normalized stroke work were reduced by only 4.48% and 3.9%, respectively).
Conclusions
Transcatheter intervention that successfully relieves mild COA pressure gradients does not translate to decreased myocardial strain. The effects of the intervention were determined to the greatest degree by ventricular--vascular coupling hemodynamics and provide a novel valuable mechanism to evaluate patients with COA that may influence clinical practice.},
author = {Zahra Keshavarz-Motamed and Farhad {Rikhtegar Nezami} and Ramon A. Partida and Kenta Nakamura and Pedro Vin{\'\i}cius Staziaki and Eyal Ben-Assa and Brian Ghoshhajra and Ami B. Bhatt and Elazer R. Edelman},
date-added = {2021-08-31 11:10:04 -0400},
date-modified = {2021-08-31 11:10:04 -0400},
doi = {https://doi.org/10.1016/j.jcin.2016.06.054},
issn = {1936-8798},
journal = {JACC: Cardiovascular Interventions},
keywords = {aortic hemodynamics, left ventricle function, mild coarctation, peak-to-peak pressure gradient, transcatheter intervention},
number = {18},
pages = {1953-1965},
title = {Elimination of Transcoarctation Pressure Gradients Has No Impact on Left Ventricular Function or Aortic Shear Stress After Intervention in Patients With Mild Coarctation},
url = {https://www.sciencedirect.com/science/article/pii/S1936879816311876},
volume = {9},
year = {2016},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S1936879816311876},
bdsk-url-2 = {https://doi.org/10.1016/j.jcin.2016.06.054}}
@article{MotamedEtAl2014,
abstract = {Early detection and accurate estimation of aortic stenosis (AS) severity are the most important predictors of successful long-term outcomes in patients. Current clinical parameters used for evaluation of the AS severity have several limitations including flow dependency. Estimation of AS severity is specifically challenging in patients with low-flow and low transvalvular pressure gradient conditions. A proper diagnosis in these patients needs a comprehensive evaluation of the left ventricle (LV) hemodynamic loads. This study has two objectives: (1) developing a lumped-parameter model to describe the ventricular-valvular-arterial interaction and to estimate the LV stroke work (SW); (2) introducing and validating a new index, the normalized stroke work (N-SW), to assess the global hemodynamic load imposed on the LV. N-SW represents the global hemodynamic load that the LV faces for each unit volume of blood ejected. The model uses a limited number of parameters which all can be measured non-invasively using current clinical imaging modalities. The model was first validated by comparing its calculated flow waveforms with the ones measured using Cardiovascular Magnetic Resonance (CMR) in 49 patients and 8 controls. A very good correlation and concordance were found throughout the cycle (median root mean square: 12.21 mL/s) and between the peak values (r = 0.98; SEE = 0.001, p<0.001). The model was then used to determine SW using the parameters measured with transthoracic Doppler-echocardiography (TTE) and CMR. N-SW showed very good correlations with a previously-validated index of global hemodynamic load, the valvular arterial impedance (), using data from both imaging modalities (TTE: r = 0.82, SEE = 0.01, p<0.001; CMR: r = 0.74, SEE = 0.01, p<0.001). Furthermore, unlike , N-SW was almost independent from variations in the flow rate. This study suggests that considering N-SW may provide incremental diagnostic and prognostic information, beyond what standard indices of stenosis severity and provide, particularly in patients with low LV outflow.},
author = {Keshavarz-Motamed, Zahra AND Garcia, Julio AND Gaillard, Emmanuel AND Capoulade, Romain AND Le Ven, Florent AND Cloutier, Guy AND Kadem, Lyes AND Pibarot, Philippe},
date-added = {2021-08-31 11:07:08 -0400},
date-modified = {2021-08-31 11:07:19 -0400},
doi = {10.1371/journal.pone.0086793},
journal = {PLOS ONE},
month = {01},
number = {1},
pages = {1-10},
publisher = {Public Library of Science},
title = {Non-Invasive Determination of Left Ventricular Workload in Patients with Aortic Stenosis Using Magnetic Resonance Imaging and Doppler Echocardiography},
url = {https://doi.org/10.1371/journal.pone.0086793},
volume = {9},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0086793}}
@article{MotamedEtAl2015,
abstract = {Early detection and accurate estimation of the extent of coarctation of the aorta (COA) is critical to long-term outcome. Peak-to-peak trans-coarctation pressure gradient (PKdP) higher than 20mmHg is an indication for interventional/surgical repair. Patients with COA have reduced proximal and distal aortic compliances. A comprehensive study investigating the effects of variations of proximal COA and systemic compliances on PKdP, and consequently on the COA severity evaluation has never been done. This study evaluates the effect of aortic compliance on diagnostic accuracy of PKdP. Lumped parameter modeling and in vitro experiments were performed for COA severities of 50{\%}, 75{\%} and 90{\%} by area. Modeling and in vitro results were validated against retrospective clinical data of PKdP, measured in 54 patients with COA. Modeling and in vitro. PKdP increases with reduced proximal COA compliance (+36{\%}, +38{\%} and +53{\%} for COA severities of 50{\%}, 75{\%} and 90{\%}, respectively; p<0.05), but decreases with reduced systemic compliance (-62{\%}, -41{\%} and -36{\%} for COA severities of 50{\%}, 75{\%} and 90{\%}, respectively; p<0.01). Clinical study. PKdP has a modest correlation with COA severity (R=0.29). The main determinants of PKdP are COA severity, stroke volume index and systemic compliance. Systemic compliance was found to be as influential as COA severity in PKdP determination (R=0.30 vs. R =0.34). In conclusion, PKdP is highly influenced by both stroke volume index and arterial compliance. Low values of PKdP cannot be used to exclude the severe COA presence since COA severity may be masked by reduced systemic compliance and/or low flow conditions.},
author = {Keshavarz-Motamed, Zahra and Edelman, Elazer R and Motamed, Payam K and Garcia, Julio and Dahdah, Nagib and Kadem, Lyes},
date-added = {2021-08-31 11:04:07 -0400},
date-modified = {2021-08-31 11:07:26 -0400},
doi = {10.1016/j.jbiomech.2015.10.017},
journal = {Journal of biomechanics},
keywords = {Arterial compliance effect; Catheterization; Coarctation of the aorta; Peak to peak pressure gradient; Adolescent; Adult; Aorta/*physiopathology; Aortic Coarctation/*diagnosis/physiopathology/therapy; Child; Child, Preschool; Compliance; Female; Humans; Male; Retrospective Studies; Stroke Volume; Treatment Outcome; Ventricular Pressure; Young Adult},
month = {12},
number = {16},
pages = {4229--4237},
title = {The role of aortic compliance in determination of coarctation severity: Lumped parameter modeling, in vitro study and clinical evaluation},
url = {https://pubmed.ncbi.nlm.nih.gov/26596718},
volume = {48},
year = {2015},
bdsk-url-1 = {https://pubmed.ncbi.nlm.nih.gov/26596718},
bdsk-url-2 = {https://doi.org/10.1016/j.jbiomech.2015.10.017}}
@inproceedings{SmithAndCarette2021-BRIC,
author = {W. Spencer Smith and Jacques Carette},
booktitle = {Proceedings of the 1st Annual Booth Resource and Innovation Cluster (BRIC) Symposium},
date-added = {2021-07-20 22:11:32 -0400},
date-modified = {2021-10-22 16:56:19 -0400},
month = {July},
pages = {21},
title = {Sustainable Software via Generation},
year = {2021},
bdsk-file-1 = {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},
bdsk-url-1 = {https://www.eng.mcmaster.ca/sept/practice/booth-resource-and-innovation-cluster#Proceedings}}
@incollection{Newman2016,
annote = {- they argue ``that the shortcomings lie in the failure of
modellers to adopt sound Software Engineering practices, and that the
elevation of computational models into superior epistemic authorities runs
counter to principles that are common to both Science and Software
Engineering.''
},
author = {Julian Newman},
booktitle = {History and Philosophy of Computing (IFIP AICT 487)},
date-added = {2021-07-20 11:16:02 -0400},
date-modified = {2021-07-20 11:17:29 -0400},
pages = {256--272},
publisher = {Cham, Switzerland: Springer},
title = {Epistemic Opacity, Confirmation Holism and Technical Debt: Computer Simulation in the Light of Empirical Software Engineering},
year = {2016},
bdsk-url-1 = {https://www.researchgate.net/project/How-Computer-Simulation-Models-can-Provide-Scientific-Evidence/update/60f48c2f2897145fbd624f09}}
@misc{AlaminAndUddin2021,
archiveprefix = {arXiv},
author = {Md Abdullah Al Alamin and Gias Uddin},
date-added = {2021-05-05 08:11:23 -0400},
date-modified = {2021-05-05 08:11:54 -0400},
eprint = {2105.01195},
primaryclass = {cs.SE},
title = {Quality Assurance Challenges for Machine Learning Software Applications During Software Development Life Cycle Phases},
year = {2021},
bdsk-url-1 = {https://arxiv.org/pdf/2105.01195.pdf}}
@misc{TrinkenreichEtAl2021,
abstract = {Success in Open Source Software (OSS) is often perceived as an exclusively code-centric endeavor. This perception can
exclude a variety of individuals with a diverse set of skills and backgrounds, in turn helping create the current diversity & inclusion
imbalance in OSS. Because people's perspectives of success affect their personal, professional, and life choices, to be able to support
a diverse class of individuals, we must first understand what OSS contributors consider successful. Thus far, research has used a
uni-dimensional, code-centric lens to define success. In this paper, we challenge this status-quo and reveal the multi-faceted definition
of success among OSS contributors. We do so through interviews with 27 OSS contributors who are recognized as successful in their
communities, and a follow-up open survey with 193 OSS contributors. Our study provides nuanced definitions of success perceptions
in OSS, which might help devise strategies to attract and retain a diverse set of contributors, helping them attain their ``pots of gold at
the end of the rainbow''.},
annote = {Success in OSS is ``contributing more than code, [and involves] contributing documentation, processes {\ldots} the governance of the project.''},
archiveprefix = {arXiv},
author = {Bianca Trinkenreich and Mariam Guizani and Igor Wiese and Tayana Conte and Marco Gerosa and Anita Sarma and Igor Steinmacher},
date-added = {2021-06-05 10:47:57 -0400},
date-modified = {2021-06-05 10:56:48 -0400},
eprint = {2105.08789},
primaryclass = {cs.SE},
title = {The Pot of Gold at the End of the Rainbow: What is Success for Open Source Contributors?},
year = {2021},
bdsk-url-1 = {https://arxiv.org/abs/2105.08789}}
@article{Hecker1997Jun,
author = {Chris Hecker},
date-added = {2021-02-01 19:43:09 -0500},
date-modified = {2021-02-01 19:43:50 -0500},
journal = {Game Developer},
month = {June},
title = {Physics, Part 4: The Third Dimension},
year = {1997},
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@article{Hecker1997Mar,
author = {Chris Hecker},
date-added = {2021-02-01 19:42:08 -0500},
date-modified = {2021-02-01 19:43:04 -0500},
journal = {Game Developer},
month = {March},
title = {Physics, Part 3: Collision Response},
year = {1997},
bdsk-file-1 = {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}}
@article{Hecker1997Jan,
author = {Chris Hecker},
date-added = {2021-02-01 19:40:58 -0500},
date-modified = {2021-02-01 19:41:59 -0500},
journal = {Game Developer},
month = {January},
title = {Physics, Part 2: Angular Effects},
year = {1997},
bdsk-file-1 = {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}}
@article{Hecker1996,
author = {Chris Hecker},
date-added = {2021-02-01 18:17:25 -0500},
date-modified = {2021-02-01 19:40:42 -0500},
journal = {Game Developer},
month = {October/November},
title = {Physics, The Next Frontier},
year = {1997},
bdsk-file-1 = {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}}
@misc{ZabardastEtAl2021,
abstract = {When developing and maintaining software-intensive products or services, we often depend on various "assets", denoting the inherent value to selected artefacts when carrying out development and maintenance activities. When exploring various areas in Software Engineering, such as Technical Debt and our work with industry partners, we soon realised that many terms and concepts are frequently intermixed and used inconsistently. Despite the central role of assets to software engineering, management, and evolution, little thoughts are yet invested into what assets eventually are. A clear terminology of "assets" and related concepts, such as "value" or "value degradation", just to name two, are crucial for setting up effective software engineering practices. As a starting point for our own work, we had to define the terminology and concepts, and extend the reasoning around the concepts. In this position paper, we critically reflect upon the resulting notion of Assets in Software Engineering. We explore various types of assets, their main characteristics, such as providing inherent value. We discuss various types of value degradation and the possible implications of this on the planning, realisation, and evolution of software-intensive products and services over time. With our work, we aspire to contribute to a more standardised definition of Asset Management in Software Engineering and foster research endeavours and their practical dissemination in a common, more unified direction.},
annote = {Defines assets as artifacts that have persistence. Emphasizes terminology more than anything else.},
archiveprefix = {arXiv},
author = {Ehsan Zabardast and Julian Frattini and Javier Gonzalez-Huerta and Daniel Mendez and Tony Gorschek},
date-added = {2021-01-21 11:48:59 -0500},
date-modified = {2021-01-21 11:50:31 -0500},
eprint = {2101.07768},
primaryclass = {cs.SE},
title = {Asset Management in Software Engineering -- What is it after all?},
year = {2021},
bdsk-file-1 = {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},
bdsk-url-1 = {https://arxiv.org/abs/2101.07768}}
@mastersthesis{Zhao2018,
address = {Hamilton, ON, Canada},
author = {Yuzhi Zhao},
date-added = {2021-01-07 10:11:22 -0500},
date-modified = {2021-01-07 10:12:21 -0500},
month = {December},
school = {McMaster University},
title = {Automated Knowledge Extraction Based on a Scientific Computing Software Dcomentation Generation Framework},
year = {2018},
bdsk-file-1 = {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}}
@article{RaminEtAl2020,
abstract = {Motivated and competent team members are a vital part of Agile Software development and make or break any project's success. Motivation is fostered by continuous progress and recognition of efforts. These concepts are founding pillars of the Scrum methodology, which focuses on self-organizing teams. The types of contributions Scrum development team members make to a project's progress are not only technical. However, a comprehensive model comprising the varied contributions in modern software engineering teams is not yet established. We propose a model that incorporates contributions of all Scrum roles, explicitly including those which are not directly related to project artifacts. It improves the visibility of performed tasks, acts as a starting point for team retrospection, and serves as a foundation for discussion in the research community.},
annote = {From JC: That software is more than code is something we've been discussing for a while now. But taking a process look (our view is definitely more product-focused) is what these people have done:
This is a really short paper (4 pages), so they get to the point quickly. Notice how their 'Contribution' (box on first page) lines up really nicely with our definition of sustainability (and productivity).},
author = {Ramin, Frederike and Matthies, Christoph and Teusner, Ralf},
date-added = {2021-01-04 09:54:48 -0500},
date-modified = {2021-01-04 09:55:29 -0500},
doi = {10.1145/3387940.3392241},
isbn = {9781450379632},
journal = {Proceedings of the IEEE/ACM 42nd International Conference on Software Engineering Workshops},
month = {Jun},
publisher = {ACM},
title = {More than Code},
url = {http://dx.doi.org/10.1145/3387940.3392241},
year = {2020},
bdsk-url-1 = {http://dx.doi.org/10.1145/3387940.3392241}}
@mastersthesis{MacLachlan2020,
address = {Hamilton, ON, Canada},
author = {Brooks MacLachlan},
date-added = {2020-11-27 09:49:01 -0500},
date-modified = {2020-11-27 09:49:52 -0500},
month = {June},
school = {McMaster University},
title = {A Design Language for Scientific Computing Software in Drasil},
year = {2020},
bdsk-url-1 = {https://macsphere.mcmaster.ca/handle/11375/25542}}
@book{Ptolemaeus2014,
date-added = {2020-10-30 15:23:29 -0400},
date-modified = {2020-10-30 15:23:29 -0400},
editor = {Claudius Ptolemaeus},
publisher = {Ptolemy.org},
title = {System Design, Modeling, and Simulation using Ptolemy II},
url = {http://ptolemy.org/books/Systems},
year = {2014},
bdsk-url-1 = {http://ptolemy.org/books/Systems}}
@inproceedings{BakirtzisEtAl2020,
address = {Cambridge, USA},
author = {Georgios Bakirtzis and Christina Vasilakopoulou and Cody H. Fleming},
booktitle = {Proceedings of the 3rd Annual International Applied Category Theory Conference 2020 (ACT 2020)},
date-added = {2020-10-30 15:04:19 -0400},
date-modified = {2020-10-30 15:07:20 -0400},
editor = {David I. Spivak and Jamie Vicary},
month = {July},
pages = {1--13},
title = {Compositional Cyber-Physical Systems Modeling},
year = {2020},
bdsk-url-1 = {https://cgi.cse.unsw.edu.au/~eptcs/paper.cgi?ACT2020:40.pdf}}
@inproceedings{OwojaiyeEtAl2021_CSE,
abstract = {We wish to understand the sustainability of current research software development practices. Sustainability is here defined to mean production of software that meets the (explicit and implicit) requirements of the present, while also allowing for cost-effective modifications in the future. To assess current sustainability, we will:
i) analyze existing open source projects to determine what documents, code and scripts are produced;
ii) what concepts are captured by those artifacts;
iii) analyze textbooks and other authoritative sources to determine what documents, code and scripts are recommended;
iv) determine what concepts are supposed to be captured by those artifacts.
We will conduct some case studies on specific domains (such as medical imaging software and Lattice Boltzmann Solvers) via ranking representative software in pair-wise comparisons along multiple quality measures. For the top software thus identified, we will conduct simple experiments to assess usability and modifiability. For the latter, we will ask domain experts to make a small change to the software, and record the time and the details of the process used to make the change. We will then analyze the correlation between modifiability and the concepts captured in project artifacts. Preliminary results suggest a disparity between the suggested documentation and that which is actually produced for a typical research software project.},
author = {Oluwaseun Owojaiye and W. Spencer Smith and Jacques Carette and Peter Michalski and Ao Dong},
booktitle = {{SIAM-CSE} 2021 Conference on Computational Science and Engineering, Minisymposterium: Software Productivity and Sustainability for CSE},
date-added = {2020-10-15 23:14:53 -0400},
date-modified = {2021-11-26 14:49:11 -0500},
doi = {https://doi.org/10.6084/m9.figshare.14039888.v2},
month = {March},
title = {State of Sustainability for Research Software (poster)},
year = {2021},
bdsk-url-1 = {https://figshare.com/articles/poster/State_of_Sustainability_for_Research_Software_SIAM_CSE21_Minisymposterium_Software_Productivity_and_Sustainability_for_CSE/14039888?backTo=/collections/SIAM_CSE21_Minisymposterium_Software_Productivity_and_Sustainability_for_CSE/5321432},
bdsk-url-2 = {https://doi.org/10.6084/m9.figshare.14039888.v2}}
@misc{GroenEtAl2020,
archiveprefix = {arXiv},
author = {D. Groen and H. Arabnejad and V. Jancauskas and W. N. Edeling and F. Jansson and R. A. Richardson and J. Lakhlili and L. Veen and B. Bosak and P. Kopta and D. W. Wright and N. Monnieri and P. Karlshoefer and D. Suleimenova and R. Sinclair and M. Vassaux and A. Nikishova and M. Bieniek and O. O. Luk and M. Kulczewski and E. Raffin and D. Crommelin and O. Hoenen and D. P. Coster and T. Piontek and P. V. Coveney},
date-added = {2020-10-09 11:25:29 -0400},
date-modified = {2020-10-09 11:25:41 -0400},
eprint = {2010.03923},
primaryclass = {cs.MS},
title = {VECMAtk: A Scalable Verification, Validation and Uncertainty Quantification toolkit for Scientific Simulations},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2010.03923},
bdsk-url-2 = {https://arxiv.org/pdf/2010.03923.pdf}}
@misc{BarAndWang2020,
archiveprefix = {arXiv},
author = {Haim Bar and HaiYing Wang},
date-added = {2020-10-06 09:32:36 -0400},
date-modified = {2020-10-06 09:33:10 -0400},
eprint = {2010.01482},
primaryclass = {cs.SE},
title = {Reproducible Science with \LaTeX},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2010.01482},
bdsk-url-2 = {https://arxiv.org/pdf/2010.01482.pdf}}
@misc{BaoEtAl2020,
archiveprefix = {arXiv},
author = {Lingfeng Bao and Tao Li and Xin Xia and Kaiyu Zhu and Hui Li and Xiaohu Yang},
date-added = {2020-10-05 09:41:11 -0400},
date-modified = {2020-10-05 09:41:35 -0400},
eprint = {2005.13167},
primaryclass = {cs.SE},
title = {How does Working from Home Affect Developer Productivity? -- A Case Study of Baidu During COVID-19 Pandemic},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2005.13167}}
@misc{PalenzuelaEtAl2020,
archiveprefix = {arXiv},
author = {C. Palenzuela and B. Mi{\~n}ano and A. Arbona and C. Bona-Casas and C. Bona and J. Mass{\'o}},
date-added = {2020-10-05 09:37:36 -0400},
date-modified = {2020-10-05 09:37:50 -0400},
eprint = {2010.00902},
primaryclass = {physics.comp-ph},
title = {Simflowny 3: An upgraded platform for scientific modelling and simulation},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2010.00902},
bdsk-url-2 = {https://arxiv.org/pdf/2010.00902.pdf}}
@misc{SmithAndCarette2020arXiv,
archiveprefix = {arXiv},
author = {Spencer Smith and Jacques Carette},
date-added = {2020-10-03 10:23:41 -0400},
date-modified = {2021-02-12 15:44:03 -0500},
eprint = {2009.14015},
howpublished = {\url{https://arxiv.org/abs/2009.14015}},
primaryclass = {cs.SE},
title = {Long-term Productivity for Long-term Impact, arXiv report},
year = {2020},
bdsk-url-1 = {https://arxiv.org/pdf/2009.14015.pdf}}
@misc{PolitowskiEtAl2020_SofP,
abstract = {Context: Little is known of the problems faced by game developers. However, game developers do share information about their games projects through postmortems, which describe informally what happened during the projects. Objective: The software-engineering research community and game developers would benefit from a state of the problems of video game development, in particular the problems faced by game developers, their evolution in time, and their root causes. This state of the practice would allow researchers and practitioners to work towards solving these problems. Method: We analyzed more than 200 postmortems, comprising 927 problems divided in 20 types from 1997 to 2019. Through our analysis, we describe the overall landscape of game industry problems in the past 23 years and how these problems evolved over the years. We also give details on the most common problems, their root causes, and possible solutions. We finally provide recommendations for future projects. Results: We observe that (1) the game industry suffer from management and production problems in the same proportion; (2) management problems decreased over the years giving space to business problems, while production problems remained constant; (3a) technical and game design problems are decreasing over the years, the later only after the last decade; (3b) problems related to the team increase over the last decade; (3c) marketing problems are the ones that had the biggest increase over the 23 years compared to other problem types; (4) finally, the majority of the main root causes are related to people, not technologies. Conclusions: In this paper we provide a state of the practice for researchers to understand and study video-game development problems. We also offer recommendations to help practitioners to avoid the most common problems in future projects.},
archiveprefix = {arXiv},
author = {Cristiano Politowski and Fabio Petrillo and Gabriel C. Ullmann and Yann-Ga{\"e}l Gu{\'e}h{\'e}neuc},
date-added = {2020-09-08 22:45:08 -0400},
date-modified = {2020-09-08 22:46:23 -0400},
eprint = {2009.02440},
primaryclass = {cs.SE},
title = {Game Industry Problems: an Extensive Analysis on the Gray Literature},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2009.02440}}
@inproceedings{SmithAndCarette2020,
author = {Spencer Smith and Jacques Carette},
booktitle = {2020 Collegeville Workshop on Scientific Software},
date-added = {2020-08-30 11:06:45 -0400},
date-modified = {2020-08-30 11:08:21 -0400},
pages = {1--5},
title = {Long-term Productivity for Long-term Impact},
url = {\url{https://collegeville.github.io/CW20/WorkshopResources/WhitePapers/WhitePaperList.html}},
year = {2020},
bdsk-url-1 = {https://collegeville.github.io/CW20/WorkshopResources/WhitePapers/WhitePaperList.html}}
@misc{TimperleyEtAl2020,
archiveprefix = {arXiv},
author = {Christopher S. Timperley and Lauren Herckis and Claire Le Goues and Michael Hilton},
date-added = {2020-08-15 10:29:19 -0400},
date-modified = {2020-08-15 10:29:39 -0400},
eprint = {2008.01046},
primaryclass = {cs.SE},
title = {Understanding and Improving Artifact Sharing in Software Engineering Research},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2008.01046}}
@misc{NapoleaoEtAl2020,
archiveprefix = {arXiv},
author = {Bianca Minetto Napole{\~a}o and Fabio Petrillo and Sylvain Hall{\'e}},
date-added = {2020-08-13 12:43:03 -0400},
date-modified = {2020-08-13 12:43:34 -0400},
eprint = {2008.05015},
primaryclass = {cs.SE},
title = {Open Source Software Development Process: A Systematic Review},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2008.05015}}
@article{RutkauskasAndPaulavivcien2015,
author = {Jonas Rutkauskas and Eimen\.{e} Paulavi\u{c}ien\.{e}},
date-added = {2020-06-27 16:24:24 -0400},
date-modified = {2020-06-27 16:24:24 -0400},
journal = {The Engineering Economics},
pages = {35-41},
title = {Concept of Productivity in Service Sector},
volume = {43},
year = {2015},
bdsk-url-1 = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.499.3715&rep=rep1&type=pdf}}
@article{WeinbergAndSchulman1974,
abstract = { In all studies of human performance, the experimenter must be certain that the subject is performing the task that the experimenter believes he has set; otherwise results become uninterpretable. Early studies of computer programming have shown such wide variations in individual performance that one might suspect that subjects differed in their interpretation of the task. Experiments are reported which show how programming performance can be strongly influenced by slight differences in performing objectives. Conclusions are drawn from these results regarding both future experimentation and management practices in computer programming. },
author = {Gerald M. Weinberg and Edward L. Schulman},
date-added = {2020-06-24 20:25:15 -0400},
date-modified = {2020-06-24 20:25:29 -0400},
doi = {10.1177/001872087401600108},
eprint = {https://doi.org/10.1177/001872087401600108},
journal = {Human Factors},
number = {1},
pages = {70-77},
title = {Goals and Performance in Computer Programming},
url = {https://doi.org/10.1177/001872087401600108},
volume = {16},
year = {1974},
bdsk-url-1 = {https://doi.org/10.1177/001872087401600108}}
@misc{Lines2019,
author = {Dan Lines},
date-added = {2020-06-22 23:06:55 -0400},
date-modified = {2020-06-22 23:07:36 -0400},
howpublished = {\url{https://linearb.io/blog/how-to-measure-productivity-in-software-engineering-organizations/}},
month = {February},
title = {How to Measure Productivity In Software Engineering Organizations},
year = {2019},
bdsk-url-1 = {https://linearb.io/blog/how-to-measure-productivity-in-software-engineering-organizations/}}
@misc{WikipediaProgProd2020,
author = {Wikipedia},
date-added = {2020-06-22 23:05:04 -0400},
date-modified = {2020-06-22 23:06:22 -0400},
howpublished = {\url{https://en.wikipedia.org/wiki/Programming_productivity}},
title = {Programming Productivity},
year = {2020},
bdsk-url-1 = {https://en.wikipedia.org/wiki/Programming_productivity}}
@misc{Infopulse2018,
author = {Infopulse},
date-added = {2020-06-22 23:02:58 -0400},
date-modified = {2020-06-22 23:04:07 -0400},
howpublished = {\url{https://www.infopulse.com/blog/top-10-software-development-metrics-to-measure-productivity/}},
month = {October},
title = {Top 10 Software Development Metrics to Measure Productivity},
year = {2018},
bdsk-url-1 = {https://www.infopulse.com/blog/top-10-software-development-metrics-to-measure-productivity/}}
@misc{Schlefer2017,
author = {Gwen Schlefer},
date-added = {2020-06-22 22:59:55 -0400},
date-modified = {2020-06-22 23:01:36 -0400},
howpublished = {\url{https://medium.com/static-object/3-key-metrics-to-measure-developer-productivity-c7cec44f0f67}},
month = {September},
title = {3 Key Metrics to Measure Developer Productivity},
year = {2017},
bdsk-url-1 = {https://medium.com/static-object/3-key-metrics-to-measure-developer-productivity-c7cec44f0f67}}
@article{KitchenhamAndMendes2004,
author = {B. {Kitchenham} and E. {Mendes}},
date-added = {2020-06-22 21:07:04 -0400},
date-modified = {2020-06-22 21:07:04 -0400},
doi = {10.1109/TSE.2004.104},
journal = {IEEE Transactions on Software Engineering},
keywords = {software cost estimation;software metrics;productivity;project management;regression analysis;software productivity measurement;software cost estimation;product size;project effort;regression-based effort estimation;parameter estimation;Size measurement;Software measurement;Productivity;Predictive models;Costs;Equations;Computer science;Computer Society;Application software;Production;Index Terms- Software productivity measurement;software cost estimation.},
month = {Dec},
number = {12},
pages = {1023-1035},
title = {Software productivity measurement using multiple size measures},
volume = {30},
year = {2004},
bdsk-url-1 = {https://ieeexplore.ieee.org/abstract/document/1377195},
bdsk-url-2 = {https://doi.org/10.1109/TSE.2004.104}}
@article{Boehm1987,
author = {Barry W. Boehm},
date-added = {2020-06-22 17:37:07 -0400},
date-modified = {2020-06-22 17:37:07 -0400},
journal = {Computer},
pages = {43--47},
title = {Improving Software Productivity},
year = {1987},
bdsk-file-1 = {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},
bdsk-url-1 = {http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=8A5967CE077ECB46DE9EBFC12F443C68?doi=10.1.1.365.9038}}
@article{Drucker1999,
added-at = {2008-10-05T14:15:05.000+0200},
author = {Drucker, P.F.},
biburl = {https://www.bibsonomy.org/bibtex/229dd1f744535efff731b78bf22bf9d70/diam_eter},
date-added = {2020-06-22 16:52:23 -0400},
date-modified = {2020-06-22 16:52:28 -0400},
interhash = {08a18b56b923dac98b91a03b3d10b947},
intrahash = {29dd1f744535efff731b78bf22bf9d70},
journal = {California Management Review},
keywords = {GdWM},
number = 2,
pages = {79--94},
timestamp = {2008-12-07T10:31:10.000+0100},
title = {{Knowledge-Worker Productivity: The Biggest Challenge}},
volume = 41,
year = 1999,
bdsk-file-1 = {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}}
@misc{Sundheim2020,
author = {Doug Sundheim},
date-added = {2020-06-22 16:37:29 -0400},
date-modified = {2020-06-22 16:38:52 -0400},
howpublished = {\url{https://www.execunet.com/daydreaming-enough/}},
month = {January},
title = {Are You Daydreaming Enough?},
year = {2018},
bdsk-url-1 = {https://www.execunet.com/daydreaming-enough/}}
@book{Taylor1911,
author = {Frederick Winslow Taylor},
date-added = {2020-06-22 15:23:20 -0400},
date-modified = {2020-06-22 15:24:11 -0400},
publisher = {New York, London, Harper \& Brothers},
title = {The principles of scientific management},
year = {1911},
bdsk-url-1 = {https://wps.pearsoncustom.com/wps/media/objects/2429/2487430/pdfs/taylor.pdf}}
@article{McLeodAndMacDonell2011,
address = {New York, NY, USA},
articleno = {24},
author = {McLeod, Laurie and MacDonell, Stephen G.},
date-added = {2020-06-03 15:31:09 -0400},
date-modified = {2020-06-03 15:31:27 -0400},
doi = {10.1145/1978802.1978803},
issn = {0360-0300},
issue_date = {October 2011},
journal = {ACM Comput. Surv.},
keywords = {project content, project outcomes, Development processes, institutional context, people and action},
month = oct,
number = {4},
numpages = {56},
publisher = {Association for Computing Machinery},
title = {Factors That Affect Software Systems Development Project Outcomes: A Survey of Research},
url = {https://doi.org/10.1145/1978802.1978803},
volume = {43},
year = {2011},
bdsk-url-1 = {https://doi.org/10.1145/1978802.1978803},
bdsk-url-2 = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.214.9834&rep=rep1&type=pdf}}
@misc{SmithEtAl2019_arXiv_AC,
author = {W. Spencer Smith and Mojdeh Sayari Nejad and Alan Wassyng},
date-added = {2020-06-03 15:26:15 -0400},
date-modified = {2021-10-25 13:25:47 -0400},
eprint = {1912.13308},
howpublished = {\url{https://arxiv.org/abs/1912.13308}},
month = dec,
title = {Building Confidence in Scientific Computing Software Via Assurance Cases},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1912.13308}}
@article{FeinbergEtAl2020,
abstract = {Although reproducibility--the idea that a valid scientific experiment can be repeated with similar results--
is integral to our understanding of good scientific practice, it has remained a difficult concept to define
precisely. Across scientific disciplines, the increasing prevalence of large datasets, and the computational
techniques necessary to manage and analyze those datasets, has prompted new ways of thinking about
reproducibility. We present findings from a qualitative study of a NSF--funded two-week workshop developed
to introduce an interdisciplinary group of domain scientists to data-management techniques for data-intensive
computing, with a focus on reproducible science. Our findings suggest that the introduction of data-related
activities promotes a new understanding of reproducibility as a mechanism for local knowledge transfer and
collaboration, particularly as regards efficient software reuse.},
address = {New York, NY, USA},
annote = {{- about reproducibility related to data, but some mention of code as well}
- two research question: * How do data tools and practices shape workshop participants` understanding of reproducibility?
* How do workshop participants articulate the benefits of computational reproducibility?
- paper makes the statement that increased automation means increased reproducibility},
articleno = {035},
author = {Feinberg, Melanie and Sutherland, Will and Nelson, Sarah Beth and Jarrahi, Mohammad Hossein and Rajasekar, Arcot},
date-added = {2020-06-02 16:34:26 -0400},
date-modified = {2020-06-02 17:02:44 -0400},
doi = {10.1145/3392840},
issue_date = {May 2020},
journal = {Proc. ACM Hum.-Comput. Interact.},
keywords = {replicability, scientific software development, reproducibility, data work},
month = may,
number = {CSCW1},
numpages = {22},
publisher = {Association for Computing Machinery},
title = {The New Reality of Reproducibility: The Role of Data Work in Scientific Research},
url = {https://doi.org/10.1145/3392840},
volume = {4},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1145/3392840},
bdsk-url-2 = {https://dl.acm.org/doi/pdf/10.1145/3392840}}
@article{NouwensEtAl2020,
author = {Nouwens, Midas and Borowski, Marcel and Fog, Bjarke Vognstrup and Klokmose, Clemens Nylandsted},
date-added = {2020-05-29 10:39:58 -0400},
date-modified = {2020-05-29 10:41:45 -0400},
journal = {Proceedings of Acm Chi 2020},
keywords = {Computational media; Computational notebook; Electronic laboratory notebook; Participatory design},
language = {eng},
month = {April},
pages = {1--13},
publisher = {Association for Computing Machinery, Inc.},
title = {Between Scripts and Applications: Computational Media for the Frontier of Nanoscience},
year = {2020},
bdsk-url-1 = {https://dl.acm.org/doi/pdf/10.1145/3313831.3376287}}
@misc{vanWerkhovenEtAl2020,
abstract = {After years of using Graphics Processing Units (GPUs) to
accelerate scientific applications in fields as varied as tomography, computer vision, climate modeling, digital forensics, geospatial databases,
particle physics, radio astronomy, and localization microscopy, we noticed
a number of technical, socio-technical, and non-technical challenges that
Research Software Engineers (RSEs) may run into. While some of these
challenges, such as managing different programming languages within a
project, or having to deal with different memory spaces, are common
to all software projects involving GPUs, others are more typical of scientific software projects. Among these challenges we include changing
resolutions or scales, maintaining an application over time and making
it sustainable, and evaluating both the obtained results and the achieved performance.},
annote = {- has two interesting references about sofware sustainability},
author = {Ben van Werkhoven and Willem Jan Palenstijn and Alessio Sclocco},
date-added = {2020-05-28 11:58:30 -0400},
date-modified = {2020-05-28 12:04:41 -0400},
howpublished = {\url{https://arxiv.org/abs/2005.13227}},
journal = {arXiv},
note = {14 pp.},
title = {Lessons learned in a decade of research software engineering GPU applications},
year = {2020},
bdsk-url-1 = {https://arxiv.org/pdf/2005.13227.pdf}}
@misc{BizopoulosAndBizopoulos2020,
archiveprefix = {arXiv},
author = {Paschalis Bizopoulos and Dimitris Bizopoulos},
date-added = {2020-05-27 09:29:31 -0400},
date-modified = {2020-05-27 09:29:50 -0400},
eprint = {2005.12660},
primaryclass = {cs.SE},
title = {Reconciler: A Workflow for Certifying Computational Research Reproducibility},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2005.12660}}
@misc{TrisovicEtAl2020,
archiveprefix = {arXiv},
author = {Ana Trisovic and Philip Durbin and Tania Schlatter and Gustavo Durand and Sonia Barbosa and Danny Brooke and Merc{\`e} Crosas},
date-added = {2020-05-07 12:24:39 -0400},
date-modified = {2020-05-07 12:26:57 -0400},
eprint = {2005.02985},
howpublished = {\url{https://arxiv.org/abs/2005.02985}},
primaryclass = {cs.DL, cs.SE},
title = {Advancing computational reproducibility in the Dataverse data repository platform},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2005.02985}}
@misc{AnztEtAl2020,
archiveprefix = {arXiv},
author = {Hartwig Anzt and Felix Bach and Stephan Druskat and Frank L{\"o}ffler and Axel Loewe and Bernhard Y. Renard and Gunnar Seemann and Alexander Struck and Elke Achhammer and Piush Aggarwal and Franziska Appel and Michael Bader and Lutz Brusch and Christian Busse and Gerasimos Chourdakis and Piotr W. Dabrowski and Peter Ebert and Bernd Flemisch and Sven Friedl and Bernadette Fritzsch and Maximilian D. Funk and Volker Gast and Florian Goth and Jean-No{\"e}l Grad and Sibylle Hermann and Florian Hohmann and Stephan Janosch and Dominik Kutra and Jan Linxweiler and Thilo Muth and Wolfgang Peters-Kottig and Fabian Rack and Fabian H. C. Raters and Stephan Rave and Guido Reina and Malte Rei{\ss}ig and Timo Ropinski and Joerg Schaarschmidt and Heidi Seibold and Jan P. Thiele and Benjamin Uekerman and Stefan Unger and Rudolf Weeber},
date-added = {2020-05-05 11:24:08 -0400},
date-modified = {2020-05-05 11:24:18 -0400},
eprint = {2005.01469},
primaryclass = {cs.GL},
title = {An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2005.01469}}
@phdthesis{Rossel2013,
author = {Pedro O. Rossel},
date-added = {2020-05-05 11:05:56 -0400},
date-modified = {2020-05-05 11:08:14 -0400},
school = {Universidad Cat{\'o}lica de la Sant{\'\i}sima Concepci{\'o}n, Chile},
title = {Sofware Product Line Model for the Meshing Tool Domain},
year = {2013},
bdsk-url-1 = {https://www.researchgate.net/publication/261171254_Software_Product_Line_Model_for_the_Meshing_Tool_Domain/references}}
@article{PolitowskiEtAl2020,
author = {Cristiano Politowski and Fabio Petrillo and Jo{\~a}o Eduardo Montandon and Marco Tulio Valente and Yann-Gael Gu'eh'eneuc},
date-added = {2020-04-23 09:08:47 -0400},
date-modified = {2020-04-23 09:08:59 -0400},
journal = {ArXiv},
title = {Are Game Engines Software Frameworks? A Three-perspective Study},
volume = {abs/2004.05705},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2004.05705}}
@techreport{IEEEStdGlossarySET1990,
author = {IEEE},
date-added = {2020-04-23 08:52:05 -0400},
date-modified = {2020-04-23 08:52:05 -0400},
institution = {IEEE},
key = {IEEE Std 610.12-1990},
title = {IEEE Standard Glossary of Software Engineering Terminology},
type = {Standard},
year = {1991},
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@book{MacKenzie2013,
address = {San Francisco, CA, USA},
author = {MacKenzie, I. Scott},
date-added = {2020-04-02 16:07:45 -0400},
date-modified = {2020-04-02 16:07:53 -0400},
edition = {1st},
isbn = {0124058655},
publisher = {Morgan Kaufmann Publishers Inc.},
title = {Human-Computer Interaction: An Empirical Research Perspective},
year = {2013},
bdsk-file-1 = {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}}
@misc{MolnarandMotogna2020,
archiveprefix = {arXiv},
author = {Arthur-Jozsef Molnar and Simona Motogna},
date-added = {2020-03-14 11:21:54 -0400},
date-modified = {2020-03-14 11:23:10 -0400},
eprint = {2003.00447},
month = {Mar},
primaryclass = {cs.SE},
title = {Longitudinal Evaluation of Open-Source Software Maintainability},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2003.00447}}
@misc{AguilaEtAl2020,
archiveprefix = {arXiv},
author = {Isabel M. del {\'A}guila and Jos{\'e} del Sagrado and Joaqu{\'\i}n Ca{\~n}adas},
date-added = {2020-03-13 20:14:24 -0400},
date-modified = {2020-03-13 20:16:30 -0400},
eprint = {2002.10163},
month = {Feb},
primaryclass = {cs.SE},
title = {Software Engineering Timeline: major areas of interest and multidisciplinary trends},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2002.10163}}
@misc{RamakrishnaEtAl2020,
archiveprefix = {arXiv},
author = {Shreyas Ramakrishna and Charles Hartsell and Abhishek Dubey and Partha Pal and Gabor Karsai},
date-added = {2020-03-13 17:42:18 -0400},
date-modified = {2020-03-13 17:42:18 -0400},
eprint = {2003.05388},
primaryclass = {cs.RO},
title = {A Methodology for Automating Assurance Case Generation},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2003.05388}}
@misc{VofelsangEtAl2020,
archiveprefix = {arXiv},
author = {Andreas Vogelsang and Jonas Eckhardt and Daniet Mendez and Moritz Berger},
date-added = {2020-03-13 15:13:14 -0400},
date-modified = {2020-03-13 20:16:06 -0400},
eprint = {2002.02793},
month = {Feb},
primaryclass = {cs.SE},
title = {Views on Quality Requirements in Academia and Practice: Commonalities, Differences, and Context-Dependent Grey Areas},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2002.02793}}
@misc{TuEtAl2020,
archiveprefix = {arXiv},
author = {Huy Tu and Rishabh Agrawal and Tim Menzies},
date-added = {2020-03-13 09:38:22 -0400},
date-modified = {2020-03-13 09:38:32 -0400},
eprint = {2003.05922},
primaryclass = {cs.SE},
title = {The Changing Nature of Computational Science Software},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2003.05922}}
@book{FreemanEtAl2004,
author = {Freeman, Elisabeth and Freeman, Eric and Bates, Bert and Sierra, Kathy},
date-added = {2020-03-03 22:35:42 -0500},
date-modified = {2020-03-03 22:47:25 -0500},
isbn = {0596007124},
publisher = {O' Reilly \& Associates, Inc.},
title = {Head First Design Patterns},
year = {2004},
bdsk-file-1 = {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}}
@misc{GarousiEtAl2020,
author = {Vahid Garousi and Ehsan Abbasi and Bedir Tekinerdogan},
date-added = {2020-03-03 10:10:33 -0500},
date-modified = {2020-03-03 10:11:54 -0500},
howpublished = {https://arxiv.org/abs/2003.00463},
month = {March},
title = {Experience in engineering of scientific software: The case of an optimization software for oil pipelines},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2003.00463}}
@book{ShullEtAl2010,
author = {Shull, Forrest and Singer, Janice and Sjberg, Dag I. K.},
date-added = {2020-02-19 10:24:23 -0500},
date-modified = {2020-02-19 10:24:44 -0500},
edition = {1st},
isbn = {1849967121},
publisher = {Springer Publishing Company, Incorporated},
title = {Guide to Advanced Empirical Software Engineering},
year = {2010},
bdsk-file-1 = {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}}
@phdthesis{Remmel2014,
annote = {- says Smith and Yu are the first to do SPLE for scientific software
- Chapter 4 shows a high level view of the domain analysis steps},
author = {Hanna Remmel},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/phd/dnb/Remmel14.bib},
date-added = {2020-02-19 09:27:40 -0500},
date-modified = {2020-02-19 09:53:12 -0500},
school = {University of Heidelberg, Germany},
timestamp = {Wed, 12 Feb 2020 16:41:48 +0100},
title = {Supporting the quality assurance of a scientific framework},
url = {http://www.ub.uni-heidelberg.de/archiv/17171},
year = {2014},
bdsk-url-1 = {http://www.ub.uni-heidelberg.de/archiv/17171}}
@misc{BauerEtAl2020,
archiveprefix = {arXiv},
author = {Martin Bauer and Harald K{\"o}stler and Ulrich R{\"u}de},
date-added = {2020-02-18 14:27:23 -0500},
date-modified = {2020-02-18 14:27:34 -0500},
eprint = {2001.11806},
primaryclass = {cs.MS},
title = {lbmpy: A flexible code generation toolkit for highly efficient lattice Boltzmann simulations},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2001.11806}}
@misc{KonkolEtAl2020,
archiveprefix = {arXiv},
author = {Markus Konkol and Daniel N{\"u}st and Laura Goulier},
date-added = {2020-01-09 10:59:09 -0500},
date-modified = {2020-01-09 10:59:20 -0500},
eprint = {2001.00484},
primaryclass = {cs.DL},
title = {Publishing computational research -- A review of infrastructures for reproducible and transparent scholarly communication},
year = {2020},
bdsk-url-1 = {https://arxiv.org/abs/2001.00484}}
@article{Meyer1985,
address = {Los Alamitos, CA, USA},
author = {Bertrand Meyer},
date-added = {2020-01-03 08:54:04 -0500},
date-modified = {2020-01-03 08:54:42 -0500},
doi = {10.1109/MS.1985.229776},
issn = {1937-4194},
journal = {IEEE Software},
keywords = {null},
month = {jan},
number = {01},
pages = {6-26},
publisher = {IEEE Computer Society},
title = {On Formalism in Specifications},
volume = {2},
year = {1985},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1109/MS.1985.229776}}
@misc{Baber2002,
author = {Robert Baber},
date-added = {2020-01-03 08:50:41 -0500},
date-modified = {2020-01-03 08:51:24 -0500},
month = {October},
title = {Translating English to Mathematics},
year = {2002},
bdsk-file-1 = {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}}
@misc{YeEtAl2019,
archiveprefix = {arXiv},
author = {Y. Ye and R. D. Boyce and M. K. Davis and K. Elliston and C. Davatzikos and A. Fedorov and J. C. Fillion-Robin and I. Foster and J. Gilbertson and M. Heiskanen and J. Klemm and A. Lasso and J. V. Miller and M. Morgan and S. Pieper and B. Raumann and B. Sarachan and G. Savova and J. C. Silverstein and D. Taylor and J. Zelnis and G. Q. Zhang and M. J. Becich},
date-added = {2020-01-02 15:49:40 -0500},
date-modified = {2020-01-02 15:49:52 -0500},
eprint = {1912.12371},
primaryclass = {q-bio.OT},
title = {Open Source Software Sustainability Models: Initial White Paper from the Information Technology for Cancer Research Sustainability and Industry Partnership Work Group},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1912.12371}}
@misc{MaljaarsEtAl2019,
archiveprefix = {arXiv},
author = {Jakob M. Maljaars and Chris N. Richardson and Nathan Sime},
date-added = {2020-01-02 15:45:29 -0500},
date-modified = {2020-01-02 15:45:52 -0500},
eprint = {1912.13375},
primaryclass = {cs.MS},
title = {LEoPart: a particle library for FEniCS},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1912.13375}}
@misc{BarthelsEtAl2019,
archiveprefix = {arXiv},
author = {Henrik Barthels and Christos Psarras and Paolo Bientinesi},
date-added = {2020-01-02 15:43:08 -0500},
date-modified = {2020-01-02 15:43:22 -0500},
eprint = {1912.12924},
primaryclass = {cs.MS},
title = {Linnea: Automatic Generation of Efficient Linear Algebra Programs},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1912.12924}}
@article{SmithEtAl2020,
abstract = {Assurance cases provide an organized and explicit argument for correctness. They can dramatically improve the quality of scientific software. Assurance cases are already effectively used for real-time safety critical systems. Their advantages for scientific software include engaging domain experts, producing only necessary documentation, and providing evidence that can be verified/replicated. This article illustrates assurance cases through the correctness case for 3dfim+, software for analyzing activity in the brain. The example justifies the value of assurance cases for scientific software, since the existing documentation is shown to have ambiguities and omissions, such as an incompletely defined ranking function and missing details on the coordinate system. We identified a serious concern for 3dfim+: running the software does not produce any warning about the necessity of using data that matches the parametric statistical model employed for the correlation calculations. Raising the bar for scientific software is both feasible and necessary.},
author = {W. Spencer Smith and Mojdeh Sayari Nejad and Alan Wassyng},
date-added = {2020-01-02 15:32:13 -0500},
date-modified = {2022-10-04 11:06:43 -0400},
journal = {Computing in Science and Engineering},
month = Feb,
number = {1},
pages = {47--57},
title = {Raising the Bar: Assurance Cases for Scientific Computing Software},
volume = {23},
year = {2020},
bdsk-file-1 = {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},
bdsk-url-1 = {https://ieeexplore.ieee.org/document/9178774}}
@misc{DiskinEtAl2019,
archiveprefix = {arXiv},
author = {Zinovy Diskin and Nicholas Annable and Alan Wassyng and Mark Lawford},
date-added = {2019-12-30 12:13:46 -0500},
date-modified = {2019-12-30 12:13:59 -0500},
eprint = {1912.09912},
primaryclass = {cs.SE},
title = {Assurance via workflow+ modelling and conformance},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1912.09912}}
@article{CrouchEtAl2013,
abstract = {To effect change, the Software Sustainability Institute works with researchers, developers, funders, and infrastructure providers to identify and address key issues with research software.},
author = {S. {Crouch} and N. C. {Hong} and S. {Hettrick} and M. {Jackson} and A. {Pawlik} and S. {Sufi} and L. {Carr} and D. {De Roure} and C. {Goble} and M. {Parsons}},
date-added = {2019-12-18 10:27:47 -0500},
date-modified = {2019-12-18 10:28:39 -0500},
doi = {10.1109/MCSE.2013.133},
issn = {1558-366X},
journal = {Computing in Science Engineering},
keywords = {research and development;software engineering;Software Sustainability Institute;research software attitudes;research software practices;Software development;Software engineering;Training;Scientific computing;Software reliability;Programming;Domain engineering;Software development;Software engineering;Training;Scientific computing;Software reliability;Programming;Domain engineering;scientific computing;software engineering;domain engineering;reliability;maintainability},
month = {Nov},
number = {6},
pages = {74-80},
title = {The Software Sustainability Institute: Changing Research Software Attitudes and Practices},
volume = {15},
year = {2013},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1109/MCSE.2013.133}}
@inproceedings{SehestedtEtAl2014,
acmid = {2578226},
address = {New York, NY, USA},
articleno = {5},
author = {Sehestedt, Stephan and Cheng, Chih-Hong and Bouwers, Eric},
booktitle = {Proceedings of the WICSA 2014 Companion Volume},
date-added = {2019-12-18 09:51:28 -0500},
date-modified = {2019-12-18 09:51:39 -0500},
doi = {10.1145/2578128.2578226},
isbn = {978-1-4503-2523-3},
keywords = {clarity, completeness, consistency, correctness, evolvability, quality attributes, software architecture, sustainability},
location = {Sydney, Australia},
numpages = {4},
pages = {5:1--5:4},
publisher = {ACM},
series = {WICSA '14 Companion},
title = {Towards Quantitative Metrics for Architecture Models},
url = {http://doi.acm.org/10.1145/2578128.2578226},
year = {2014},
bdsk-file-1 = {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},
bdsk-url-1 = {http://doi.acm.org/10.1145/2578128.2578226},
bdsk-url-2 = {https://doi.org/10.1145/2578128.2578226}}
@misc{RieschEtAl2019,
archiveprefix = {arXiv},
author = {Michael Riesch and Tien Dat Nguyen and Christian Jirauschek},
date-added = {2019-12-13 14:06:32 -0500},
date-modified = {2019-12-13 14:07:23 -0500},
eprint = {1912.01640},
primaryclass = {cs.MS},
title = {bertha: Project Skeleton for Scientific Software},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1912.01640},
bdsk-url-2 = {https://arxiv.org/pdf/1912.01640.pdf}}
@article{LeiteEtAl2019,
author = {Leite, Leonardo and Rocha, Carla and Kon, Fabio and Milojicic, Dejan and Meirelles, Paulo},
date-added = {2019-12-12 16:22:19 -0500},
date-modified = {2019-12-12 16:22:25 -0500},
doi = {10.1145/3359981},
issn = {0360-0300},
journal = {ACM Computing Surveys},
month = {Nov},
number = {6},
pages = {1--35},
publisher = {Association for Computing Machinery (ACM)},
title = {A Survey of DevOps Concepts and Challenges},
url = {http://dx.doi.org/10.1145/3359981},
volume = {52},
year = {2019},
bdsk-url-1 = {http://dx.doi.org/10.1145/3359981},
bdsk-url-2 = {https://arxiv.org/pdf/1909.05409.pdf}}
@book{ISO9126,
added-at = {2014-07-08T11:07:29.000+0200},
annote = {``ISO/IEC 9126 consists of the following parts, under the general title Information technology --- Software product quality:
--- Part 1: Quality model
--- Part 2: External metrics
--- Part 3: Internal metrics
--- Part 4: Quality in use metrics''
``Comprehensive specification and evaluation of software product quality is a key factor in ensuring adequate quality.''
- they call the different qualities, quality characteristics
- like Ghezzi, they distinguish internal and external qualities, they also add ``quality in use''
- like Van Vleit they distinguish direct and indirect measures
- external metrics corresponds to what Ghezzi et al calls dynamic measures of verification and validation
- discusses quality, which is made up of quality characteristics. The characteristics in turn can be divided into sub-characteristics. The subcharacteristics are determined by attributes. The attributes may contribute to more than one subcharacteristiccs. The characteristics, subcharacteristics, and attributers can be internal or external. Metrics are used to measure quality. There are internal and external metrics. Metrics can be direct or indirect. It seems that metrics are typically tied to attributes, but I don't see that written out explicity.
- does not follow the usual distinction between verification and validation (the two definitions are almost identifical)
- examples would really help make the distinction between all of the terminology (attribute, measure, indicator, metric, internal, external, direct, indirect, etc.)
- In a sense they punted the real work to the definition of the attributes and the measures of the attributes, and the means for combining the attribute measures to come up with the quality measures
- the ISO definition of accuracy is defined in terms of precision, but in scientific computing accuracy and precision are two different concepts.},
author = {{ISO/IEC}},
biburl = {https://www.bibsonomy.org/bibtex/2a7b775cd08a9182a7b88d5ca68657a4a/andiv},
date-added = {2019-12-03 22:05:58 -0500},
date-modified = {2021-09-22 16:56:15 -0400},
interhash = {ef6f58a2241715facdfa7424be170ea3},
intrahash = {a7b775cd08a9182a7b88d5ca68657a4a},
keywords = {ISO functional non},
publisher = {ISO/IEC},
timestamp = {2014-07-08T11:07:50.000+0200},
title = {{ISO/IEC} 9126. Software engineering -- Product quality},
year = 2001,
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@misc{CaretteEtAl2019,
author = {Jacques Carette and Brooks MacLachlan and W. Spencer Smith},
date-added = {2019-11-27 08:37:45 -0500},
date-modified = {2019-11-28 09:42:43 -0500},
howpublished = {https://arxiv.org/abs/1911.11824},
month = nov,
title = {{GOOL}: A Generic Object-Oriented Language},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.11824}}
@inproceedings{CaretteEtAl2020,
abstract = {We present the design and implementation of a generative geometric kernel. The kernel generator is generic, type-safe, parametrized by many design-level choices and extensible. The resulting code has minimal traces of the design abstractions. We achieve genericity through a layered design deriving concepts from affine geometry, linear algebra and abstract algebra. We achieve parametrization and type-safety by using OCaml's module system, including higher order modules. The cost of abstraction is removed by using MetaOCaml's support for code generation coupled with some annotations atop the code type.},
author = {Jacques Carette and Brooks MacLachlan and W. Spencer Smith},
booktitle = {ACM SIGPLAN 2020 Workshop on Partial Evaluation and Program Manipulation (PEPM'20)},
date-added = {2019-11-27 08:34:08 -0500},
date-modified = {2019-11-27 08:36:02 -0500},
keywords = {Code Generation, Domain Specific Language, Haskell, Documentation},
month = jan,
pages = {1--6},
title = {{GOOL}: A Generic Object-Oriented Language},
year = {2020},
bdsk-file-1 = {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},
bdsk-url-1 = {https://github.com/JacquesCarette/Drasil/tree/master/Papers/GOOL}}
@misc{Prechelt2019,
archiveprefix = {arXiv},
author = {Lutz Prechelt},
date-added = {2019-11-26 22:18:09 -0500},
date-modified = {2019-11-26 22:18:19 -0500},
eprint = {1911.09971},
primaryclass = {cs.SE},
title = {Four presumed gaps in the software engineering research community's knowledge},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.09971}}
@misc{PsarrasEtAl2019,
archiveprefix = {arXiv},
author = {Christos Psarras and Henrik Barthels and Paolo Bientinesi},
date-added = {2019-11-22 14:43:13 -0500},
date-modified = {2019-11-22 14:43:29 -0500},
eprint = {1911.09421},
primaryclass = {cs.MS},
title = {The Linear Algebra Mapping Problem},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.09421}}
@misc{AndersonEtAl2019,
archiveprefix = {arXiv},
author = {Robert Anderson and Julian Andrej and Andrew Barker and Jamie Bramwell and Jean-Sylvain Camier and Jakub Cerveny and Veselin Dobrev and Yohann Dudouit and Aaron Fisher and Tzanio Kolev and Will Pazner and Mark Stowell and Vladimir Tomov and Johann Dahm and David Medina and Stefano Zampini},
date-added = {2019-11-22 14:34:23 -0500},
date-modified = {2019-11-22 14:34:35 -0500},
eprint = {1911.09220},
primaryclass = {cs.MS},
title = {MFEM: a modular finite element methods library},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.09220}}
@book{Pressman2010,
author = {Roger S. Pressman},
date-added = {2019-11-20 15:11:36 -0500},
date-modified = {2019-11-20 16:34:34 -0500},
edition = {7},
publisher = {McGraw-Hill},
title = {Software Engineering, A Practitioner's Approach},
year = {1999},
bdsk-file-1 = {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}}
@misc{GallardEtAl2019,
archiveprefix = {arXiv},
author = {Jean-Matthieu Gallard and Lukas Krenz and Leonhard Rannabauer and Anne Reinarz and Michael Bader},
date-added = {2019-11-19 09:28:50 -0500},
date-modified = {2019-11-19 09:29:06 -0500},
eprint = {1911.06817},
primaryclass = {cs.MS},
title = {Role-Oriented Code Generation in an Engine for Solving Hyperbolic PDE Systems},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.06817}}
@misc{PermannEtAl2019,
archiveprefix = {arXiv},
author = {Cody J. Permann and Derek R. Gaston and David Andrs and Robert W. Carlsen and Fande Kong and Alexander D. Lindsay and Jason M. Miller and John W. Peterson and Andrew E. Slaughter and Roy H. Stogner and Richard C. Martineau},
date-added = {2019-11-13 14:45:22 -0500},
date-modified = {2019-11-13 14:45:34 -0500},
eprint = {1911.04488},
primaryclass = {cs.MS},
title = {MOOSE: Enabling Massively Parallel Multiphysics Simulation},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.04488}}
@misc{BastianEtAl2019,
abstract = {In the Exa-Dune project we have developed, implemented and optimised numerical algorithms and software for the scalable solution of partial differential equations (PDEs) on future exascale systems exhibiting a heterogeneous massively parallel architecture. In order to cope with the increased probability of hardware failures, one aim of the project was to add flexible, application-oriented resilience capabilities into the framework. Continuous improvement of the underlying hardware-oriented numerical methods have included GPU-based sparse approximate inverses, matrix-free sum-factorisation for high-order discontinuous Galerkin discretisations as well as partially matrix-free preconditioners. On top of that, additional scalability is facilitated by exploiting massive coarse grained parallelism offered by multiscale and uncertainty quantification methods where we have focused on the adaptive choice of the coarse/fine scale and the overlap region as well as the combination of local reduced basis multiscale methods and the multilevel Monte-Carlo algorithm. Finally, some of the concepts are applied in a land-surface model including subsurface flow and surface runoff.},
annote = {- not really anything on the design, or on software engineering},
archiveprefix = {arXiv},
author = {Peter Bastian and Mirco Altenbernd and Nils-Arne Dreier and Christian Engwer and Jorrit Fahlke and Ren{\'e} Fritze and Markus Geveler and Dominik G{\"o}ddeke and Oleg Iliev and Olaf Ippisch and Jan Mohring and Steffen M{\"u}thing and Mario Ohlberger and Dirk Ribbrock and Nikolay Shegunov and Stefan Turek},
date-added = {2019-11-08 15:39:33 -0500},
date-modified = {2019-11-08 15:42:13 -0500},
eprint = {1911.01492},
primaryclass = {cs.MS},
title = {Exa-Dune -- Flexible PDE Solvers, Numerical Methods and Applications},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1911.01492}}
@misc{Daversin-Catty2019,
archiveprefix = {arXiv},
author = {C\'{e}cile Daversin-Catty and Chris N. Richardson and Ada J. Ellingsrud and Marie E. Rognes},
date-added = {2019-11-05 08:07:28 -0500},
date-modified = {2019-11-05 08:09:18 -0500},
eprint = {1911.01166},
primaryclass = {cs.MS},
title = {Abstractions and automated algorithms for mixed domain finite element methods},
year = {2019},
bdsk-url-1 = {https://arxiv.org/pdf/1911.01166.pdf}}
@misc{JayEtAl2019,
archiveprefix = {arXiv},
author = {Caroline Jay and Robert Haines and Daniel S. Katz and Jeffrey Carver and James C. Phillips and Anshu Dubey and Sandra Gesing and Matthew Turk and Hui Wan and Hubertus van Dam and James Howison and Vitali Morozov and Steven R. Brandt},
date-added = {2019-11-03 08:36:46 -0500},
date-modified = {2019-11-03 08:36:59 -0500},
eprint = {1910.09902},
primaryclass = {cs.SE},
title = {Theory-Software Translation: Research Challenges and Future Directions},
year = {2019},
bdsk-url-1 = {https://arxiv.org/pdf/1910.09902.pdf}}
@misc{ArndtEtAl2019,
annote = {- OO library
- uses templates
- has a comparison of different design approaches for FEM in other libraries
- highlights problems with DEAL.II - could likely be addressed by a generative approach},
archiveprefix = {arXiv},
author = {Daniel Arndt and Wolfgang Bangerth and Denis Davydov and Timo Heister and Luca Heltai and Martin Kronbichler and Matthias Maier and Jean-Paul Pelteret and Bruno Turcksin and David Wells},
date-added = {2019-11-03 08:15:43 -0500},
date-modified = {2019-11-03 08:25:09 -0500},
eprint = {1910.13247},
primaryclass = {cs.MS},
title = {The deal.II finite element library},
year = {2019},
bdsk-url-1 = {https://arxiv.org/pdf/1910.13247.pdf}}
@mastersthesis{Fadhel2019,
address = {Hamilton, Ontario, Canada},
author = {Muntazir Fadhel},
date-added = {2019-10-31 15:31:09 -0400},
date-modified = {2019-10-31 15:32:37 -0400},
month = {October},
school = {McMaster University},
title = {Towards Automating Code Reviews},
year = {2019},
bdsk-file-1 = {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}}
@book{Sommerville2010,
address = {USA},
author = {Sommerville, Ian},
date-added = {2019-10-30 15:13:54 -0400},
date-modified = {2019-10-30 15:14:03 -0400},
edition = {9th},
isbn = {0137035152, 9780137035151},
publisher = {Addison-Wesley Publishing Company},
title = {Software Engineering},
year = {2010},
bdsk-url-1 = {http://iips.icci.edu.iq/images/exam/Software-Engineering-9th-Edition-by-Ian-Sommerville.pdf}}
@inproceedings{DiskinEtAl2018,
author = {Zinovy Diskin and Tom Maibaum and Alan Wassyng and Stephen Wynn-Williams and Mark Lawford},
booktitle = {Proceedings of the 21st International Conference on Models Driven Engineering Languages and Systems, MODELS 2018, Copenhagen, Denmark, October 14-19, 2018},
date = {2018-11-21},
date-added = {2019-10-25 12:46:05 -0400},
date-modified = {2019-10-25 12:46:25 -0400},
keywords = {assurance case, block diagram, decomposition, model transformation, safety assurance, substitution},
pages = {426 - 436},
publisher = {ACM},
pubstate = {published},
title = {Assurance via model transformations and their hierarchical refinement},
tppubtype = {inproceedings},
url = {https://www.mcscert.ca/wp-content/uploads/2018/12/p426-diskin-1.pdf},
year = {2018},
bdsk-url-1 = {https://www.mcscert.ca/wp-content/uploads/2018/12/p426-diskin-1.pdf}}
@misc{InranAndKosar2019,
archiveprefix = {arXiv},
author = {Asif Imran and Tevfik Kosar},
date-added = {2019-10-17 08:57:52 -0400},
date-modified = {2019-10-17 08:58:05 -0400},
eprint = {1910.06109},
primaryclass = {cs.SE},
title = {Software Sustainability: A Systematic Literature Review and Comprehensive Analysis},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1910.06109}}
@misc{RusanovskyEtAl2019,
archiveprefix = {arXiv},
author = {Matan Rusanovsky and Re'em Harel and Lee-or Alon and Idan Mosseri and Harel Levin and Gal Oren},
date-added = {2019-10-16 08:33:53 -0400},
date-modified = {2019-10-16 08:34:10 -0400},
eprint = {1910.06415},
primaryclass = {cs.DC},
title = {BACKUS: Comprehensive High-Performance Research Software Engineering Approach for Simulations in Supercomputing Systems},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1910.06415}}
@article{Krueger1992,
acmid = {130856},
address = {New York, NY, USA},
author = {Krueger, Charles W.},
date-added = {2019-10-09 09:40:55 -0400},
date-modified = {2019-10-09 09:41:03 -0400},
doi = {10.1145/130844.130856},
issn = {0360-0300},
issue_date = {June 1992},
journal = {ACM Comput. Surv.},
keywords = {abstraction, cognitive distance, software reuse},
month = jun,
number = {2},
numpages = {53},
pages = {131--183},
publisher = {ACM},
title = {Software Reuse},
url = {http://doi.acm.org/10.1145/130844.130856},
volume = {24},
year = {1992},
bdsk-url-1 = {http://doi.acm.org/10.1145/130844.130856},
bdsk-url-2 = {https://doi.org/10.1145/130844.130856},
bdsk-url-3 = {http://www.ebizstrategy.org/research/resources/610_Sp02/IS_Const2/ab/Research/Krueger%20-%20Software%20Reuse.pdf}}
@article{OberEtAl2018,
abstract = {This paper reports on a four-year project that aims to raise the abstraction level through the use of model-driven engineering (MDE) techniques in the development of scientific applications relying on high-performance computing. The development and maintenance of high-performance scientific computing software is reputedly a complex task. This complexity results from the frequent evolutions of supercomputers and the tight coupling between software and hardware aspects. Moreover, current parallel programming approaches result in a mixing of concerns within the source code. Our approach relies on the use of MDE and consists in defining domain-specific modeling languages targeting various domain experts involved in the development of HPC applications, allowing each of them to handle their dedicated model in a both user-friendly and hardware-independent way. The different concerns are separated thanks to the use of several models as well as several modeling viewpoints on these models. Depending on the targeted execution platforms, these abstract models are translated into executable implementations by means of model transformations. To make all of these effective, we have developed a tool chain that is also presented in this paper. The approach is assessed through a multi-dimensional validation that focuses on its applicability, its expressiveness and its efficiency. To capitalize on the gained experience, we analyze some lessons learned during this project.},
author = {Ober, Ileana and Palyart, Marc and Bruel, Jean-Michel and Lugato, David},
date-added = {2019-10-08 11:18:57 -0400},
date-modified = {2019-10-08 11:19:07 -0400},
day = {01},
doi = {10.1007/s10270-016-0518-0},
issn = {1619-1374},
journal = {Software {\&} Systems Modeling},
month = {Feb},
number = {1},
pages = {319--342},
title = {On the use of models for high-performance scientific computing applications: an experience report},
url = {https://doi.org/10.1007/s10270-016-0518-0},
volume = {17},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1007/s10270-016-0518-0},
bdsk-url-2 = {https://link.springer.com/content/pdf/10.1007%2Fs10270-016-0518-0.pdf}}
@misc{VerdugoAndBadia2019,
archiveprefix = {arXiv},
author = {Francesc Verdugo and Santiago Badia},
date-added = {2019-10-04 08:24:58 -0400},
date-modified = {2019-10-04 08:25:10 -0400},
eprint = {1910.01412},
primaryclass = {cs.MS},
title = {A user-guide to Gridap -- grid-based approximation of partial differential equations in Julia},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1910.01412}}
@inproceedings{Cunningham1992,
acmid = {157715},
address = {New York, NY, USA},
author = {Cunningham, Ward},
booktitle = {Addendum to the Proceedings on Object-oriented Programming Systems, Languages, and Applications (Addendum)},
date-added = {2019-10-03 09:39:16 -0400},
date-modified = {2019-10-03 09:39:27 -0400},
doi = {10.1145/157709.157715},
isbn = {0-89791-610-7},
location = {Vancouver, British Columbia, Canada},
numpages = {2},
pages = {29--30},
publisher = {ACM},
series = {OOPSLA '92},
title = {The WyCash Portfolio Management System},
url = {http://doi.acm.org/10.1145/157709.157715},
year = {1992},
bdsk-url-1 = {http://doi.acm.org/10.1145/157709.157715},
bdsk-url-2 = {https://doi.org/10.1145/157709.157715}}
@misc{MGPG2005,
author = {{Math Gateway Partners Group}},
date-added = {2019-10-02 13:02:49 -0400},
date-modified = {2019-10-02 13:02:49 -0400},
howpublished = {\url{https://www.maa.org/book/export/html/115342}},
month = {April},
title = {Core Subject Taxonomy for Mathematical Sciences Education},
year = {2005},
bdsk-url-1 = {https://www.maa.org/book/export/html/115342}}
@misc{VentersEtAl2014,
abstract = {The development of sustainable software has been identified as one of the key challenges in the field of computational science and engineering. However, there is currently no agreed definition of the concept. Current definitions range from a composite, non-functional requirement to simply an emergent property. This lack of clarity leads to confusion, and potentially to ineffective and inefficient efforts to develop sustainable software systems. The aim of this paper is to explore the emerging definitions of software sustainability from the field of software engineering in order to contribute to the question, what is software sustainability? The preliminary analysis suggests that the concept of software sustainability is complex and multifaceted with any consensus towards a shared definition within the field of software engineering yet to be achieved.},
author = {CC Venters and C Jay and LMS Lau and MK Griffiths and V Holmes and RR Ward and J Austin and CE Dibsdale and J Xu},
booktitle = {RE4SuSy: Third International Workshop on Requirements Engineering for Sustainable Systems},
date-added = {2019-10-01 12:06:02 -0400},
date-modified = {2019-10-01 12:06:12 -0400},
editor = {B Penzenstadler and M Mahaux and C Salinesi},
journal = {CEUR Workshop Proceedings},
keywords = {Non-functional requirements; Quality attributes; Software engineering; Software sustainability; Sustainability},
note = {(c) 2014, The Author(s). This is an author produced version of a paper published in CEUR Workshop Proceedings. Uploaded in accordance with the publisher's self-archiving policy},
pages = {7 -- 12},
publisher = {CEUR},
title = {Software Sustainability: The Modern Tower of Babel},
url = {http://eprints.whiterose.ac.uk/84941/},
volume = {1216},
year = {2014},
bdsk-url-1 = {http://ceur-ws.org/Vol-1216/paper2.pdf},
bdsk-url-2 = {http://eprints.whiterose.ac.uk/84941/}}
@inproceedings{Parnas1994a,
abstract = {Programs, like people, get old. We can't prevent aging, but we can understand its causes, take steps to limits its effects, temporarily reverse some of the damage it has caused, and prepare for the day when the software is no longer viable. A sign that the software engineering profession has matured will be that we lose our preoccupation with the first release and focus on the long-term health of our products. Researchers and practitioners must change their perception of the problems of software development. Only then will software engineering deserve to be called "engineering".<>},
author = {D. L. {Parnas}},
booktitle = {Proceedings of 16th International Conference on Software Engineering},
date-added = {2019-10-01 11:36:21 -0400},
date-modified = {2019-10-01 11:36:57 -0400},
doi = {10.1109/ICSE.1994.296790},
keywords = {software engineering;professional aspects;software aging;software viability;software engineering profession;professional maturity;product release;long term product health;software development problems;Aging;Humans;Engineering profession;Mathematics;Machinery;Impedance;Product design;Programming profession;Command languages;Embedded software},
month = {May},
pages = {279-287},
title = {Software aging},
year = {1994},
bdsk-url-1 = {https://doi.org/10.1109/ICSE.1994.296790},
bdsk-url-2 = {https://www.cs.drexel.edu/~yfcai/CS451/RequiredReadings/SoftwareAging.pdf}}
@inproceedings{PenzenstadlerAndHenning2013,
acmid = {2451609},
address = {New York, NY, USA},
annote = {``Technical sustainability From a point of view of (software) systems engineering, there is another dimension that has to be considered. Technical sustainability has the central objective of long-time
usage of systems and their adequate evolution with changing surrounding conditions and respective requirements.For SE: How can
software be created so that it can easily adapt to future change?''},
author = {Penzenstadler, Birgit and Femmer, Henning},
booktitle = {Proceedings of the 2013 Workshop on Green in/by Software Engineering},
date-added = {2019-10-01 11:23:50 -0400},
date-modified = {2019-10-01 11:26:22 -0400},
doi = {10.1145/2451605.2451609},
isbn = {978-1-4503-1866-2},
keywords = {case study, definition, generic reference model, requirements, sustainability},
location = {Fukuoka, Japan},
numpages = {6},
pages = {3--8},
publisher = {ACM},
series = {GIBSE '13},
title = {A Generic Model for Sustainability with Process- and Product-specific Instances},
url = {http://doi.acm.org/10.1145/2451605.2451609},
year = {2013},
bdsk-url-1 = {https://www.researchgate.net/publication/255949688_A_Generic_Model_for_Sustainability_with_Process-_and_Product-specific_Instances},
bdsk-url-2 = {http://doi.acm.org/10.1145/2451605.2451609},
bdsk-url-3 = {https://doi.org/10.1145/2451605.2451609}}
@mastersthesis{Hygerth2016,
abstract = {is study has focused on the technical sustainability dimension of sustainable soware engineering. Sustainabilitywithin soware engineering is something that has recently started to gain traction, where most of theresearch has focused on the environmental dimension.e purpose of this study was to investigate the technicalsustainability dimension, and contribute by continuing to build upon previous research which has suggestedsustainability as a part of non-functional requirements and as a part of soware quality.is study was conducted with a qualitative approach. is approach used interviews with people withexperience of working in soware development to collect data. e interviews were used to gain in-depthinformation of the dierent aspects in soware development, e.g. development processes.e results, based on the interviews, showed that from a technical sustainability perspective there are issueswith where the focus of the work is in soware development and also problems related to how timemanagementis used.e results also showed that there was some lacking in understanding the benets and tradeos ofdecisions made in the project, for example regarding the soware design, which can result in unnecessarycomplexity is acquired.e study found that the culture within soware development projects and companies needs to be changedtowards a culture which promotes the development of high quality soware. Because non-functional requirementsand soware quality are components of technical sustainability, therefore is the technical sustainabilityhigher if the quality is high. It was further found that this culture would be possible if changes were made tothe way prioritisations are made, and the way testing is performed should be extended. Finally it was foundthat the understanding of the benets and tradeos of decisions and ideas needs to be increased and extendedcollectively.e study concluded that the technical sustainability dimension can be achieved through these changes andthat the problem and solution therefore are not small and local but rather a big and complex issue where thesolution spans several solutions that encompasses dierent aspects and perspectives. },
annote = {"The technical sustainability dimension considers the long-term usage of systems and
their capacity to evolve with changing conditions and requirements [78]." - it looks like they got the reference wrong, it should probably be reference 76!},
author = {Hygerth, Henrik},
date-added = {2019-10-01 11:10:52 -0400},
date-modified = {2019-10-01 11:12:04 -0400},
institution = {KTH, Sustainability and Industrial Dynamics},
keywords = {Sustainable software engineering, technical sustainability, sustainability, software maintainability, software development process, software quality, software design, non-functional requirements},
pages = {65},
school = {KTH, Sustainability and Industrial Dynamics},
title = {Sustainable Software Engineering : An Investigation Into the Technical Sustainability Dimension},
year = {2016},
bdsk-url-1 = {http://www.diva-portal.org/smash/record.jsf?pid=diva2%3A946937&dswid=-6115},
bdsk-url-2 = {http://www.diva-portal.org/smash/get/diva2:946937/FULLTEXT01.pdf}}
@inproceedings{WolframEtAl2017,
annote = {``Sustainability is commonly
divided into different dimensions, depending on the type of
effects a product or process has. Normally considered are the
environmental, economic and social dimensions of sustainability. Apart from this, we also add technical sustainability as
a fourth dimension to this list {\ldots}''},
author = {Nina Wolfram and Patricia Lago and Francesco Osborne},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/conf/ifip6-3/WolframLO17},
booktitle = {2017 Sustainable Internet and {ICT} for Sustainability, SustainIT 2017, Funchal, Portugal, December 6-7, 2017},
date-added = {2019-10-01 10:44:46 -0400},
date-modified = {2019-10-01 12:11:09 -0400},
doi = {10.23919/SustainIT.2017.8379798},
pages = {55--61},
timestamp = {Wed, 25 Sep 2019 18:20:40 +0200},
title = {Sustainability in software engineering},
url = {https://doi.org/10.23919/SustainIT.2017.8379798},
year = {2017},
bdsk-url-1 = {http://dl.ifip.org/db/conf/ifip6-3/sustainit2017/08_P08_S21_SustainIT2017.pdf},
bdsk-url-2 = {https://doi.org/10.23919/SustainIT.2017.8379798}}
@book{Brundtland1987,
abstract = {Most of today's decision makers will be dead before the planet suffers the full consequences of acid rain, global warning, ozone depletion, widespread desertification, and species loss. Most of today's young voters, however, will be alive. In this, perhaps the most important document of the decade on the future of the world, the urgency of changing certain policy decisions, some of which threaten the very survival of the human race, is made abundantly clear. The World Commission on Environment and Development, headed by Gro Harlem Brundtland, Prime Minister of Norway, was set up as an independent body in 1983 by the United Nations. Its brief was to re-examine the critical environment, to develop proposals to solve them, and to ensure that human progress will be sustained through development without bankrupting the resources of future generations. In Our Common Future, the Commission serves notice that the time has come for a marriage of economy and ecology, so that governments and their people can take responsibility not just for environmental damage, but for the policies that cause the damage. It is not too late to change these policies; but, it warns, we must act now.},
annote = {Their definition characterizes sustainability as
``the ability to meet the needs of the present without compromising the ability of
future generations to meet their own needs''},
author = {G. H. Brundtland},
date-added = {2019-10-01 10:30:19 -0400},
date-modified = {2019-10-01 11:43:26 -0400},
editor = {World Commission on Environment and Development},
publisher = {Oxford University Press},
title = {Our Common Future},
url = {https://EconPapers.repec.org/RePEc:oxp:obooks:9780192820808},
year = {1987},
bdsk-url-1 = {https://EconPapers.repec.org/RePEc:oxp:obooks:9780192820808}}
@misc{IISD2019,
annote = {"Sustainable development is development that meets the needs of the present without compromising the ability of future generations to meet their own needs." - from Brundtland report},
author = {IISD {International Institute for Sustainable Development}},
date-added = {2019-10-01 10:20:39 -0400},
date-modified = {2019-10-01 10:26:44 -0400},
howpublished = {\url{https://www.iisd.org/topic/sustainable-development}},
month = {October},
title = {Sustainable Development},
year = {2019},
bdsk-url-1 = {https://www.iisd.org/topic/sustainable-development}}
@misc{Heine2017,
annote = {``The concept of sustainability is based on three pillars: the ecological, the economical and the social. This means that for a software to be sustainable, we must take all of its effects -- direct and indirect -- on the environment, the economy and the society into account. In addition, the entire life cycle of a software has to be considered: from planning and conception to programming, distribution, installation, usage and disposal. ``
- sustainable in this case has a ``green'' focus},
author = {Robert Heine},
date-added = {2019-10-01 10:02:08 -0400},
date-modified = {2019-10-01 10:05:12 -0400},
howpublished = {\url{https://www.energypedia-consult.com/en/blog/robert-heine/what-sustainable-software}},
month = {July},
title = {What is Sustainable Software?},
year = {2017},
bdsk-url-1 = {https://www.energypedia-consult.com/en/blog/robert-heine/what-sustainable-software}}
@book{Tate2005,
annote = {``Sustainable development is a mindset (principles) and an accompanying set of practices that enable a team to achieve and maintain an optimal development pace indefinitely. ``
},
author = {Tate, Kevin},
date-added = {2019-10-01 10:00:41 -0400},
date-modified = {2019-10-01 10:01:19 -0400},
isbn = {0321286081},
publisher = {Addison-Wesley Professional},
title = {Sustainable Software Development: An Agile Perspective},
year = {2005},
bdsk-url-1 = {http://catalogue.pearsoned.co.uk/samplechapter/0321286081.pdf}}
@misc{Katz2016,
annote = {Definition of software sustainability by Katz: ``The capacity of the software to endure. In other words, sustainability means that the software will continue to be available in the future, on new platforms, meeting new needs.''
Definition by Neil Chue Hong:
``Sustainable software is software which is:
-- Easy to evolve and maintain
-- Fulfils its intent over time
-- Survives uncertainty
-- Supports relevant concerns (Political, Economic, Social, Technical,
Legal, Environmental)''},
author = {Daniel Katz},
date-added = {2019-10-01 08:56:33 -0400},
date-modified = {2019-10-01 09:21:00 -0400},
howpublished = {\url{https://danielskatzblog.wordpress.com/2016/09/13/defining-software-sustainability/}},
month = {September},
title = {Defining Software Sustainability},
year = {2016},
bdsk-url-1 = {https://danielskatzblog.wordpress.com/2016/09/13/defining-software-sustainability/}}
@inproceedings{Dubey2019,
author = {Anshu Dubey},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:10 -0400},
date-modified = {2019-09-30 16:22:24 -0400},
title = {Software Engineering Research for Exploratory Research Software},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/DubeyAnshu_whitepaper.pdf}}
@inproceedings{Dyadechko2019,
author = {Vadim Dyadechko},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:09 -0400},
date-modified = {2019-09-30 16:23:01 -0400},
title = {Random Thoughts on Software Sustainability},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/vdyadec-CS3S19.pdf}}
@inproceedings{GesingAndBenham2019,
author = {Sandra Gesing and David R. Benham},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:08 -0400},
date-modified = {2019-09-30 16:23:51 -0400},
title = {OneSciencePlace: Sustainability Measures for a Science Gateway Framework},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/SustainabilityOneSciencePlace.pdf}}
@inproceedings{Heroux2019,
author = {Michael Heroux},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:07 -0400},
date-modified = {2019-09-30 16:25:11 -0400},
title = {Research Software Science: A New Approach to Understanding and Improving How We Develop and Use Software for Research},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/HerouxResearchSoftwareScientist.pdf}}
@inproceedings{Jacob2019,
author = {Robert Jacob},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:07 -0400},
date-modified = {2019-09-30 16:26:20 -0400},
title = {Impediments to regular testing of scientific software},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/JacobTestingCW3S19.pdf}}
@inproceedings{Katz2019,
author = {Daniel Katz},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:06 -0400},
date-modified = {2019-09-30 16:27:43 -0400},
title = {Data-driven software sustainability},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/KatzDanielS_CW3S19_white_paper.pdf}}
@inproceedings{KnepperAndStory,
author = {Sarah Knepper and Shane Story},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:05 -0400},
date-modified = {2019-09-30 16:28:28 -0400},
title = {Software Sustainability Considerations for a Performance Library},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/Knepper_Intel_MKL_Software_Sustainability.pdf}}
@inproceedings{Li2019,
author = {X. Sherry Li},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:05 -0400},
date-modified = {2019-09-30 16:30:30 -0400},
title = {Making Correctness Testing and Performance Autotuning Integral Parts of Software},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/LiSherry_CWS319_whitepaper.pdf}}
@inproceedings{CurfmanEtAl2019,
author = {Lois Curfman McInnes and David E. Bernholdt and Rinku Gupta and Michael Heroux and Mark C. Miller},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:04 -0400},
date-modified = {2019-09-30 16:31:33 -0400},
title = {2014 DOE Report on Software Productivity for Extreme-Scale Science: Perspectives on Recommendations, Progress, and Urgent Needs},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/swp4xs-perspectives-2019.pdf}}
@inproceedings{Milewicz2019,
author = {Reed Milewicz},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:03 -0400},
date-modified = {2019-09-30 16:32:23 -0400},
title = {Wickedness, Trust, and Sustainability},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/MilewiczWickednessTrustSustainability.pdf}}
@inproceedings{Miller2019,
author = {Mark C. Miller},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:03 -0400},
date-modified = {2019-09-30 16:33:03 -0400},
title = {Continuous Technology Refreshment: a Sustainable Software Best Practice},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/markcmiller86_ctr.html}}
@inproceedings{Quillen2019,
author = {Pat Quillen},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:02 -0400},
date-modified = {2019-09-30 16:33:37 -0400},
title = {Sustainable Software Practices in Developing Matlab},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/quillenCW3S19.pdf}}
@inproceedings{Watson2019,
author = {Gregory R. Watson},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:01 -0400},
date-modified = {2019-09-30 16:34:17 -0400},
title = {A Scientific Approach to Developing Scientific Software},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/CW3S19_watson.pdf}}
@inproceedings{Willenbring2019,
author = {James M. Willenbring},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:00 -0400},
date-modified = {2019-09-30 16:34:46 -0400},
title = {The Layers of CSE Software Sustainability},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/CSEswSustainabilityLayers.pdf}}
@inproceedings{WindusAndCrawford2019,
author = {Theresa L. Windus and T. Daniel Crawford},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:13:00 -0400},
date-modified = {2019-09-30 16:35:25 -0400},
title = {Software Sustainability in the Molecular Sciences},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/WindusSustainabilityInMolecularSciences.pdf}}
@inproceedings{Carver2019,
annote = {``{\ldots} a scientific developer needs to be convinced of the value of any SE practice before he or she will allocate any precious time to employing that practice.''},
author = {Jeffrey Carver},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:12:57 -0400},
date-modified = {2019-09-30 16:50:25 -0400},
title = {Software Engineering for Sustainable Scientific Software},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/Carver-SoftwareEngineering.pdf}}
@inproceedings{Cowan2019,
author = {Benjamin Cowan},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:12:56 -0400},
date-modified = {2019-09-30 16:21:53 -0400},
title = {The need for software deployability: Broadening community tools for industry use},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/CowanBenjamin_Deployability.pdf}}
@inproceedings{ChueHong2019b,
author = {Neil Chue Hong},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:12:55 -0400},
date-modified = {2019-09-30 16:18:53 -0400},
title = {Software undead: a bestiary of software that somehow manages to stay alive},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/ChueHongSoftwareUndead.pdf}}
@inproceedings{ChueHong2019,
author = {Neil Chue Hong},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:12:53 -0400},
date-modified = {2019-09-30 16:18:04 -0400},
title = {Making open source research software visible: new models for sustaining research software development},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/ChueHongMakingOpenSourceResearchSoftwareVisible.pdf}}
@inproceedings{CohoonAndHowison2019,
author = {Johanna Cohoon and James Howison},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:12:29 -0400},
date-modified = {2019-10-01 13:22:47 -0400},
title = {Routes to Sustainable Software in Science: Transitioning from Peer Production},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/CohoonHandoutAOM.pdf}}
@inproceedings{Bernholdt2019,
author = {David Bernholdt},
booktitle = {2019 Collegeville Workshop on Sustainable Scientific Software},
date-added = {2019-09-30 16:10:50 -0400},
date-modified = {2019-09-30 16:12:04 -0400},
title = {Open Sourcing Your Software is Not a Sustainability Strategy -- Until it Is!},
year = {2019},
bdsk-url-1 = {https://collegeville.github.io/CW3S19/WorkshopResources/WhitePapers/bernholdt-open-source-v02.pdf}}
@inproceedings{FrappierEtAl1994,
author = {Marc Frappier and Stan Matwin and Ali Mili},
date-modified = {2019-09-29 23:05:07 -0400},
title = {Software Metrics for Predicting Maintainability},
url = {http://www.dmi.usherb.ca/~frappier/Papers/tm2.pdf},
year = {1994},
bdsk-url-1 = {http://www.dmi.usherb.ca/~frappier/Papers/tm2.pdf}}
@misc{TashtoushEtAl2014,
archiveprefix = {arXiv},
author = {Yahya Tashtoush and Mohammed Al-Maolegi and Bassam Arkok},
date-modified = {2019-09-29 23:04:39 -0400},
eprint = {1408.4523},
primaryclass = {cs.SE},
title = {The Correlation among Software Complexity Metrics with Case Study},
url = {https://arxiv.org/pdf/1408.4523.pdf},
year = {2014},
bdsk-url-1 = {https://arxiv.org/pdf/1408.4523.pdf}}
@misc{AlawadEtAl2019,
archiveprefix = {arXiv},
author = {Duaa Alawad and Manisha Panta and Minhaz Zibran and Md Rakibul Islam},
date-modified = {2019-09-29 23:03:52 -0400},
eprint = {1909.01760},
primaryclass = {cs.SE},
title = {An Empirical Study of the Relationships between Code Readability and Software Complexity},
url = {https://arxiv.org/ftp/arxiv/papers/1909/1909.01760.pdf},
year = {2019},
bdsk-url-1 = {https://arxiv.org/ftp/arxiv/papers/1909/1909.01760.pdf}}
@inproceedings{AlMumunEtAl2017,
author = {Mamun, Md Abdullah and Berger, Christian and Hansson, J{\"o}rgen},
date-modified = {2019-09-29 23:02:15 -0400},
doi = {10.1145/3143434.3143445},
month = {10},
pages = {255--266},
title = {Correlations of software code metrics: an empirical study},
url = {https://www.researchgate.net/publication/321091593_Correlations_of_software_code_metrics_an_empirical_study},
year = {2017},
bdsk-url-1 = {https://www.researchgate.net/publication/321091593_Correlations_of_software_code_metrics_an_empirical_study},
bdsk-url-2 = {https://doi.org/10.1145/3143434.3143445}}
@article{ShollerEtAl2019,
annote = {Rule 4: Keep knowledge up to date and findable},
author = {Sholler, Dan AND Steinmacher, Igor AND Ford, Denae AND Averick, Mara AND Hoye, Mike AND Wilson, Greg},
date-added = {2019-09-17 08:12:49 -0400},
date-modified = {2019-09-17 08:13:30 -0400},
doi = {10.1371/journal.pcbi.1007296},
journal = {PLOS Computational Biology},
month = {09},
number = {9},
pages = {1-10},
publisher = {Public Library of Science},
title = {Ten simple rules for helping newcomers become contributors to open projects},
url = {https://doi.org/10.1371/journal.pcbi.1007296},
volume = {15},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1371/journal.pcbi.1007296}}
@misc{FehrEtAl2019,
archiveprefix = {arXiv},
author = {J{\"o}rg Fehr and Christian Himpe and Stephan Rave and Jens Saak},
date-added = {2019-09-24 10:18:15 -0400},
date-modified = {2019-09-24 10:18:27 -0400},
eprint = {1909.09469},
primaryclass = {cs.GL},
title = {Sustainable Research Software Hand-Over},
year = {2019},
bdsk-file-1 = {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},
bdsk-url-1 = {https://arxiv.org/abs/1909.09469#}}
@book{Anton1987,
author = {Anton, Howard},
date-added = {2019-09-23 12:32:51 -0400},
date-modified = {2019-09-23 12:34:12 -0400},
edition = {Fifth},
keywords = {linear.algebra matrix textbook},
publisher = {Wiley},
title = {Elementary Linear Algebra},
year = 1987}
@article{MilewiczAndRaybourn2018,
abstract = {Large-scale collaborative scientific software projects require more knowledge than any one person typically possesses. This makes coordination and communication of knowledge and expertise a key factor in creating and safeguarding software quality, without which we cannot have sustainable software. However, as researchers attempt to scale up the production of software, they are confronted by problems of awareness and understanding. This presents an opportunity to develop better practices and tools that directly address these challenges. To that end, we conducted a case study of developers of the Trilinos project. We surveyed the software development challenges addressed and show how those problems are connected with what they know and how they communicate. Based on these data, we provide a series of practicable recommendations, and outline a path forward for future research.},
annote = {- cites Drasil (Dan's position paper) and Thulasi's work (5 redevelopment projects)
- seems like MandR assumed the potential problems - should have provided an opportunity for new problems to emerge from user feedback
- they implied that Drasil cannot capture tacit knowledge that cannot be codefied, likely because they misunderstood Drasil
- if Drasil is successful, much of the knowledge they are referring to only has to be entered once, the communication is through documentation, mistakes cannot be repeated in the same way as the anecdote in the paper because the code is generated},
author = {Reed Milewicz and Elaine M. Raybourn},
date-added = {2019-09-10 15:12:48 -0400},
date-modified = {2019-09-10 15:12:48 -0400},
journal = {ArXiv e-prints},
month = {September},
title = {Talk to Me: A Case Study on Coordinating Expertise in Large-Scale Scientific Software Projects},
year = {2018},
bdsk-file-1 = {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}}
@misc{PHA2009,
author = {PHA, Public Health Agency of Canada},
date-added = {2019-08-23 10:24:18 -0400},
date-modified = {2019-08-23 10:24:18 -0400},
howpublished = {\href{https://www.canada.ca/content/dam/phac-aspc/migration/phac-aspc/publicat/2009/cvd-avc/pdf/CVD_report-eng.pdf}{https://www.canada.ca/content/dam/phac-aspc/migration/phac-aspc/publicat/2009/cvd-avc/pdf/CVD\_report-eng.pdf}},
title = {Tracking heart disease and stroke in {C}anada},
year = {2009}}
@misc{AmericanHeartAssociation2017,
author = {AHA, American Heart Association},
date-added = {2019-08-23 09:37:40 -0400},
date-modified = {2019-08-23 10:09:48 -0400},
howpublished = {\href{https://healthmetrics.heart.org/wp-content/uploads/2017/06/Heart-Disease-and-Stroke-Statistics-2017-ucm_491265.pdf}{https://healthmetrics.heart.org/wp-content/uploads/2017/06/Heart-Disease-and-Stroke-Statistics-2017-ucm\_491265.pdf}},
title = {Heart Disease and Stroke Statistics -- at-a-glace},
year = {2017}}
@article{Marsden2013,
author = {Marsden, A. L.},
date-added = {2019-08-21 23:34:27 -0400},
date-modified = {2019-08-21 23:38:15 -0400},
journal = {Physics of Fluids},
month = {September},
number = {101303},
title = {Simulation based planning of surgical interventions in pediatric cardiology},
volume = {25},
year = {2013}}
@article{CasasEtAl2017,
author = {Casas, B. Et Al},
date-added = {2019-08-21 23:32:41 -0400},
date-modified = {2019-08-21 23:33:54 -0400},
journal = {Sci. Rep.},
number = {6214},
title = {Bridging the gap between measurements and modelling: a cardiovascular functional avatar},
volume = {7},
year = {2017}}
@article{DiCarliEtAl2016,
author = {Di Carli, M. F. and Geva, T. and Davidoff, R.},
date-added = {2019-08-21 23:30:07 -0400},
date-modified = {2019-08-21 23:31:46 -0400},
journal = {Circulatiom},
pages = {2640--2661},
title = {The Future of Cardiovascular Imaging},
volume = {133},
year = {2016}}
@inproceedings{Voelter2018,
annote = {- observes that models can be descriptive or prescriptive {it is interesting that the prescriptive models in Drasil are for scientific models, which are descriptive - we are prescribing the software that will be used to experiment with a descriptive model of some physical phenomenon}
- Model Driven: The ``driven'' expresses that the to-be-developed system is automatically constructed3 from its prescriptive model. In other words, from the perspective of a user, only the model has to be adapted for the system to change. This can be achieved through (multi-step) transformation/generation/compilation or through interpretation.
- Model-driven refers to a way of developing a software system S where users change a set of prescriptive models Mi representing concerns Ci at an appropriate abstraction level to affect the behavior of S. An automatic process constructs a full implementation of S that relies on a platform P.
- in MPS they define numbers types with a range and precision {this would be useful for Drasil}
},
author = {Markus Voelter},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/conf/isola/Voelter18},
booktitle = {Leveraging Applications of Formal Methods, Verification and Validation. Modeling - 8th International Symposium, ISoLA 2018, Limassol, Cyprus, November 5-9, 2018, Proceedings, Part {I}},
crossref = {DBLP:conf/isola/2018-1},
date-added = {2019-08-13 11:20:34 -0400},
date-modified = {2019-08-13 11:37:18 -0400},
doi = {10.1007/978-3-030-03418-4\_19},
pages = {309--339},
timestamp = {Tue, 14 May 2019 10:00:41 +0200},
title = {Fusing Modeling and Programming into Language-Oriented Programming - Our Experiences with {MPS}},
url = {https://doi.org/10.1007/978-3-030-03418-4\_19},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1007/978-3-030-03418-4%5C_19}}
@article{RunesonAndHost2009,
abstract = {Case study is a suitable research methodology for software engineering research since it studies contemporary phenomena in its natural context. However, the understanding of what constitutes a case study varies, and hence the quality of the resulting studies. This paper aims at providing an introduction to case study methodology and guidelines for researchers conducting case studies and readers studying reports of such studies. The content is based on the authors' own experience from conducting and reading case studies. The terminology and guidelines are compiled from different methodology handbooks in other research domains, in particular social science and information systems, and adapted to the needs in software engineering. We present recommended practices for software engineering case studies as well as empirically derived and evaluated checklists for researchers and readers of case study research.},
annote = {- Case studies do not generate the same results on e.g. causal relationships as controlled experiments do, but they provide deeper understanding of the phenomena under study.
- case study is an empirical method aimed at investigating contemporary phenomena in their context. - uses multiple sources of evidence, boundary between the phenomenon and its context may be unclear, information gathering from few entities (people, groups, organizations), lack of experimental control.
- a case study may contain elements of other research methods, e.g. a survey may be conducted within a case study, literature search often precede a case study and archival analyses may be a part of its data collection. Ethnographic methods, like interviews and observations are mostly used for data collection in case studies.
- Action research, with its purpose to ``influence or change some aspect of whatever is the focus of the research'' (Robson 2002), is closely related to case study. More strictly, a case study is purely observational while action research is focused on and involved in the change process. {Research using Drasil seems to be Action research} - when studying the effects of a change, e.g. in pre- and post-event studies, we classify the methodology as case study.
We distinguish between four types of purposes for research based on Robson's (2002) classification:
& Exploratory---finding out what is happening, seeking new insights and generating ideas and hypotheses for new research.
& Descriptive---portraying a situation or phenomenon.
& Explanatory---seeking an explanation of a situation or a problem, mostly but not necessary in the form of a causal relationship.
& Improving---trying to improve a certain aspect of the studied phenomenon. - case studies in software engineering often take an improvement approach, similar to action research
{Research on using Drasil will be of the Exploratory and Improving classifications}
- Case studies are by definition conducted in real world settings, and thus have a high degree of realism, mostly at the expense of the level of control.
Case studies tend mostly to be based on qualitative data, as these provide a richer and deeper description. However, a combination of qualitative and quantitative data often provides better understanding of the studied phenomenon (Seaman 1999), i.e. what is sometimes called ``mixed methods'' (Robson 2002).
The research process may be characterized as fixed or flexible according to Anastas and MacDonald (1994) and Robson (2002). In a fixed design process, all parameters are defined at the launch of the study, while in a flexible design process key parameters of the study may be changed during the course of the study. Case studies are typically flexible design studies, while experiments and surveys are fixed design studies.
Four different types of triangulation may be applied (Stake 1995):
& Data (source) triangulation---using more than one data source or collecting the same data at different occasions.
& Observer triangulation---using more than one observer in the study.
& Methodological triangulation---combining different types of data collection methods,
e.g. qualitative and quantitative methods.
& Theory triangulation---using alternative theories or viewpoints.
{For Drasil NSERC - collect data from different sources, use more than one observer? combine different types of data collection methods, theory triangulation - Drasil versus Epsilon}
Perry et al. define similar criteria for a case study (Perry et al. 2005). It is expected that a case study:
- ``Has research questions set out from the beginning of the study
- Data is collected in a planned and consistent manner
- Inferences are made from the data to answer the research question
- Explores a phenomenon, or produces an explanation, description, or causal analysis of it
- Threats to validity are addressed in a systematic way.''
- In summary, the key characteristics of a case study are that 1) it is of flexible type, coping with the complex and dynamic characteristics of real world phenomena, like software engineering, 2) its conclusions are based on a clear chain of evidence, whether qualitative or quantitative, collected from multiple sources in a planned and consistent manner, and 3) it adds to existing knowledge by being based on previously established theory, if such exist, or by building theory.
When conducting a case study, there are five major process steps to be walked through:
1. Case study design: objectives are defined and the case study is planned.
2. Preparation for data collection: procedures and protocols for data collection are defined.
3. Collecting evidence: execution with data collection on the studied case.
4. Analysis of collected data
5. Reporting
Definitions:
- The overall objective is a statement of what is expected to be achieved in the case study.
- The objective is refined into a set of research questions, which are to be answered through the case study analysis.
- A case may be based on a software engineering theory.
- A research question may be related to a hypothesis
- A case study protocol defines the detailed procedures for collection and analysis of the raw data, sometimes called field procedures.
A plan for a case study should at least contain the following elements (Robson 2002):
& Objective (goal) ---what to achieve?
& The case (context) ---what is studied?
& Theory---frame of reference
& Research questions---what to know?
& Methods---how to collect data?
& Selection strategy---where to seek data?
{There are case study protocol templates available on-line}
},
author = {Runeson, Per and H{\"o}st, Martin},
date-added = {2019-07-25 09:06:04 -0400},
date-modified = {2020-04-08 15:03:55 -0400},
day = {19},
doi = {10.1007/s10664-008-9102-8},
issn = {1573-7616},
journal = {Empirical Software Engineering},
month = {Dec},
number = {2},
pages = {131--164},
title = {Guidelines for conducting and reporting case study research in software engineering},
url = {https://doi.org/10.1007/s10664-008-9102-8},
volume = {14},
year = {2009},
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bdsk-url-1 = {https://doi.org/10.1007/s10664-008-9102-8}}
@article{EbertAndJones2009,
abstract = {Due to the complex system context of embedded-software applications, defects can cause life-threatening situations, delays can create huge costs, and insufficient productivity can impact entire economies. Providing better estimates, setting objectives, and identifying critical hot spots in embedded-software engineering requires adequate benchmarking data.},
annote = {- systematic code inspections of embedded software have a defect removal effectiveness of 85\%~\cite{EbertAndJones2009}},
author = {C. {Ebert} and C. {Jones}},
date-added = {2019-07-19 14:54:36 -0400},
date-modified = {2019-07-19 14:55:27 -0400},
doi = {10.1109/MC.2009.118},
issn = {0018-9162},
journal = {Computer},
keywords = {embedded systems;software engineering;embedded-software engineering;benchmarking data;Embedded software;Automotive engineering;Embedded system;Microprocessors;Linux;Kernel;Software measurement;Costs;Size control;Control systems;Embedded software;Software measurement;Software process;Function points;Estimation;Quality control;CMMI},
month = {April},
number = {4},
pages = {42-52},
title = {Embedded Software: Facts, Figures, and Future},
volume = {42},
year = {2009},
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bdsk-url-1 = {https://doi.org/10.1109/MC.2009.118}}
@article{KitchenhamEtAl2002,
acmid = {636197},
address = {Piscataway, NJ, USA},
annote = {1. INTRODUCTION
- paper published in 2002 - at the time the authors observed that the standard for empirical software engineering resarch was poor
- empirical studies are challenging - medical and phychiatric fields still struggle (citations given to show this)
- would expect different guildelines for different purposes (randomized trials, surveys, exploratory stides, etc.)
- guidelines under six basic topic areas:
- experimental context
- experimental design
- conduct of experiment and data collection
- analysis
- presentation of results
- interpretation of results
2. EXPERIMENTAL CONTEXT
- experimental context has three elements: background information about the industrial circumstances in which am empicral study takes place, discuss the research hypotheses, information about related research
- C1: Be sure to specify as much of the industrial context as possible. In particular, clearly define the entities, attributes, and measures that are capturing the contextual information
- two types of empirical studies: observational and formal experiments
2.2.1 Observational Studies
- researchers need to identify the particular factors that might ffect the generality and utlility of the conclusions, such as: the industry in which products are made, nature of software dev organization, skills and experience of software staff, type of software products, software process being used
- important not only to identify appropriate contextual variables, but also to measure them consistently - followed by discussion that even lines of code is defined differently by different researchers
2.2.2 Formal Experiments
- make sure that the experiments are not too much of an oversimplification of reality
- make sure to not ignore other measures - for instance, even if the intervention has no effect on performance, it might have an affect on other benefits (example given of inspection techniques)
- C2: If a specific hypothesis is being tested, state it clearly prior to performing the study and discuss the theory from which it is derived, so that its implications are apparent
- avoid shallow hypothesis - relate hyptheses to theory
- C3: If the research is exploratory, state clearly and, prior to data analysis, what questions the investigation is intended to address and how it will address them.
- define research questions in advance
- C4: Describe resarch that is similar to, or has a bearing on, the current research and how current work relates to it.
3 EXPERIMENTAL DESIGN
- describe the products, resources and processes involved in the study
- D1: Identify the population from which the subjects and objects are drawn.
- D2: Define the process by which the subjects and objects were selected.
- D3: Define the process by which the subjects and objects are assigned to treatments.
- make the assignment unbiased
- if use more complex designs, or non-randomized design, include a statistics expert on the team
- D4: Restrict yourself to simply study design, or consult a statistician
- D6: For formal experiments, perform a pre-experiment or precalcuation to identify or estimate the minimum required sample size,
- D7: Use appropriate levels of blinding
- not always possible, since subjects will know what technique they are using (unlike a patient taking medicine)
- D8: If you cannot avoid evaluationg your own work, then make explicit any vested interests (including your sources of support) and report what you have done to minimize bias.
- D9: Avoid the use of controls unless you are sure the control situation can be unambiguously defined
- usually there is no common default technology - cannot really compare ``with'' a technology to ``without'' the technology, because the ``without'' will be different for different groups, organization, companies, individuals. Can compare two techniques.
- D10: Fully define all treatments (interventions)
- D11: Justify the choice of outcomes measures in terms of their relevance to the objectives of the empirical study
Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, presentation, outliers etc.
},
author = {Kitchenham, Barbara A. and Pfleeger, Shari Lawrence and Pickard, Lesley M. and Jones, Peter W. and Hoaglin, David C. and Emam, Khaled El and Rosenberg, Jarrett},
date-added = {2019-07-18 23:14:57 -0400},
date-modified = {2019-07-22 13:34:27 -0400},
doi = {10.1109/TSE.2002.1027796},
issn = {0098-5589},
issue_date = {August 2002},
journal = {IEEE Trans. Softw. Eng.},
keywords = {empirical software research, research guidelines, statistical mistakes},
month = aug,
number = {8},
numpages = {14},
pages = {721--734},
publisher = {IEEE Press},
title = {Preliminary Guidelines for Empirical Research in Software Engineering},
url = {https://doi.org/10.1109/TSE.2002.1027796},
volume = {28},
year = {2002},
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bdsk-url-1 = {https://doi.org/10.1109/TSE.2002.1027796}}
@misc{Drasil2019,
author = {Drasil Team},
date-added = {2019-06-25 14:02:40 -0400},
date-modified = {2019-06-25 14:06:01 -0400},
howpublished = {\url{https:// github.com/JacquesCarette/Drasil}},
month = {June},
title = {Drasil Software: Generate All The Things (Focusing on Scientific Software)},
year = {2019},
bdsk-url-1 = {https://github.com/JacquesCarette/Drasil}}
@misc{SmithEtAl2019_arXiv,
author = {Spencer Smith and Malavika Srinivasan and Sumanth Shankar},
date-added = {2019-06-20 00:15:58 -0400},
date-modified = {2019-06-20 00:18:58 -0400},
howpublished = {\url{https://arxiv.org/abs/1906.07812}},
month = {June},
title = {Debunking the Myth that Upfront Requirements are Infeasible for Scientific Computing Software Debunking the Myth that Upfront Requirements are Infeasible for Scientific Computing Software},
year = {2019},
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@inproceedings{MilewiczAndRodeghero2019,
author = {Reed Milewicz and Paige Rodeghero},
booktitle = {2019 International Workshop on Software Engineering for Science (held in conjunction with ICSE'19)},
date-added = {2019-06-14 10:31:01 -0400},
date-modified = {2019-06-14 10:32:08 -0400},
pages = {1--2},
title = {Position Paper: Towards Usability as a First-Class Quality of HPC Scientific Software},
year = {2019},
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@inproceedings{BadreddinEtAl2019,
author = {Omar Badreddin and Wahab Hamou-Lhadj and Swapnil Chauhan},
booktitle = {2019 International Workshop on Software Engineering for Science (held in conjunction with ICSE'19)},
date-added = {2019-06-14 10:29:26 -0400},
date-modified = {2019-06-14 10:30:20 -0400},
pages = {1--4},
title = {Susereum: Towards a Reward Structure for Sustainable Scientific Research Software},
year = {2019},
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@inproceedings{DanishEtAl2019,
author = {Matthew Danish and Miltiadis Allamanis and Marc Brockschmidt and Andrew Rice and Dominic Orchard},
booktitle = {2019 International Workshop on Software Engineering for Science (held in conjunction with ICSE'19)},
date-added = {2019-06-14 10:26:55 -0400},
date-modified = {2019-06-14 10:28:37 -0400},
pages = {1--4},
title = {Learning units-of-measure from scientific code},
year = {2019},
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@inproceedings{VogelEtAl2019,
author = {Thomas Vogel and Stephan Druskat and Markus Scheidgen and Claudia Draxl and Lars Grunske},
booktitle = {2019 International Workshop on Software Engineering for Science (held in conjunction with ICSE'19)},
date-added = {2019-06-14 10:24:40 -0400},
date-modified = {2019-06-14 10:25:40 -0400},
number = {1--8},
title = {Challenges for Verifying and Validating Scientific Software in Computational Materials Science},
year = {2019},
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@inproceedings{KempfAndBastian2019,
author = {Dominic Kempf and Peter Bastian},
booktitle = {2019 International Workshop on Software Engineering for Science (held in conjunction with ICSE'19)},
date-added = {2019-06-14 10:22:05 -0400},
date-modified = {2019-06-14 10:23:40 -0400},
pages = {1--8},
title = {An {HPC} Perspective on Generative Programming},
year = {2019},
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@inproceedings{SmithEtAl2019,
author = {Spencer Smith and Malavika Srinivasan and Sumanth Shankar},
booktitle = {2019 International Workshop on Software Engineering for Science (held in conjunction with ICSE'19)},
date-added = {2019-06-03 11:26:43 -0400},
date-modified = {2019-06-03 11:28:18 -0400},
pages = {1--8},
title = {Debunking the Myth that Upfront Requirements are Infeasible for Scientific Computing Software},
year = {2019},
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@article{DioszegiAndHattel2004,
author = {Di{\'o}szegi, Attila and Hattel, Jesper},
date-added = {2019-05-27 17:08:45 -0400},
date-modified = {2019-05-27 17:08:45 -0400},
journal = {International Journal of Cast Metals Research},
number = {5},
pages = {311--318},
publisher = {Taylor \& Francis},
title = {Inverse thermal analysis method to study solidification in cast iron},
volume = {17},
year = {2004},
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@article{BarreraEtAl2019,
abstract = {A wide range of engineering applications uses optimisation techniques as part of their
solution process. The researcher uses specialized software that implements well-known
optimisation techniques to solve his problem. However, when it comes to develop original optimisation techniques that fit a particular problem the researcher has no option
but to implement his own new method from scratch. This leads to large development
times and error prone code that, in general, will not be reused for any other application. In this work, we present a novel methodology that simplifies, fasten and
improves the development process of scientific software. This methodology guide us
on the identification of design patterns. The application of this methodology generates reusable, flexible and high quality scientific software. Furthermore, the produced
software becomes a documented tool to transfer the knowledge on the development
process of scientific software. We apply this methodology for the design of an optimisation framework implementing Newton's type methods which can be used as a fast
prototyping tool of new optimisation techniques based on Newton's type methods.
The abstraction, re-useability and flexibility of the developed framework is measured by means of Martin's metric. The results indicate that the developed software is highly
reusable},
author = {Ricardo Serrato Barrera and Gustavo Rodr{\'\i}guez G{\'o}mez and Julio C{\'e}sar P{\'e}rez Sansalvador and Saul E. Pomares Hern{\'a}ndez and Leticia Flores Pulido and Antonio Mu{\~n}oz},
date-added = {2019-05-22 08:37:01 -0400},
date-modified = {2019-05-22 08:41:38 -0400},
journal = {ArXiv e-prints},
keywords = {Scientific Software Design, Object--Oriented Programming, Design Patterns, Newton's methods, Optimization techniques},
pages = {1--19},
title = {Software System Design based on Patterns for Newton-Type Methods},
volume = {arXiv:1905.04642},
year = {2019},
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@article{Morales-TrujilloEtAl2018,
author = {Miguel Morales Trujillo and Hanna Oktaba and Francisco Hern{\'{a}}ndez Quiroz and Boris Escalante{-}Ram{\'{\i}}rez},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/journals/cai/TrujilloOQE18},
date-added = {2019-05-21 10:54:57 -0400},
date-modified = {2019-05-21 10:55:50 -0400},
journal = {Computing and Informatics},
number = {1},
pages = {109--141},
timestamp = {Tue, 22 May 2018 01:00:00 +0200},
title = {Towards a Formalization of a Framework to Express and Reason about Software Engineering Methods},
url = {http://www.cai.sk/ojs/index.php/cai/article/view/2018\_1\_109},
volume = {37},
year = {2018},
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bdsk-url-1 = {http://www.cai.sk/ojs/index.php/cai/article/view/2018%5C_1%5C_109}}
@inproceedings{DubeyEtAl2019,
author = {Anshu Dubey and Alvaro Coutinho and Roscoe Bartlett and Sandra Gesing and Spencer Smith},
booktitle = {{SIAM-CSE} 2019 Conference on Computational Science and Engineering},
date-added = {2019-05-10 11:25:15 -0400},
date-modified = {2019-05-10 11:36:22 -0400},
title = {Scientific Software: Practices, Concerns, and Solution Strategies (Panel Discussion)},
year = {2019}}
@article{WieseEtAl2019,
abstract = {The scientific software community is eagerly embracing software development practices and tools. However, the lack of Computer Science background, in general, and Software Engineering training, in particular, pose a toll on scientists that need to develop software. Although some of the problems that scientific software developers face when developing scientific software are already known in the literature, we believe that a comprehensive characterization of this complex landscape is still missing. In this paper we build a taxonomy of 2,110 problems (the so called ``pains'') reported by 1,577 scientific software developers. These problems are grouped into three major axes: technical-related, social-related, and scientific-related problems. Our report helps to better understand the needs and challenges of this so far not fully understood community.},
annote = {``Technical-related problems are by far the most common problems that our scientific software developers face. As Figure 1 shows, technical-related problems represent more than 70% of the overall set of problems. The percentages represent the share of respondents that mentioned each pain.''
``According to our respondents, Software Requirements and Management is the software engineering discipline that most hurts scientific developers (they account for 23% of the technical problems reported).''
``Problems related to the evolution of Functional Requirements (e.g., ``The objective changes after having worked on it for months'') was cited by many respondents. Moreover, in spite of its importance, we perceived that writing a good Documentation also poses a major issue. For instance, one respondent mentioned that ``I work with biologists that have little knowledge of programming. Therefore, the software must be easy to use. Write a clear documentation is always a challenge''. Documentation issues are 8.7% of the total problems raised by the respondents, considering the technical, social and scientific-related problems group.''
``Scientific developers also face a hard time when conducting Software Testing and Debugging activities, which represents more than 14% of the total pains presented. This is particularly relevant due to the intrinsic non-deterministic nature of exploring research questions, as one respondent mentioned: ``It's frequently difficult to test scientific software, since you might not even know in advance what the answer should be''.''
``Finally, the Other category groups pains associated with, for instance, the lack of programming background (e.g., ``not having a software development background (i.e.: learning on the fly)''), the algorithms' performance (e.g., ``optimizing code that is not running fast enough (pure engineering issue)''), and the user experience (e.g., ``anticipating user behavior and designing [a good] user interface''). Note that, problems regarding Programming Background and software Performance represent more than 9% of the total problems cited.''},
author = {I. S. {Wiese} and I. {Polato} and G. {Pinto}},
date-added = {2019-05-01 10:26:31 -0400},
date-modified = {2022-02-07 14:45:27 -0500},
doi = {10.1109/MS.2019.2899838},
issn = {0740-7459},
journal = {IEEE Software},
keywords = {Pain;Documentation;Programming;Software packages;Software engineering;Encoding;Scientific Software Developers;Pain points;Survey},
pages = {1-1},
title = {Naming the Pain in Developing Scientific Software},
year = {2019},
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bdsk-url-1 = {https://doi.org/10.1109/MS.2019.2899838}}
@article{deSouzaEtAl2019,
abstract = {Software is now a vital scientific instrument, provid- ing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the human- ities. The software used in research is often home-grown and bespoke: it is constructed for a particular project, and rarely maintained beyond this, leading to rapid decay, and frequent `reinvention of the wheel'. Understanding how to develop sus- tainable research software, such that it is suitable for future reuse, is therefore of interest to both researchers and funders, but how to achieve this remains an open question. Here we report the results of an interview study examining how research software engineers -- the people actively developing software in an academic research environment -- subjectively define soft- ware sustainability. Thematic analysis of the data reveals two interacting dimensions: intrinsic sustainability, which relates to internal qualities of software, such as modularity, encapsulation and testability, and extrinsic sustainability, concerning cultural and organisational factors, including how software is resourced, supported and shared. Research software engineers believe an increased focus on quality and discoverability are key factors in increasing the sustainability of academic research software.},
annote = {- clearly shows the importance of documentation, modularizaiton, readable code, etc.},
archiveprefix = {arXiv},
author = {Mario Rosado de Souza and Robert Haines and Markel Vigo and Caroline Jay},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/journals/corr/abs-1903-06039},
date-added = {2019-04-17 08:42:00 -0400},
date-modified = {2019-04-24 16:20:11 -0400},
eprint = {1903.06039},
journal = {CoRR},
timestamp = {Sun, 31 Mar 2019 19:01:24 +0200},
title = {What Makes Research Software Sustainable? An Interview Study With Research Software Engineers},
url = {http://arxiv.org/abs/1903.06039},
volume = {abs/1903.06039},
year = {2019},
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bdsk-url-1 = {http://arxiv.org/abs/1903.06039}}
@article{Bjorner2019,
author = {Bj\⊘rner, Dines},
date-added = {2019-04-09 16:31:49 -0400},
date-modified = {2019-04-09 16:34:36 -0400},
journal = {ACM Trans. Softw. Eng. Methodol.},
keywords = {domain engineering, domain analysis and description calculi, transcendental deduction},
month = {March},
number = {2},
pages = {8:1--8:67},
title = {Domain Analysis and Description Principles, Techniques, and Modelling Languages},
volume = {28},
year = {2019},
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@inproceedings{Farmer2004,
abstract = {Undefined terms are commonplace in mathematics, particularly in calculus. The traditional approach to undefinedness in mathematical practice is to treat undefined terms as legitimate, nondenoting terms that can be components of meaningful statements. The traditional approach enables statements about partial functions and undefined terms to be stated very concisely. Unfortunately, the traditional approach cannot be easily employed in a standard logic in which all functions are total and all terms are defined, but it can be directly formalized in a standard logic if the logic is modified slightly to admit undefined terms and statements about definedness. This paper demonstrates this by defining a version of simple type theory called Simple Type Theory with Undefinedness (sttwu) and then formalizing in sttwu examples of undefinedness arising in calculus. The examples are taken from M. Spivak's well-known textbook Calculus.},
address = {Berlin, Heidelberg},
author = {Farmer, William M.},
booktitle = {Automated Reasoning},
date-added = {2019-03-14 08:51:32 -0400},
date-modified = {2019-03-14 08:51:40 -0400},
editor = {Basin, David and Rusinowitch, Micha{\"e}l},
isbn = {978-3-540-25984-8},
pages = {475--489},
publisher = {Springer Berlin Heidelberg},
title = {Formalizing Undefinedness Arising in Calculus},
year = {2004},
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@incollection{Patrick2016,
address = {Boca Raton, FL},
author = {Matthew Patrick},
booktitle = {Software Engineering for Science},
chapter = {Examples of the Application of Traditional Software Engineering Practices to Science},
date-added = {2019-02-08 20:30:34 -0500},
date-modified = {2019-02-08 20:31:59 -0500},
editor = {Jeffrey C. Carver and Neil Chue Hong and George Thiruvathukal},
pages = {53--88},
publisher = {Taylor \& Francis},
series = {Chapman \& Hall/{CRC} Computational Science},
title = {Making Scientific Software Easier to Understand, Test, and Communicate through Software Engineering},
year = {2016},
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@inproceedings{Smith2019_CSE,
author = {W. Spencer Smith},
booktitle = {{SIAM-CSE} Conference on Computational Science and Engineering, Minisymposium scientific software: practices, concerns, and solution strategies},
date-added = {2019-01-30 12:03:03 -0500},
date-modified = {2019-01-30 12:15:49 -0500},
month = {Feb},
title = {Toward Automatic Generation of Scientific Software Artifacts},
year = {2019},
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bdsk-url-1 = {https://figshare.com/articles/Toward_Automatic_Generation_of_Scientific_Software_Artifacts_SIAM_CS19_MS2_Scientific_Software_Practices_Concerns_and_Solution_Strategies_February_25_2019/7771061}}
@inproceedings{SmithEtAl2019_CSE,
author = {W. Spencer Smith and Malavika Srinivasan and Sumanth Shankar},
booktitle = {{SIAM-CSE} 2019 Conference on Computational Science and Engineering, Minisymposterium: Software Productivity and Sustainability for CSE and Data Science},
date-added = {2019-01-30 11:59:12 -0500},
date-modified = {2019-02-22 11:53:26 -0500},
doi = {https://doi.org/10.6084/m9.figshare.7757246.v2},
month = {Feb},
title = {No Need for Excuses: Applying Software Engineering Principles to Facilitate Scientific Software Documentation},
year = {2019},
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@article{SahinEtAl2005,
author = {{\c{S}}ahin, Hac{\i} Mehmet and Kocatepe, Kadir and Kay{\i}kc{\i}, Ramazan and Akar, Ne{\c{s}}et},
date-added = {2019-02-07 15:40:41 -0500},
date-modified = {2019-02-07 15:40:41 -0500},
journal = {Energy conversion and management},
number = {1},
pages = {19--34},
publisher = {Elsevier},
title = {Determination of unidirectional heat transfer coefficient during unsteady-state solidification at metal casting--chill interface},
volume = {47},
year = {2006},
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@mastersthesis{Srinivasan2018,
author = {Malavika Srinivasan},
date-added = {2019-02-04 16:41:56 -0500},
date-modified = {2019-02-04 16:43:10 -0500},
school = {McMaster University, Hamilton, Ontario, Canada},
title = {Investigating Common Perceptions of Software Engineering Methods Applied to Scientific Computing Software},
year = {2018},
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@article{Lange2013,
acmid = {2590217},
address = {Amsterdam, The Netherlands, The Netherlands},
author = {Lange, Christoph},
date-added = {2019-01-20 14:41:45 -0500},
date-modified = {2019-01-20 14:41:59 -0500},
issn = {1570-0844},
issue_date = {April 2013},
journal = {Semant. web},
keywords = {Formalization, Knowledge Representation, Linked Data, Mathematical Knowledge Management, Mathematics, Ontologies, Xml},
month = apr,
number = {2},
numpages = {40},
pages = {119--158},
publisher = {IOS Press},
title = {Ontologies and Languages for Representing Mathematical Knowledge on the Semantic Web},
url = {http://dl.acm.org/citation.cfm?id=2590215.2590217},
volume = {4},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2590215.2590217}}
@inproceedings{SouagEtAl2015,
abstract = {Security is an important issue that needs to be taken into account at all stages of information system development, including early requirements elicitation. Early analysis of security makes it possible to predict threats and their impacts and define adequate security requirements before the system is in place. Security requirements are difficult to elicit, analyze, and manage. The fact that analysts' knowledge about security is often tacit makes the task of security requirements elicitation even harder. Ontologies are known for being a good way to formalize knowledge. Ontologies, in particular, have been proved useful to support reusability. Requirements engineering based on predefined ontologies can make the job of requirement engineering much easier and faster. However, this very much depends on the quality of the ontology that is used. Some security ontologies for security requirements have been proposed in the literature. None of them stands out as complete. This paper presents a core and generic security ontology for security requirements engineering. Its core and generic status is attained thanks to its coverage of wide and high-level security concepts and relationships. We implemented the ontology and developed an interactive environment to facilitate the use of the ontology during the security requirements engineering process. The proposed security ontology was evaluated by checking its validity and completeness compared to other ontologies. Moreover, a controlled experiment with end-users was performed to evaluate its usability.},
address = {Cham},
author = {Souag, Amina and Salinesi, Camille and Mazo, Ra{\'u}l and Comyn-Wattiau, Isabelle},
booktitle = {Engineering Secure Software and Systems},
date-added = {2019-01-20 14:35:24 -0500},
date-modified = {2019-01-20 14:35:54 -0500},
editor = {Piessens, Frank and Caballero, Juan and Bielova, Nataliia},
isbn = {978-3-319-15618-7},
pages = {157--177},
publisher = {Springer International Publishing},
title = {A Security Ontology for Security Requirements Elicitation},
year = {2015},
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@inproceedings{OfenbeckEtAl2017,
annote = {- space is referring to design space - list of design choices and specialization
- meta stage, current stage, code generation at run-time - get size of fft (n) at run-time - now treat yourself as compile time instead of run-time - compile a good fft and then link it in - generate it somewhere else, compile it and then link it},
author = {Georg Ofenbeck and Tiark Rompf and Markus P{\"{u}}schel},
booktitle = {{GPCE}},
date-added = {2018-12-03 13:08:16 -0500},
date-modified = {2018-12-03 13:29:06 -0500},
pages = {15--28},
publisher = {{ACM}},
title = {Staging for generic programming in space and time},
year = {2017},
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@inproceedings{ButlerEtAl2017,
acmid = {3102076},
address = {New York, NY, USA},
articleno = {6},
author = {Butler, Eric and Siu, Kristin and Zook, Alexander},
booktitle = {Proceedings of the 12th International Conference on the Foundations of Digital Games},
date-added = {2018-11-26 11:02:41 -0500},
date-modified = {2018-11-26 11:02:54 -0500},
doi = {10.1145/3102071.3102076},
isbn = {978-1-4503-5319-9},
keywords = {generative grammars, generative methods, procedural content generation, program synthesis},
location = {Hyannis, Massachusetts},
numpages = {10},
pages = {6:1--6:10},
publisher = {ACM},
series = {FDG '17},
title = {Program Synthesis As a Generative Method},
url = {http://doi.acm.org/10.1145/3102071.3102076},
year = {2017},
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bdsk-url-1 = {http://doi.acm.org/10.1145/3102071.3102076},
bdsk-url-2 = {https://doi.org/10.1145/3102071.3102076}}
@inproceedings{ZhuEtAl2016,
author = {Zirun Zhu and Yongzhe Zhang and Hsiang{-}Shang Ko and Pedro Martins and Jo{\~{a}}o Saraiva and Zhenjiang Hu},
booktitle = {{SLE}},
date-added = {2018-11-23 13:08:36 -0500},
date-modified = {2018-11-23 13:08:45 -0500},
pages = {2--14},
publisher = {{ACM}},
title = {Parsing and reflective printing, bidirectionally},
year = {2016},
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@article{KanewalaAndChen2018,
author = {Upulee Kanewala and Tsong Yueh Chen},
date-added = {2018-11-09 15:26:35 -0500},
date-modified = {2018-11-09 15:27:32 -0500},
journal = {Computing in Science \& Engineering},
title = {Metamorphic Testing: A Simple yet Effective Approach for Testing Scientific Software},
year = {2018},
bdsk-file-1 = {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}}
@inproceedings{ReisAndJarvi2005,
author = {Gabriel Dos Reis and Jaakko Jarvi},
booktitle = {In LibraryCentric Software Design, OOPSLA workshop},
date-added = {2018-11-09 12:58:30 -0500},
date-modified = {2018-11-09 12:59:26 -0500},
title = {What is generic programming?},
year = {2005},
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@inproceedings{MayerhoferEtAl2016,
abstract = {Although several software modeling languages permit the representation of key aspects of physical entities, such as units, precision or measurement uncertainty, these aspects are not typically incorporated into their type systems. Therefore, operating with such properties is normally cumbersome and contrived. This paper shows how both data uncertainty and units can be captured in software models and naturally incorporated into their type systems. In particular, we present extensions of the UML/OCL type Real and define a set of operations on values of these new types. Furthermore, we show how they can be used in software models to carry out computations that consider measurement uncertainty and permit the detection of unit mismatches when trying to operate with their values.},
acmid = {2997376},
address = {New York, NY, USA},
annote = {- units as an 8 tuple, together with converstion factor and offset},
author = {Mayerhofer, Tanja and Wimmer, Manuel and Vallecillo, Antonio},
booktitle = {Proceedings of the 2016 ACM SIGPLAN International Conference on Software Language Engineering},
date-added = {2018-11-08 15:09:30 -0500},
date-modified = {2018-11-29 15:00:38 -0500},
doi = {10.1145/2997364.2997376},
isbn = {978-1-4503-4447-0},
keywords = {dimensions, measurement uncertainty, model-based engineering, modeling quantities, units},
location = {Amsterdam, Netherlands},
numpages = {14},
pages = {118--131},
publisher = {ACM},
series = {SLE 2016},
title = {Adding Uncertainty and Units to Quantity Types in Software Models},
url = {http://doi.acm.org/10.1145/2997364.2997376},
year = {2016},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2997364.2997376},
bdsk-url-2 = {https://doi.org/10.1145/2997364.2997376}}
@inproceedings{DiFranco2017,
acmid = {3155627},
address = {Piscataway, NJ, USA},
author = {Di Franco, Anthony and Guo, Hui and Rubio-Gonz\'{a}lez, Cindy},
booktitle = {Proceedings of the 32Nd IEEE/ACM International Conference on Automated Software Engineering},
date-added = {2018-11-07 14:16:00 -0500},
date-modified = {2018-11-07 14:16:08 -0500},
isbn = {978-1-5386-2684-9},
keywords = {empirical study, numerical bugs},
location = {Urbana-Champaign, IL, USA},
numpages = {11},
pages = {509--519},
publisher = {IEEE Press},
series = {ASE 2017},
title = {A Comprehensive Study of Real-world Numerical Bug Characteristics},
url = {http://dl.acm.org/citation.cfm?id=3155562.3155627},
year = {2017},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=3155562.3155627}}
@inproceedings{Gibbons2006,
acmid = {1159863},
address = {New York, NY, USA},
annote = {- builder has the stuff before it is all built, add as go along - can do the same thing in functional programming with lazy evaluation - wait until you have the thing you need and then have code for them
- bi-map is an fmap with an Either},
author = {Gibbons, Jeremy},
booktitle = {Proceedings of the 2006 ACM SIGPLAN Workshop on Generic Programming},
date-added = {2018-11-05 09:49:41 -0500},
date-modified = {2018-11-05 13:39:56 -0500},
doi = {10.1145/1159861.1159863},
isbn = {1-59593-492-8},
keywords = {design patterns, folds, functional programming, generic programming, higher-order functions, unfolds},
location = {Portland, Oregon, USA},
numpages = {12},
pages = {1--12},
publisher = {ACM},
series = {WGP '06},
title = {Design Patterns As Higher-order Datatype-generic Programs},
url = {http://doi.acm.org/10.1145/1159861.1159863},
year = {2006},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1159861.1159863},
bdsk-url-2 = {https://doi.org/10.1145/1159861.1159863}}
@inproceedings{Smith1999,
author = {Douglas R. Smith},
booktitle = {Client Resources on the Internet, IEEE Multimedia Systems '99},
date-added = {2018-10-29 13:10:41 -0400},
date-modified = {2018-10-29 13:10:52 -0400},
pages = {302--307},
title = {Mechanizing the Development of Software},
year = {1999},
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@article{CaretteEtAl2009,
acmid = {1630626},
address = {New York, NY, USA},
author = {Carette, Jacques and Kiselyov, Oleg and Shan, Chung-chieh},
date-added = {2018-10-29 13:08:08 -0400},
date-modified = {2018-10-29 13:08:17 -0400},
doi = {10.1017/S0956796809007205},
issn = {0956-7968},
issue_date = {September 2009},
journal = {J. Funct. Program.},
month = sep,
number = {5},
numpages = {35},
pages = {509--543},
publisher = {Cambridge University Press},
title = {Finally Tagless, Partially Evaluated: Tagless Staged Interpreters for Simpler Typed Languages},
url = {http://dx.doi.org/10.1017/S0956796809007205},
volume = {19},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1017/S0956796809007205}}
@article{HemelAndVisser2011,
acmid = {2048121},
address = {New York, NY, USA},
author = {Hemel, Zef and Visser, Eelco},
date-added = {2018-10-22 13:00:08 -0400},
date-modified = {2018-10-22 13:04:26 -0400},
doi = {10.1145/2076021.2048121},
issn = {0362-1340},
issue_date = {October 2011},
journal = {SIGPLAN Not.},
keywords = {domain-specific language, mobile, mobile development, mobile web},
month = oct,
number = {10},
numpages = {18},
pages = {695--712},
publisher = {ACM},
title = {Declaratively Programming the Mobile Web with Mobl},
url = {http://doi.acm.org/10.1145/2076021.2048121},
volume = {46},
year = {2011},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2076021.2048121},
bdsk-url-2 = {https://doi.org/10.1145/2076021.2048121}}
@inproceedings{SmithEtAl2009,
acmid = {1536548},
address = {New York, NY, USA},
author = {Smith, Gillian and Treanor, Mike and Whitehead, Jim and Mateas, Michael},
booktitle = {Proceedings of the 4th International Conference on Foundations of Digital Games},
date-added = {2018-10-15 13:07:09 -0400},
date-modified = {2018-10-15 13:07:20 -0400},
doi = {10.1145/1536513.1536548},
isbn = {978-1-60558-437-9},
keywords = {2D platformers, games, levels, procedural generation},
location = {Orlando, Florida},
numpages = {8},
pages = {175--182},
publisher = {ACM},
series = {FDG '09},
title = {Rhythm-based Level Generation for 2D Platformers},
url = {http://doi.acm.org/10.1145/1536513.1536548},
year = {2009},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1536513.1536548},
bdsk-url-2 = {https://doi.org/10.1145/1536513.1536548}}
@inproceedings{MouratoEtAl2011,
acmid = {2071433},
address = {New York, NY, USA},
articleno = {8},
author = {Mourato, Fausto and dos Santos, Manuel Pr\'{o}spero and Birra, Fernando},
booktitle = {Proceedings of the 8th International Conference on Advances in Computer Entertainment Technology},
date-added = {2018-10-12 12:19:53 -0400},
date-modified = {2018-10-12 12:20:03 -0400},
doi = {10.1145/2071423.2071433},
isbn = {978-1-4503-0827-4},
keywords = {automated game design, platform videogames, procedural content generation},
location = {Lisbon, Portugal},
numpages = {8},
pages = {8:1--8:8},
publisher = {ACM},
series = {ACE '11},
title = {Automatic Level Generation for Platform Videogames Using Genetic Algorithms},
url = {http://doi.acm.org/10.1145/2071423.2071433},
year = {2011},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2071423.2071433},
bdsk-url-2 = {https://doi.org/10.1145/2071423.2071433}}
@mastersthesis{Hanebach2009,
author = {Alicja Hanebach},
date-added = {2018-10-12 11:06:32 -0400},
date-modified = {2018-10-12 11:07:38 -0400},
month = {July},
school = {Civil Engineering Department, McMaster University},
title = {Flexible Pavement Response Modelling Using the Indirect Boundary Element Method},
year = {2009},
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@mastersthesis{El-Sewify2012,
address = {Hamilton, ON, Canada},
author = {Hesham El-Sewify},
date-added = {2018-10-12 11:02:48 -0400},
date-modified = {2018-10-12 11:04:15 -0400},
month = {April},
school = {School of Computational Science and Engineering, McMaster University},
title = {Multi-particle Collision Dynamics},
year = {2012},
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@article{RudeEtAl2018,
author = {R{\"u}de, U. and Willcox, K. and McInnes, L. and Sterck, H.},
date-added = {2018-10-10 10:24:37 -0400},
date-modified = {2018-10-11 11:50:20 -0400},
doi = {10.1137/16M1096840},
eprint = {https://doi.org/10.1137/16M1096840},
journal = {SIAM Review},
number = {3},
pages = {707-754},
title = {Research and Education in Computational Science and Engineering},
url = {https://doi.org/10.1137/16M1096840},
volume = {60},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1137/16M1096840}}
@misc{HettrickEtAl2014,
abstract = {This spreadsheet contains the anonymised data collected as part of a survey of UK researchers in their use of research software.
We asked people specifically about ``research software'' which we defined as:
``Software that is used to generate, process or analyse results that you intend to appear in a publication (either in a journal, conference paper, monograph, book or thesis). Research software can be anything from a few lines of code written by yourself, to a professionally developed software package. Software that does not generate, process or analyse results - such as word processing software, or the use of a web search - does not count as `research software' for the purposes of this survey.''
We contacted 1,000 randomly selected researchers at each of 15 Russell Group universities. From the 15,000 invitations to complete the survey, we received 417 responses -- a rate of 3% which is fairly normal for a blind survey. We used Google Forms to collect responses.
The responses have good representation from across the disciplines, seniorities and genders. This is a statistically significant number of responses that can be used to represent the views of people in research-intensive universities in the UK.
An overview of the data is available on the worksheet "Summary data". Responses to questions are ordered by unique respondent ID. Please read the "README" worksheet for additional information about the collection and processing of this data.
This survey data is licensed under a Creative Commons by Attribution licence. Copyright resides with The University of Edinburgh on behalf of the Software Sustainability Institute.},
annote = {- 92% of academic use research software
- 69% say that their research would not be pratical without it
- 56% develop their own software},
author = {Hettrick, Simon and Antonioletti, Mario and Carr, Les and Chue Hong, Neil and Crouch, Stephen and De Roure, David and Emsley, Iain and Goble, Carole and Hay, Alexander and Inupakutika, Devasena and Jackson, Mike and Nenadic, Aleksandra and Parkinson, Tim and Parsons, Mark I and Pawlik, Aleksandra and Peru, Giacomo and Proeme, Arno and Robinson, John and Sufi, Shoaib},
date-added = {2018-10-09 10:52:48 -0400},
date-modified = {2018-10-09 10:55:21 -0400},
doi = {10.5281/zenodo.14809},
month = dec,
title = {UK Research Software Survey 2014},
url = {https://doi.org/10.5281/zenodo.14809},
year = 2014,
bdsk-url-1 = {https://doi.org/10.5281/zenodo.14809}}
@misc{KapurAndMusser1992,
annote = {- one of authors of this paper worked on the STL for C++ - the idea of concepts and traits were distilled out of STL and now are part of Scala
- interesting that Tecton was inspired by OBJ and IMPS (from Bill Farmer) (little theories from Bill Farmer)
- morphisms for specifications
[|(plus(a, b)|] = [| a |] + [| b |] - relation between syntax and semantics
- traits are like theories
- what they call a sort is what other people would call a type},
author = {Deepak Kapur and David R. Musser},
date-added = {2018-10-05 08:10:20 -0400},
date-modified = {2018-10-05 14:09:44 -0400},
title = {Tecton: A Framework for Specifying and Verifying Generic System Components},
year = {1992},
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@inproceedings{KatsAndVisser2010,
annote = {- students say that the paper is repetitive
IDEs are not that easy - try writing something that has the following for a given prog. lang:
- parser, pretty printing, type checking, syntax highlighting
- code folding, inline error, auto complete, matching,
Spoofax provides a metalanguage of PL
Spoofax also has a meta description of ``editing'' features of PLs
- generating a parser is not a solved problem (yacc and bison exist (and others), but not easy to use for all problems)
- Spoofax isn't commonly used by anyone outside of the research group
- MPS is a competitor to Spoofax
- not projectional editing - allowed to create programs that are not syntactically correct
- Scratch is a projectional editor (good for teaching)
- if an IDE can be provided, what else can be provided (generated)?},
author = {Lennart C. L. Kats and Eelco Visser},
booktitle = {Proceedings of the 25th Annual ACM SIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications (OOPSLA 2010)},
date = {October 17-21, 2010},
date-added = {2018-09-27 23:27:35 -0400},
date-modified = {2018-09-28 13:56:09 -0400},
editor = {Martin Rinard},
location = {Reno, NV, USA},
tags = {Spoofax, language workbench},
title = {The {Spoofax} Language Workbench. {Rules} for Declarative Specification of Languages and {IDEs}},
year = {2010},
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@article{LucivEtAl2018,
abstract = {Contemporary software documentation is as complicated as the software itself. During its lifecycle, the documentation accumulates a lot of ``near duplicate'' fragments, i.e. chunks of text that were copied from a single source and were later modified in different ways. Such near duplicates decrease documentation quality and thus hamper its further utilization. At the same time, they are hard to detect manually due to their fuzzy nature. In this paper we give a formal definition of near duplicates and present an algorithm for their detection in software documents. This algorithm is based on the exact software clone detection approach: the software clone detection tool Clone Miner was adapted to detect exact duplicates in documents. Then, our algorithm uses these exact duplicates to construct near ones. We evaluate the proposed algorithm using the documentation of 19 open source and commercial projects. Our evaluation is very comprehensive -- it covers various documentation types: design and requirement specifications, programming guides and API documentation, user manuals. Overall, the evaluation shows that all kinds of software documentation contain a significant number of both exact and near duplicates. Next, we report on the performed manual analysis of the detected near duplicates for the Linux Kernel Documentation. We present both quantative and qualitative results of this analysis, demonstrate algorithm strengths and weaknesses, and discuss the benefits of duplicate management in software documents.},
author = {Luciv, D. V. and Koznov, D. V. and Chernishev, G. A. and Terekhov, A. N. and Romanovsky, K. Yu. and Grigoriev, D. A.},
date-added = {2018-09-27 15:27:12 -0400},
date-modified = {2018-09-27 19:28:07 -0400},
day = {01},
doi = {10.1134/S0361768818050079},
issn = {1608-3261},
journal = {Programming and Computer Software},
month = {Sep},
number = {5},
pages = {335--343},
title = {Detecting Near Duplicates in Software Documentation},
url = {https://doi.org/10.1134/S0361768818050079},
volume = {44},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1134/S0361768818050079}}
@article{Zwart2018,
author = {Simon Portegies Zwart},
date-added = {2018-09-25 14:28:40 -0400},
date-modified = {2018-09-25 14:30:04 -0400},
journal = {Science},
month = {September},
number = {6406},
pages = {979--980},
title = {Computational Astrophysics for the Future},
volume = {361},
year = {2018},
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@article{Keshavarz-MotamedEtAl2014,
annote = {{the derivation of the ODEs is unclear.}
{the actual ODEs are unclear, although a circuit diagram analogy helps}},
author = {Zahra Keshavarz-Motamed and Julio Garcia and Emmanuel Gaillard and Romain Capoulade and Florent LeVen and Guy Cloutier and Lyes Kadem and Philippe Pibarot},
date-added = {2018-09-25 13:25:17 -0400},
date-modified = {2018-09-25 13:44:29 -0400},
doi = {doi:10.1371/journal.pone.0086793},
journal = {{PLoS ONE}},
note = {10 pp},
number = {1},
title = {Non-Invasive Determination of Left Ventricular Workload in Patients with Aortic Stenosis Using Magnetic Resonance Imaging and Doppler Echocardiography},
volume = {9},
year = {2014},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0086793}}
@article{Keshavarz-MotamedEtAl2011,
author = {Zahra Keshavarz-Motamed and J. Garcia and P. Pibarot and E. Larose and L. Kadem},
date-added = {2018-09-25 13:22:54 -0400},
date-modified = {2018-09-25 13:24:28 -0400},
journal = {Journal of Biomechanics},
pages = {2817--2825},
title = {Modeling the impact of concomitant aortic stenosis and coarctation of the aorta on left ventricular workload},
volume = {44},
year = {2011},
bdsk-file-1 = {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}}
@article{MilewiczAndRayborn2018,
abstract = {Large-scale collaborative scientific software projects require more knowledge than any one person typically possesses. This makes coordination and communication of knowledge and expertise a key factor in creating and safeguarding software quality, without which we cannot have sustainable software. However, as researchers attempt to scale up the production of software, they are confronted by problems of awareness and understanding. This presents an opportunity to develop better practices and tools that directly address these challenges. To that end, we conducted a case study of developers of the Trilinos project. We surveyed the software development challenges addressed and show how those problems are connected with what they know and how they communicate. Based on these data, we provide a series of practicable recommendations, and outline a path forward for future research.},
annote = {- cites Drasil (Dan's position paper) and Thulasi's work (5 redevelopment projects)
- seems like MandR assumed the potential problems - should have provided an opportunity for new problems to emerge from user feedback
- they implied that Drasil cannot capture tacit knowledge that cannot be codefied, likely because they misunderstood Drasil
- if Drasil is successful, much of the knowledge they are referring to only has to be entered once, the communication is through documentation, mistakes cannot be repeated in the same way as the anecdote in the paper because the code is generated},
author = {Reed Milewicz and Elaine M. Raybourn},
date-added = {2018-09-24 14:41:10 -0400},
date-modified = {2019-05-22 08:40:04 -0400},
journal = {ArXiv e-prints},
keywords = {Scientific Software Design, Object--Oriented Programming, Design Patterns, Newton's methods, Optimization techniques},
month = {September},
pages = {1--19},
title = {Talk to Me: A Case Study on Coordinating Expertise in Large-Scale Scientific Software Projects},
volume = {arXiv:1905.04642},
year = {2018},
bdsk-file-1 = {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}}
@article{RompfAndOdersky2010,
abstract = {Software engineering demands generality and abstraction, performance demands specialization and concretization. Generative programming can provide both, but the effort required to develop high-quality program generators likely offsets their benefits, even if a multi-stage programming language is used. We present lightweight modular staging, a library-based multi-stage programming approach that breaks with the tradition of syntactic quasi-quotation and instead uses only types to distinguish between binding times. Through extensive use of component technology, lightweight modular staging makes an optimizing compiler framework available at the library level, allowing programmers to tightly integrate domain-specific abstractions and optimizations into the generation process. We argue that lightweight modular staging enables a form of language virtualization, i.e. allows to go from a pure-library embedded language to one that is practically equivalent to a stand-alone implementation with only modest effort.},
author = {Rompf, Tiark and Odersky, Martin},
date-added = {2018-09-24 11:25:33 -0400},
date-modified = {2018-09-24 11:26:09 -0400},
journal = {Acm Sigplan Notices},
pages = {127-136},
title = {Lightweight Modular Staging: A Pragmatic Approach to Runtime Code Generation and Compiled DSLs},
volume = {46},
year = {2010},
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@inbook{PueschelEtAl2011,
abstract = {Spiral is a program generation system (software that generates other software) for linear transforms and
an increasing list of other mathematical functions. The goal of Spiral is to automate the development and
porting of performance libraries. Linear transforms include the discrete Fourier transform (DFT), discrete
cosine transforms, convolution, and the discrete wavelet transform. The input to Spiral consists of a highlevel
mathematical algorithm specification and selected architectural and microarchitectural parameters. The
output is performance-optimized code in a high-level language such as C, possibly augmented with vector
intrinsics and threading instructions.},
annote = {- preprint version of the paper
- representation is pointfree - means it can be left to the compiler - focuses on operators, rather than the typical ``sea'' of indicies usual in this type of code},
author = {Markus P{\"u}schel and Franz Franchetti and Yevgen Voronenko},
chapter = {Spiral},
date-added = {2018-09-21 13:12:01 -0400},
date-modified = {2018-09-21 13:24:10 -0400},
publisher = {Springer},
title = {Encyclopedia of Parallel Computing},
year = {2011},
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@misc{MernikEtAl2003,
abstract = {Domain-specific languages (DSLs) are languages tailored to a specific application domain. They offer substantial gains in expressiveness and ease of use compared with general purpose programming languages in their domain of application. DSL development is hard, requiring both domain knowledge and language development expertise. Few people have both. Not surprisingly, the decision to develop a DSL is often postponed indefinitely, if considered at all, and most DSLs never get beyond the application library stage. While many articles have been written on the development of particular DSLs, there is very limited literature on DSL development methodologies and many questions remain regarding when and how to develop a DSL. To aid the DSL developer, we identify patterns in the decision, analysis, design, and implementation phases of DSL development. Our patterns try to improve on and extend earlier work on DSL design patterns, in particular by Spinellis (2001). We also discuss domain analysis tools and language development systems that may help to speed up DSL development. Finally, we state a number of open problems.},
annote = {{- the actual DSL for Drasil is not obvious}
- JC mentioned gradually type languages, both static and dynamic types - challenge is creating meaningful error messages
- JC mentioned a book on the history of notations
- JC make is a great example of a DSL (not a good language)
- JC mentioned Matthias Fellesein},
author = {M. Mernik and J. Heering and A.M. Sloane and Marjan Mernik and Anthony M. Sloane},
date-added = {2018-09-17 09:27:57 -0400},
date-modified = {2018-09-17 14:22:59 -0400},
title = {When And How To Develop Domain-Specific Languages},
year = {2003},
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@misc{Soergel2014,
author = {David Soergel},
date-added = {2018-09-16 21:34:35 -0400},
date-modified = {2018-09-16 21:35:30 -0400},
howpublished = {\url{http://davidsoergel.com/posts/confirmation-depth-as-a-measure-of-reproducible-scientific-research}},
month = {October},
title = {Confirmation Depth as a measure of reproducible scientific research},
year = {2014},
bdsk-url-1 = {http://davidsoergel.com/posts/confirmation-depth-as-a-measure-of-reproducible-scientific-research}}
@article{Grunwald2004,
author = {Peter Gr{\"u}nwald},
date-added = {2018-09-16 21:23:36 -0400},
date-modified = {2018-09-16 21:26:48 -0400},
journal = {ArXiv e-prints},
month = {June},
title = {A tutorial introduction to the minimum description length principle},
year = {2004},
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@article{PostAndVotta2005,
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
adsurl = {http://adsabs.harvard.edu/abs/2005PhT....58a..35P},
annote = {``Verification, validation, and quality management, we found, are all crucial to the success of a large-scale code- writing project. Although some computational science projects---those illustrated by figures 1−4, for example---stress all three requirements, many other current and planned projects give them insufficient attention. In the absence of any one of those requirements, one doesn't have the assurance of independent assessment, confirmation, and repeatability of results. Because it's impossible to judge the validity of such results, they often have little credibility and no impact.''
- more examples of failures - missed discovery
- emphasizes verification and validation},
author = {{Post}, D.~E. and {Votta}, L.~G.},
date-added = {2018-09-10 13:25:52 -0400},
date-modified = {2018-09-10 14:10:18 -0400},
doi = {10.1063/1.1881898},
journal = {Physics Today},
keywords = {computer applications, physics, societies, data analysis, parallel processing, codes, white dwarfs, software selection, supernovae, magnetosphere, bridges (structures)},
month = jan,
number = 1,
pages = {35-41},
title = {{Computational Science Demands a New Paradigm}},
volume = 58,
year = 2005,
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bdsk-url-1 = {https://doi.org/10.1063/1.1881898}}
@article{FaulkEtAl2009,
abstract = {Hardware improvements do little to improve real productivity in scientific programming. Indeed, the dominant barriers to productivity improvement are now in the software processes. To break the gridlock, we must establish a degree of cooperation and collaboration with the software engineering community that does not yet exist.},
annote = {``The development environment's unique goals and constraints have led the scien- tific programming community to evolve its own characteristic software development approach. As our workflow studies show, this approach cre- ates bottlenecks{\ldots}''
``we saw many mani- festations of a productivity crisis: frustratingly long and troubled software development times, a growing shortage of expertise in critical areas,5 a dysfunctional market in supporting tools,6 acute problems in achieving required portability (both portable software and portable programming skills), and growing concern about the reliability of scientific results based on that software.''
``When asked about strategies for building con- fidence in their codes, the scientific programmers we studied answered strictly in terms of the sci- ence. Typical responses? That the output ``looked right'' to the domain scientist, and confidence in the code grew over time.''
- say can address productivity gridlock through automation (page 35, bottom) and abstraction - this is the idea behind DSL and generative programming - also says that measurement is important
- did a redevelopment experiment similar to ones done by Smith et al, but seem to have completely ignored documentation, focused on code},
author = {S. Faulk and E. Loh and M. L. V. D. Vanter and S. Squires and L. G. Votta},
date-added = {2018-09-10 11:25:54 -0400},
date-modified = {2018-09-10 11:58:34 -0400},
doi = {10.1109/MCSE.2009.205},
issn = {1521-9615},
journal = {Computing in Science Engineering},
keywords = {Scientific computing;Productivity;Software engineering;Hardware;Programming;Sun;Assembly;Humans;Computer industry;Machinery production industries;Sciences;scientific programming;software engineering},
month = {Nov},
number = {6},
pages = {30-39},
title = {Scientific Computing's Productivity Gridlock: How Software Engineering Can Help},
volume = {11},
year = {2009},
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bdsk-url-1 = {https://doi.org/10.1109/MCSE.2009.205}}
@article{HealyAndCaudell2006,
abstract = {We propose category theory, the mathematical theory of structure, as a vehicle for defining ontologies in an unambiguous language with analytical and constructive features. Specifically, we apply categorical logic and model theory, based upon viewing an ontology as a sub-category of a category of theories expressed in a formal logic. In addition to providing mathematical rigor, this approach has several advantages. It allows the incremental analysis of ontologies by basing them in an interconnected hierarchy of theories, with an operation on the hierarchy that expresses the formation of complex theories from simple theories that express first principles. Another operation forms abstractions expressing the shared concepts in an array of theories. The use of categorical model theory makes possible the incremental analysis of possible worlds, or instances, for the theories, and the mapping of instances of a theory to instances of its more abstract parts. We describe the theoretical approach by applying it to the semantics of neural networks.},
author = {Healy, Michael John and Caudell, Thomas Preston},
date-added = {2018-09-10 10:00:41 -0400},
date-modified = {2018-09-10 10:01:08 -0400},
day = {01},
doi = {10.1007/s10516-005-5474-1},
issn = {1572-8390},
journal = {Axiomathes},
month = {Mar},
number = {1},
pages = {165--214},
title = {Ontologies and Worlds in Category Theory: Implications for Neural Systems},
url = {https://doi.org/10.1007/s10516-005-5474-1},
volume = {16},
year = {2006},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1007/s10516-005-5474-1}}
@article{KatzEtAl2018,
author = {Daniel S. Katz and Stephan Druskat and Robert Haines and Caroline Jay and Alexander Struck},
date-added = {2018-08-03 15:07:38 -0400},
date-modified = {2018-08-03 15:09:40 -0400},
journal = {ArXiv},
pages = {1--19},
title = {The State of Sustainable Research Software: Results from the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1)},
year = {2018},
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@article{MillsEtAl2018,
annote = {- has good references on traceability},
author = {Chris Mills and Javier Escobar-Avila and Sonia Haiduc},
date-added = {2018-08-02 13:47:27 -0400},
date-modified = {2018-08-02 13:49:41 -0400},
journal = {arXiv},
pages = {1--12},
title = {Automatic Traceability Maintenance via Machine Learning Classification},
year = {2018},
bdsk-file-1 = {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}}
@inproceedings{BezzecchiEtAl2018,
address = {Toulouse, France},
author = {Bezzecchi, Sergio and Crisafulli, Paolo and pichot, charlotte and Wolff, Burkhart},
booktitle = {{9th European Congress on Embedded Real Time Software and Systems (ERTS 2018)}},
date-added = {2018-08-02 09:42:18 -0400},
date-modified = {2018-08-02 09:42:32 -0400},
hal_id = {hal-01702815},
hal_version = {v1},
keywords = {Development Processes ; Certification ; Formal Methods ; Isabelle/HOL ; seL4},
month = Jan,
pdf = {https://hal.archives-ouvertes.fr/hal-01702815/file/2018erts-agile-fm.pdf},
title = {{Making Agile Development Processes fit for V-style Certification Procedures}},
url = {https://hal.archives-ouvertes.fr/hal-01702815},
year = {2018},
bdsk-file-1 = {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},
bdsk-url-1 = {https://hal.archives-ouvertes.fr/hal-01702815}}
@phdthesis{Bagge2009,
address = {PB 7803, 5020 Bergen, Norway},
annote = {- has a good overview of abstraction, separation of concerns etc.},
author = {Anya Helene Bagge},
category = {testing,languages,sle,transformation,concepts},
date-added = {2018-07-13 15:53:05 +0000},
date-modified = {2018-08-03 16:49:23 -0400},
isbn = {978-82-308-0887-0},
kind = {thesis},
school = {Research School in Information and Communication Technology, Department of Informatics, University of Bergen, Norway},
title = {Constructs \& {C}oncepts: Language Design for Flexibility and Reliability},
url = {http://www.ii.uib.no/~anya/phd/},
year = 2009,
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bdsk-url-1 = {http://www.ii.uib.no/~anya/phd/}}
@article{JinAndParnas2010,
acmid = {1837670},
address = {Amsterdam, The Netherlands, The Netherlands},
author = {Jin, Ying and Parnas, David Lorge},
date-added = {2018-06-13 21:16:58 +0000},
date-modified = {2018-06-13 21:17:10 +0000},
doi = {10.1016/j.scico.2009.12.009},
issn = {0167-6423},
issue_date = {November, 2010},
journal = {Sci. Comput. Program.},
keywords = {Expression semantics, Mathematical documentation, Software documentation, Software engineering, Tabular expressions},
month = nov,
number = {11},
numpages = {21},
pages = {980--1000},
publisher = {Elsevier North-Holland, Inc.},
title = {Defining the Meaning of Tabular Mathematical Expressions},
url = {http://dx.doi.org/10.1016/j.scico.2009.12.009},
volume = {75},
year = {2010},
bdsk-file-1 = {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},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.scico.2009.12.009}}
@article{JohansonAndHasselbring2018,
author = {Arne N. Johanson and Wilhelm Hasselbring},
date-added = {2018-06-04 20:03:31 +0000},
date-modified = {2018-06-04 20:05:26 +0000},
journal = {Computing in Science \& Engineering},
pages = {1--31},
title = {Software Engineering for Computational Science: Past, Present, Future},
volume = {Accepted},
year = {2018},
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@inproceedings{SimmEtAl2018,
author = {W. A. Simm and F. Samreen and R. Bassett and M. A. Ferrario and G. Blair and J. Whittle and P. J. Young},
booktitle = {2018 ACM/IEEE 40th International Conference on Software Engineering: Software Engineering in Society},
date-added = {2018-06-04 18:05:39 +0000},
date-modified = {2018-06-04 18:07:17 +0000},
pages = {1--10},
title = {SE in ES: Opportunities for Software Engineering and Cloud Computing in Environmental Science},
year = {2018},
bdsk-file-1 = {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}}
@inproceedings{LinEtAl2018,
author = {Xuanyi Lin and Michelle Simon and Nan Niu},
booktitle = {2018 International Workshop on Software Engineering for Science (held in conjunction with ICSE'18)},
date-added = {2018-06-04 17:54:15 +0000},
date-modified = {2018-06-04 17:54:55 +0000},
pages = {1--8},
title = {Hierarchical Metamorphic Relations for Testing Scientific Software},
year = {2018},
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@inproceedings{HauptEtAl2018,
abstract = {Software is a vital part of modern research. The competence to develop sustainable software becomes increasingly important for research organizations. The DLR - a large research organization in Germany - has set up a software engineering initiative to address typical obstacles in this regard such as missing long-term funding, lack of incentives, or missing knowledge about essential software development practices. In this paper, we describe the concept and activities of the initiative as well as discuss the impact of these activities on the identified obstacles.},
annote = {A related paper is available at:
https://elib.dlr.de/114050/
- Has some summary of the checklist that they use - sounds like a capabiliy maturity model of sorts},
author = {Carina Haupt and Tobias Schlauch and Michael Meinel},
booktitle = {2018 International Workshop on Software Engineering for Science (held in conjunction with ICSE'18)},
date-added = {2018-06-04 17:52:25 +0000},
date-modified = {2018-06-06 15:46:43 +0000},
pages = {1--4},
title = {The Software Engineering Initiative of DLR},
year = {2018},
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@inproceedings{DubeyAndWan2018,
abstract = {Computational science and engineering communities develop com- plex application software with multiple mathematical models that need to interact with one another. Partly due to complexity of veri- fying scientific software, and partly because of the way incentives work in science, there has been insufficient testing of these codes. With a spotlight on the results produced with scientific software, and increasing awareness of software testing and verification as a critical contributor to the reliability of these results, testing is gaining more attention by the developing teams. However, many science teams struggle to find a good solution for themselves due either to lack of training or lack of resources within the team. In this experience paper we describe test development methodologies utilized in two different scenarios: one explains a methodology for building granular tests where none existed before, while the second demonstrates a methodology for selecting test cases that build con- fidence in the software through a process similar to scaffolding. The common insight from both the experiences is that testing should be a part of software design from the beginning for better software and scientific productivity.},
annote = {Conclusion - testing should be part of the software design from the beginning for better software and scientific productivity
- she used stubs and drivers to isolate some of the units for testing purposes},
author = {Anshu Dubey and Hui Wan},
booktitle = {2018 International Workshop on Software Engineering for Science (held in conjunction with ICSE'18)},
date-added = {2018-06-04 17:50:33 +0000},
date-modified = {2018-06-06 15:35:14 +0000},
pages = {1--7},
title = {Methodology for Building Granular Testing in Multicomponent Scientific Software},
year = {2018},
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@inproceedings{BicketEtAl2018,
author = {Isobel C. Bicket and Alexandre Pofelski and Spencer Smith and Gianluigi A. Botton},
booktitle = {Advanced Electron Microscopy Conference: From Steels to DNA},
date-added = {2018-06-01 07:56:05 +0000},
date-modified = {2018-06-01 08:09:48 +0000},
organization = {Canadian Centre for Electron Microscopy (CCEM)},
title = {Enhancing Trust in Electron Microscopy Data Analysis Software Through Software Engineering Principles, Tools and Techniques (Poster)},
year = {2018},
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@inproceedings{Smith2018,
author = {W. Spencer Smith},
booktitle = {2018 International Workshop on Software Engineering for Science (held in conjunction with ICSE'18)},
date-added = {2018-05-20 14:21:55 +0000},
date-modified = {2018-05-21 15:59:34 +0000},
pages = {1--8},
title = {Beyond Software Carpentry},
year = {2018},
bdsk-file-1 = {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}}
@article{ShackleyEtAl1998,
author = {Shackley, S. and Young, P. and Parkinson, S. and Wynne, B.},
journal = {Climatic Change},
note = {Shackley, S Young, P Parkinson, S Wynne, B},
number = {2},
pages = {159-205},
title = {Uncertainty, complexity and concepts of good science in climate change modelling: Are GCMs the best tools?},
volume = {38},
year = {1998}}
@techreport{ShaonEtAl2009,
author = {A. Shaon and Jim Woodcock and E. Conway},
institution = {The University of York},
title = {Tools and Guidelines for Preserving and Accessing Software as a Research Output Report II: Case Studies.},
year = {2009}}
@techreport{StephanAndStevenson2009,
author = {Matthew Stephan and Andrew Stevenson},
institution = {Queen's University},
title = {A Comparative Look at Model Transformation Languages},
year = {2009}}
@article{Shull2011,
author = {F. Shull},
doi = {10.1109/MS.2011.135},
issn = {0740-7459},
journal = {IEEE Software},
keywords = {Software validation; modeling and simulation; climate studies; Robert Jacob; Gavin Schmidt; Argonne National Laboratory and NASA Goddard Institute for Space Studies},
month = nov,
pages = {4-8},
title = {Assuring the Future? A Look at Validating Climate Model Software},
url = {doi.ieeecomputersociety.org/10.1109/MS.2011.135},
volume = {28},
year = {2011},
bdsk-url-1 = {doi.ieeecomputersociety.org/10.1109/MS.2011.135},
bdsk-url-2 = {https://doi.org/10.1109/MS.2011.135}}
@conference{Singer2011,
address = {New York, NY, USA},
author = {Singer, Jeremy},
booktitle = {Proceedings of the 10th SIGPLAN symposium on New ideas, new paradigms, and reflections on programming and software},
doi = {10.1145/2048237.2048249},
isbn = {978-1-4503-0941-7},
keywords = {experimental write-up, literate programming},
organization = {ACM},
pages = {91{\textendash}102},
publisher = {ACM},
series = {ONWARD {\textquoteright}11},
title = {A literate experimentation manifesto},
url = {http://doi.acm.org/10.1145/2048237.2048249},
year = {2011},
bdsk-url-1 = {http://doi.acm.org/10.1145/2048237.2048249},
bdsk-url-2 = {https://doi.org/10.1145/2048237.2048249}}
@inproceedings{SletholtEtAl2011,
acmid = {1985784},
address = {New York, NY, USA},
author = {Sletholt, Magnus Thorstein and Hannay, Jo and Pfahl, Dietmar and Benestad, Hans Christian and Langtangen, Hans Petter},
booktitle = {Proceedings of the 4th International Workshop on Software Engineering for Computational Science and Engineering},
doi = {10.1145/1985782.1985784},
isbn = {978-1-4503-0598-3},
keywords = {agile software development, literature review, scientific software, scrum, xp},
location = {Waikiki, Honolulu, HI, USA},
numpages = {9},
pages = {1--9},
publisher = {ACM},
series = {SECSE '11},
title = {A Literature Review of Agile Practices and Their Effects in Scientific Software Development},
url = {http://doi.acm.org/10.1145/1985782.1985784},
year = {2011},
bdsk-url-1 = {http://doi.acm.org/10.1145/1985782.1985784},
bdsk-url-2 = {https://doi.org/10.1145/1985782.1985784}}
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journal = {Computing in Science \& Engineering},
keywords = {Software development; literature review; case study; agile practice; computational science; scientific computing},
month = nov,
pages = {24-37},
title = {What Do We Know about Scientific Software Development's Agile Practices?},
url = {doi.ieeecomputersociety.org/10.1109/MCSE.2011.113},
volume = {14},
year = {2012},
bdsk-url-1 = {doi.ieeecomputersociety.org/10.1109/MCSE.2011.113},
bdsk-url-2 = {https://doi.org/10.1109/MCSE.2011.113}}
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title = {Lessons from Space},
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bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0067111}}
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title = {Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research},
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year = {2013}}
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author = {Michael Stonebraker and Daniel Bruckner and Ihab F. Ilyas and George Beskales and Mitch Cherniack and Stanley B. Zdonik and Alexander Pagan and Shan Xu},
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year = {2013},
bdsk-url-1 = {http://cidrdb.org/cidr2013/Papers/CIDR13_Paper28.pdf}}
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address = {Albuquerque, New Mexico},
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institution = {Sandia National Laboratories},
title = {Software Engineering Intersections with Verification and Validation (V\&V) of High Performance Computational Science Software: Some Observations},
year = {2005}}
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acmid = {1524479},
address = {Washington, DC, USA},
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doi = {10.1109/CSEET.2009.44},
isbn = {978-0-7695-3539-5},
keywords = {bioinformatics, software engineering, education, open source, survey},
numpages = {8},
pages = {216--223},
publisher = {IEEE Computer Society},
series = {CSEET '09},
title = {Software Engineering Education for Bioinformatics},
url = {https://doi.org/10.1109/CSEET.2009.44},
year = {2009},
bdsk-url-1 = {https://doi.org/10.1109/CSEET.2009.44}}
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author = {Van Gorp, Pieter and Mazanek, Steffen},
doi = {10.1016/j.procs.2011.04.062},
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journal = {Procedia Computer Science},
keywords = {active papers,replication,tools},
mendeley-tags = {active papers,replication,tools},
month = jan,
pages = {589--597},
title = {SHARE: a web portal for creating and sharing executable research papers},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1877050911001207},
volume = {4},
year = {2011},
bdsk-url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S1877050911001207},
bdsk-url-2 = {https://doi.org/10.1016/j.procs.2011.04.062}}
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author = {Vigder, Mark and Stewart, Darlene and Singer Janice},
date-modified = {2018-05-19 18:00:49 +0000},
month = may,
title = {Software Automation in Scientific Research Organizations},
year = {2008}}
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issue_date = {January 2013},
journal = {Environ. Model. Softw.},
keywords = {Calibration, Components, Integral modeling, Integrated modeling, Modularity, Module linking},
month = jan,
number = {C},
numpages = {10},
pages = {149--158},
publisher = {Elsevier Science Publishers B. V.},
title = {'Integronsters', Integral and Integrated Modeling},
url = {http://dx.doi.org/10.1016/j.envsoft.2012.05.014},
volume = {39},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.envsoft.2012.05.014}}
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address = {Piscataway, NJ, USA},
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booktitle = {Proceedings of the 2015 International Workshop on Software Engineering for High Performance Computing in Science},
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location = {Florence, Italy},
numpages = {8},
pages = {16--23},
publisher = {IEEE Press},
series = {SE4HPCS '15},
title = {A Scientific Function Test Framework for Modular Environmental Model Development: Application to the Community Land Model},
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month = mar,
number = {4},
numpages = {29},
pages = {5--33},
publisher = {M. E. Sharpe, Inc.},
title = {Beyond Accuracy: What Data Quality Means to Data Consumers},
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volume = {12},
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bdsk-url-1 = {http://dx.doi.org/10.1080/07421222.1996.11518099}}
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author = {Weyuker, Elaine J.},
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journal = {The Computer Journal},
number = {4},
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title = {On Testing Non-Testable Programs},
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author = {Wilson, Greg and Lumsdaine, Andrew},
doi = {10.1109/MCSE.2009.206},
issn = {1521-9615},
issue_date = {November 2009},
journal = {Computing in Science and Engg.},
keywords = {Software Engineering and Computational Science},
month = nov,
number = {6},
numpages = {2},
pages = {12--13},
publisher = {IEEE Educational Activities Department},
title = {Software Engineering and Computational Science},
url = {http://dx.doi.org/10.1109/MCSE.2009.206},
volume = {11},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.206}}
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issue_date = {June 2012},
journal = {SIGMOD Rec.},
month = aug,
number = {2},
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pages = {37--46},
publisher = {ACM},
title = {Erich Neuhold Speaks out: On Industry Research Versus Academic Research, Funding Projects, and More},
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volume = {41},
year = {2012},
bdsk-url-1 = {http://doi.acm.org/10.1145/2350036.2350043},
bdsk-url-2 = {https://doi.org/10.1145/2350036.2350043}}
@inproceedings{WoollardEtAl2009,
acmid = {1556937},
address = {Washington, DC, USA},
author = {Woollard, David and Mattmann, Chris and Medvidovic, Nenad},
booktitle = {Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering},
doi = {10.1109/SECSE.2009.5069164},
isbn = {978-1-4244-3737-5},
numpages = {7},
pages = {65--71},
publisher = {IEEE Computer Society},
series = {SECSE '09},
title = {Injecting Software Architectural Constraints into Legacy Scientific Applications},
url = {http://dx.doi.org/10.1109/SECSE.2009.5069164},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1109/SECSE.2009.5069164}}
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acmid = {1907732},
address = {Piscataway, NJ, USA},
author = {{Yale Law School Roundtable on Data and Code Sharing}},
doi = {10.1109/MCSE.2010.113},
issn = {1521-9615},
issue_date = {September 2010},
journal = {Computing in Science and Engg.},
key = {{$\!\!$}},
keywords = {Computational science, Computational science, scientific method, reproducible research, data sharing, code sharing, scientific integrity, code sharing, data sharing, reproducible research, scientific integrity, scientific method},
month = sep,
number = {5},
numpages = {6},
pages = {8--13},
publisher = {IEEE Educational Activities Department},
title = {Reproducible Research},
url = {http://dx.doi.org/10.1109/MCSE.2010.113},
volume = {12},
year = {2010},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2010.113}}
@inproceedings{PintoEtAl2018,
abstract = {Although the goal of scientists is to do science, not to develop software, many scientists have extended their roles to include software development to their skills. However, since scientists have different background, it remains unclear how do they perceive software engineering practices or how do they acquire software engineering knowledge. In this paper we conducted an external replication of one influential 10 years paper about how scientists develop and use scientific software. In particular, we employed the same method (an on-line questionnaire) in a different population (R developers). When analyzing the more than 1,572 responses received, enriched with data gathered from their GitHub repositories, we correlated our findings with the original study. We found that the results were consistent in many ways, including: (1) scientists that develop software work mostly alone, (2) they decide themselves what they want to work on next, and (3) most of what they learnt came from self-study, rather than a formal education. However, we also uncover new facts, such as: some of the ``pain points'' regarding software development are not related to technical activities (e.g., interruptions, lack of collaborators, and lack of a reward system play a role). Our replication can help researchers, practitioners, and educators to better focus their efforts on topics that are important to the scientific community that develops software.},
author = {Gustavo Pinto and Igor Wiese and Luis Felipe Dias},
booktitle = {Proceedings of 25th IEEE International Conference on Software Analysis, Evolution and Reengineering},
date-added = {2018-04-11 14:32:49 +0000},
date-modified = {2022-01-12 14:10:14 -0500},
doi = {10.1109/SANER.2018.8330263},
month = feb,
pages = {582-591},
title = {How Do Scientists Develop and Use Scientific Software? An External Replication},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1109/SANER.2018.8330263}}
@techreport{ChenEtAl1998,
author = {Chen TY, Cheung SC, Yiu SM},
date-added = {2018-04-16 21:10:07 +0000},
date-modified = {2018-04-16 21:11:47 +0000},
institution = {Department of Computer Science, Hong Kong University of Science and Technology},
number = {HKUST-CS98-01},
title = {Metamorphic testing: a new approach for generating next test cases},
type = {Technical Report},
year = {1998},
bdsk-file-1 = {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}}
@article{BenureauAndRougier2017,
abstract = {- there isn't one},
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170808205B},
annote = {``A re-runnable code is one that can be run again when needed, and in particular more than the one time that was needed to produce the results. It is important to notice that the re-runnability of a code is not an intrinsic property. Rather, it depends on the context, and becomes increasingly difficult as the code ages. Therefore, to be and remain re-runnable on other researchers' computers, a re-runnable code should describe---with enough details to be recreated---an execution environment in which it is executable. ``
``The code is running and producing the expected results. The next step is to make sure that you can pro-
duce the same output over successive runs of your program. In other words, the next step is to make your program deterministic, producing repeatable output. Repeatability is valuable. If a run of the program produces a particularly puzzling result, repeatability allows you to scrutinize any step of the execution of the program by re-running it again with extraneous prints, or inside a debugger. Repeata- bility is also useful to prove that the program did indeed produce the published results. Repeatability is not always possible or easy (Diethelm, 2012; Courte`s & Wurmus, 2015). But for sequential programs not depending on analog inputs, it often comes down to controlling the initialization of the pseudo- random number generators (RNG).''
``A result is said to be reproducible if another researcher can take the original code and input data, execute it, and re-obtain the same result ``
``To recap, reproducibility implies re-runnability and repeatability and availability, yet imposes ad- ditional conditions. Dependencies and platforms must be described as precisely and as specifically as possible. Parameters values and inputs should accompany the result files. The data and scripts behind the graphs must be published. Unit tests are a good way to embed self-diagnostics of reproducibility in the code. Reproducibility is hard, yet tremendously necessary.''
``Making your program reusable means it can be easily used, and modified, by you and other people, in-
side and outside your lab.''
``Replicability is the implicit assumption that any article that does not provide the code source makes: that the description it provides of the algorithms is sufficiently precise and complete to re-obtain the results it presents''},
archiveprefix = {arXiv},
author = {{Benureau}, F. and {Rougier}, N.},
date-added = {2018-04-04 10:59:34 +0000},
date-modified = {2022-02-25 18:14:33 -0500},
eprint = {1708.08205},
journal = {ArXiv e-prints},
keywords = {Computer Science - General Literature, Computer Science - Computers and Society},
month = aug,
primaryclass = {cs.GL},
title = {{Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions}},
year = 2017,
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@article{DaviesEtAl2014,
author = {Jim Davies and Jeremy Gibbons and Steve Harris and Charles Crichton},
date-added = {2018-04-03 17:19:39 +0000},
date-modified = {2018-04-03 17:19:51 +0000},
doi = {10.1016/j.scico.2013.02.010},
journal = {Science of Computer Programming},
month = sep,
pages = {126-143},
title = {The CancerGrid Experience: Metadata-Based Model-Driven Engineering for Clinical Trials},
url = {http://www.comlab.ox.ac.uk/people/jeremy.gibbons/publications/cancergrid.pdf},
volume = {89B},
year = {2014},
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bdsk-url-1 = {http://www.comlab.ox.ac.uk/people/jeremy.gibbons/publications/cancergrid.pdf},
bdsk-url-2 = {https://doi.org/10.1016/j.scico.2013.02.010}}
@misc{SmithEtAl2018_arXivGIS,
author = {W. Spencer Smith and Adam Lazzarato and Jacques Carette},
date-added = {2018-02-13 20:38:25 +0000},
date-modified = {2018-02-22 05:36:01 +0000},
howpublished = {\url{https://arxiv.org/abs/1802.03422}},
month = feb,
title = {State of the Practice for {GIS} Software},
year = {2018},
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@inproceedings{Bartlett2009,
author = {Roscoe A. Bartlett},
booktitle = {Software Engineering for Computational Science and Engineering},
pages = {35--42},
publisher = {IEEE},
title = {Integration strategies for computational science \& engineering},
year = {2009}}
@article{BechhoferEtAl2013,
acmid = {2405937},
address = {Amsterdam, The Netherlands, The Netherlands},
author = {Bechhofer, Sean and Buchan, Iain and De Roure, David and Missier, Paolo and Ainsworth, John and Bhagat, Jiten and Couch, Philip and Cruickshank, Don and Delderfield, Mark and Dunlop, Ian and Gamble, Matthew and Michaelides, Danius and Owen, Stuart and Newman, David and Sufi, Shoaib and Goble, Carole},
doi = {10.1016/j.future.2011.08.004},
issn = {0167-739X},
issue_date = {February, 2013},
journal = {Future Gener. Comput. Syst.},
keywords = {Linked data, Publishing, Reproducibility, Research object, Reuse, Sharing},
month = feb,
number = {2},
numpages = {13},
pages = {599--611},
publisher = {Elsevier Science Publishers B. V.},
title = {Why Linked Data is Not Enough for Scientists},
url = {http://dx.doi.org/10.1016/j.future.2011.08.004},
volume = {29},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.future.2011.08.004}}
@book{BeckAndAndres2004,
author = {Beck, Kent and Andres, Cynthia},
isbn = {0321278658},
publisher = {Addison-Wesley Professional},
title = {Extreme Programming Explained: Embrace Change (2nd Edition)},
year = {2004}}
@book{BergdahlEtAl2007,
address = {Wiesbaden},
author = {Mats Bergdahl and Manfred Ehling and Eva Elvers and Erika F{\"o}ldesi and Thomas K{\"o}rner and Andrea Kron and Kornelia Mag and Peter Lohau{\ss} and Vera Morais and Anja Nimmergut and Hans Viggo S{\ae}b{\o} and Ulrike Timm and Maria Jo ao Zilh{\~a}o},
publisher = {European Commission},
title = {Handbook on Data Quality Assessment Methods and Tools},
year = {2007}}
@book{Brooks1995,
address = {Boston, MA, USA},
author = {Frederick P. Brooks, Jr.},
edition = {9},
isbn = {0-201-83595-9},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
title = {The Mythical Man-month (Anniversary Ed.)},
year = {1995}}
@article{BernholdtEtAl2005,
author = {David Bernholdt and Shishir Bharathi and David Brown and Kasidit Chanchio and Meili Chen and Ann Chervenak and Luca Cinquini and Bob Drach and Ian Foster and Peter Fox and Jose Garcia and Carl Kesselman and Rob Markel and Don Middleton and Veronika Nefedova and Line Pouchard and Arie Shoshani and Alex Sim and Gary Strand and Dean Williams},
journal = {Proc. IEEE},
month = mar,
number = {3},
pages = {485---494},
title = {The earth system grid: Supporting the next generation of climate modeling research},
volume = {93},
year = {2005}}
@book{BoisvertAndTang2001,
booktitle = {Proceedings of the IFIP TC2/WG2.5 Working Conference on the Architecture of Scientific Software},
editor = {Ronald F. Boisvert and Ping Tak Peter Tang},
publisher = {Springer},
series = {IFIP Advances in Information and Communication Technology},
title = {The Architecture of Scientific Software},
volume = {60},
year = {2001}}
@article{Blom2012,
author = {Martin Blom},
journal = {Procedia Computer Science},
number = {1},
pages = {1511--1517},
title = {{Is scrum and XP suitable for CSE development?}},
volume = {1},
year = {2012}}
@inproceedings{BetzAndWalker2013,
author = {R. M. Betz and R. C. Walker},
booktitle = {2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)},
doi = {10.1109/SECSE.2013.6615101},
keywords = {chemistry computing;integrated software;software engineering;software packages;user interfaces;AMBER;Web-based interface;benchmark information;computational chemistry software package;computational science projects;continuous integration server;continuous integration software;failure information;molecular dynamics software package;software engineering;Buildings;Graphics processing units;Hardware;Servers;Testing},
month = may,
pages = {68-74},
title = {Implementing continuous integration software in an established computational chemistry software package},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2013.6615101}}
@article{Billie2002,
author = {Charles Billie},
doi = {10.1109/5992.998640},
issn = {1521-9615},
journal = {Computing in Science Engineering},
keywords = {data structures;digital simulation;natural sciences computing;object-oriented programming;data structures;digital simulation;dynamic simulation;hydrodynamic chemistry tracers;object oriented software;scientific software;software patterns;Application software;Data structures;Object oriented modeling;Pattern analysis;Programming profession;Software architecture;Software design;Software maintenance;Software reusability;Software systems},
month = may,
number = {3},
pages = {48-53},
title = {Patterns in scientific software: An introduction},
volume = {4},
year = {2002},
bdsk-url-1 = {https://doi.org/10.1109/5992.998640}}
@techreport{BlackburnEtAl2012,
author = {Stephen M. Blackburn and Amer Diwan and Matthias Hauswirth and Peter F. Sweeney and Jos Nelson Amaral and Vlastimil Babka and Walter Binder and Tim Brecht and Lubomr Bulej and Lieven Eeckhout and Sebastian Fischmeister and Daniel Frampton and Robin Garner and Laurie J. Hendren and Andy Georges and Michael Hind and Antony L. Hosking and Richard E. Jones and Tomas Kalibera and Philippe Moret and Victor Pankratius and Nathaniel Nystrom and Petr Tuma},
note = {Evaluate Collaboratory},
title = {Can You Trust Your Experimental Results?},
type = {Technical Report},
year = {2012}}
@article{CluneAndRood2011,
acmid = {2068553},
address = {Los Alamitos, CA, USA},
author = {Thomas L. Clune and Richard B. Rood},
doi = {10.1109/MS.2011.117},
issn = {0740-7459},
issue_date = {November 2011},
journal = {IEEE Softw.},
keywords = {software engineering, program verification, testing strategies, testing and debugging},
month = nov,
number = {6},
numpages = {7},
pages = {49--55},
publisher = {IEEE Computer Society Press},
title = {Software Testing and Verification in Climate Model Development},
url = {http://dx.doi.org/10.1109/MS.2011.117},
volume = {28},
year = {2011},
bdsk-url-1 = {http://dx.doi.org/10.1109/MS.2011.117}}
@article{CalderEtAl2002,
abstract = {We present a case study of validating an astrophysical simulation code. Our study focuses on validating FLASH, a parallel, adaptive-mesh hydrodynamics code for studying the compressible, reactive flows found in many astrophysical environments. We describe the astrophysics problems of interest and the challenges associated with simulating these problems. We describe methodology and discuss solutions to difficulties encountered in verification and validation. We describe verification tests regularly administered to the code, present the results of new verification tests, and outline a method for testing general equations of state. We present the results of two validation tests in which we compared simulations to experimental data. The first is of a laser-driven shock propagating through a multilayer target, a configuration subject to both Rayleigh-Taylor and Richtmyer-Meshkov instabilities. The second test is a classic Rayleigh-Taylor instability, where a heavy fluid is supported against the force of gravity by a light fluid. Our simulations of the multilayer target experiments showed good agreement with the experimental results, but our simulations of the Rayleigh-Taylor instability did not agree well with the experimental results. We discuss our findings and present results of additional simulations undertaken to further investigate the Rayleigh-Taylor instability.},
author = {A. C. Calder and B. Fryxell and T. Plewa and R. Rosner and L. J. Dursi and V. G. Weirs and T. Dupont and H. F. Robey and J. O. Kane and B. A. Remington and R. P. Drake and G. Dimonte and M. Zingale and F. X. Timmes and K. Olson and P. Ricker and P. MacNeice and H. M. Tufo},
journal = {The Astrophysical Journal Supplement Series},
number = {1},
pages = {201-229},
title = {On Validating an Astrophysical Simulation Code},
url = {http://stacks.iop.org/0067-0049/143/i=1/a=201},
volume = {143},
year = {2002},
bdsk-url-1 = {http://stacks.iop.org/0067-0049/143/i=1/a=201}}
@article{Carver2009,
acmid = {2220176},
address = {Piscataway, NJ, USA},
author = {Jeffrey C. Carver},
doi = {10.1109/MCSE.2009.203},
issn = {1521-9615},
issue_date = {November 2009},
journal = {Computing in Science and Engg.},
keywords = {CSE, CSE software development, Computational science and engineering, software engineering},
month = {November/December},
number = {6},
numpages = {6},
pages = {14--19},
publisher = {IEEE Educational Activities Department},
title = {Report: The Second International Workshop on Software Engineering for CSE},
url = {http://dx.doi.org/10.1109/MCSE.2009.203},
volume = {11},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.203}}
@proceeding{Carver2009a,
editor = {Jeffrey C. Carver},
publisher = {IEEE Computer Society},
title = {Proceedings of the 2nd International Workshop on Software Engineering for Computational Science, in conjunction with the 2009 IEEE 31st International Conference on Software Engineering (ICSE'09)},
year = {2009}}
@proceeding{Carver2010,
address = {Elsevier, Amsterdam, The Netherlands},
editor = {Jeffrey C. Carver},
title = {Proceedings of the 3rd International Workshop on Software Engineering for Computational Science and Engineering},
year = {2010}}
@proceeding{Carver2011,
editor = {Jeffrey C. Carver},
publisher = {ACM},
title = {Proceedings of the 4th International Workshop on Software Engineering for Computational Science, in Conjunction with the 2011 IEEE 33rd International Conference on Software Engineering (ICSE'11)},
year = {2011}}
@proceeding{Carver2013,
editor = {Jeffrey C. Carver},
publisher = {IEEE Computer Society},
title = {Proceedings of the 5th International Workshop on Software Engineering for Computational Science, in Conjunction with the 2013 IEEE 35th International Conference on Software Engineering (ICSE'13)},
year = {2013}}
@proceeding{CarverAndChueHong2016,
editor = {Jeffrey C. Carver and Neil P. Chue Hong},
publisher = {ACM},
title = {Proceedings of the International Workshop on Software Engineering for Science (SE4Science@ICSE'16)},
year = {2016}}
@article{CarverEtAl2013,
author = {Jeffrey Carver and Dustin Heaton and Lorin Hochstein and Roscoe Bartlett},
doi = {10.1109/MCSE.2013.12},
issn = {1521-9615},
journal = {Computing in Science Engineering},
keywords = {software engineering;complex codes;software engineering practices;software engineers;software scientists;Best practices;Coding;Computational modeling;Production;Scientific computing;Software engineering;best practices;computational science;scientific computing;software engineering practices},
month = {January/February},
number = {1},
pages = {7-11},
title = {Self-Perceptions about Software Engineering: A Survey of Scientists and Engineers},
volume = {15},
year = {2013},
bdsk-file-1 = {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},
bdsk-url-1 = {https://doi.org/10.1109/MCSE.2013.12}}
@article{CastelliEtAl2013,
author = {Donatella Castelli and Paolo Manghi and Costantino Thanos},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/journals/jodl/CastelliMT13},
doi = {10.1007/s00799-013-0106-7},
journal = {Int. J. on Digital Libraries},
number = {3-4},
pages = {155--169},
timestamp = {Tue, 06 Jun 2017 22:18:14 +0200},
title = {A vision towards Scientific Communication Infrastructures - On bridging the realms of Research Digital Libraries and Scientific Data Centers},
url = {https://doi.org/10.1007/s00799-013-0106-7},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1007/s00799-013-0106-7}}
@inproceedings{ChilanaEtAl2009,
author = {Parmit K. Chilana and Carole L. Palmer and Andrew J. Ko},
booktitle = {2009 ICSE Workshop on Software Engineering for Computational Science and Engineering},
doi = {10.1109/SECSE.2009.5069165},
keywords = {bioinformatics;software engineering;bioinformatics software development;computational biology;information-seeking activities;Biochemistry;Bioinformatics;Biological information theory;Biology computing;Computational biology;North America;Open source software;Programming;Sequences;Software tools},
month = may,
pages = {72-79},
title = {Comparing bioinformatics software development by computer scientists and biologists: An exploratory study},
year = {2009},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2009.5069165}}
@inproceedings{CickovskiEtAl2008,
author = {Trevor Cickovski and Thierry Matthey and Jes{\'u}s A. Izaguirre},
booktitle = {Proceedings of the Conference for the Association for Software Testing},
title = {Design patterns for generic object-oriented scientific software},
year = {2008}}
@inproceedings{ClaerboutAndKarrenbach1992,
author = {Jon F. Claerbout and Martin Karrenbach},
booktitle = {Proceedings of the 1992 Meeting of the Society of Exploration Geophysics},
doi = {10.1190/1.1822162},
eprint = {https://library.seg.org/doi/pdf/10.1190/1.1822162},
title = {Electronic documents give reproducible research a new meaning},
url = {https://library.seg.org/doi/abs/10.1190/1.1822162},
year = {1992},
bdsk-url-1 = {https://library.seg.org/doi/abs/10.1190/1.1822162},
bdsk-url-2 = {https://doi.org/10.1190/1.1822162}}
@techreport{CMMIProductTeam2010,
address = {Pittsburgh, PA},
author = {{CMMI Product Team}},
institution = {Software Engineering Institute, Carnegie Mellon University},
title = {{CMMI for Development}},
type = {Technical Report},
year = {2010}}
@article{ColbergEtAl2013,
author = {Christian Colberg and Todd Proebsting and Gina Moraila and Akash Shankaran and Zuoming Shi and Alex M. Warren},
title = {Measuring Reproducibility in Computer Systems Research},
year = {2013}}
@article{CrichtonEtAl2012,
author = {Daniel J. Crichton and Chris A. Mattmann and Luca Cinquini and Amy Braverman and Duane Waliser and Michael Gunson and Andrew F. Hart and Cameron E. Goodale and Peter Lean and Jinwon Kim},
doi = {10.1109/MS.2012.21},
issn = {0740-7459},
journal = {IEEE Software},
keywords = {artificial satellites;climate mitigation;ecology;environmental science computing;meta data;remote sensing;satellite navigation;service-oriented architecture;software tools;5th assessment report;AR5;Earth climate processes;IPCC;climate model;climate-modeling community;distributed ecosystem;economic benefit;globally gridded datasets;heterogeneous data file formats;information aggregation;information navigation;intergovernmental panel on climate change;metadata formats;political benefit;remote sensing experts;satellite data;satellite observations sharing;societal benefit;software engineering challenges;software infrastructure;software services;software tools;swath-based remotely sensed data;Computational modeling;Data models;Distributed databases;Internet;Meteorology;Remote sensing;Satellite communication;Software development;distributed applications;domain-specific architectures;evolving Internet applications},
month = {September/October},
number = {5},
pages = {73-81},
title = {Sharing Satellite Observations with the Climate-Modeling Community: Software and Architecture},
volume = {29},
year = {2012},
bdsk-url-1 = {https://doi.org/10.1109/MS.2012.21}}
@article{Doherty2007,
author = {Tom Doherty},
month = sep,
title = {Integration of the ATLAS VOMS system with the ATLAS Metadata Interface},
year = {2007}}
@inproceedings{DubeyEtAl2013,
author = {Anshu Dubey and Katie Antypas and Alan Calder and Bruce Fryxell and Don Lamb and Paul Ricker and Lynn Reid and Katherine Riley and Robert Rosner and Andrew Siegel and Francis Timmes and Natalia Vladimirova and Klaus Weide},
booktitle = {2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)},
doi = {10.1109/SECSE.2013.6615093},
keywords = {digital simulation;physics computing;software maintenance;FLASH code;extensible scientific simulation software system;modular software system;multiphysics simulation code;software development process;software evolution process;Astrophysics;Communities;Computer architecture;Databases;Educational institutions;Production;Software;FLASH code;adaptive mesh;case study;community code;software evolution},
month = may,
pages = {1-8},
title = {The Software development process of FLASH, a multiphysics simulation code},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2013.6615093}}
@inproceedings{DanielEtAl2007,
acmid = {1287651},
author = {Brett Daniel and Danny Dig and Kely Garcia and Darko Marinov},
booktitle = {Proceedings of the the 6th Joint Meeting of the European Software Engineering Conference and the ACM SIGSOFT Symposium on The Foundations of Software Engineering},
doi = {10.1145/1287624.1287651},
isbn = {978-1-59593-811-4},
keywords = {automated testing, bounded-exhaustive testing, imperative generators, refactoring engines, test data generation},
location = {Dubrovnik, Croatia},
numpages = {10},
pages = {185--194},
publisher = {ACM Press},
series = {ESEC-FSE '07},
title = {Automated Testing of Refactoring Engines},
url = {http://doi.acm.org/10.1145/1287624.1287651},
year = {2007},
bdsk-url-1 = {http://doi.acm.org/10.1145/1287624.1287651},
bdsk-url-2 = {https://doi.org/10.1145/1287624.1287651}}
@inproceedings{StolEtAl2016,
author = {Stol, Klaas-Jan and Ralph, Paul and Fitzgerald, Brian},
booktitle = {Proceedings of 38th International Conference on Software Engineering},
date-added = {2018-02-10 01:36:09 +0000},
date-modified = {2018-02-10 01:38:29 +0000},
month = may,
title = {Grounded Theory in Software Engineering Research: A Critical Review and Guidelines},
year = {2016},
bdsk-file-1 = {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}}
@inproceedings{deOliveiraEtAl2013,
author = {Diego Caminha B. de Oliveira and Alan Humphrey and Zvonimir Rakamari and Qingyu Meng and Martin Berzins and Ganesh Gopalakrishnan},
booktitle = {2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)},
doi = {10.1109/SECSE.2013.6615102},
keywords = {chemically reactive flow; combustion; crystallisation; formal verification; graph theory; multiprocessing systems; parallel processing; problem solving; task analysis; turbulence; gpu; hpc systems testing; urv project; uintah runtime verification; asynchronous task graph based problem solving environment; fluid structure interaction; formal correctness checking method; formal method; high performance computing; innovative design feature; million cpu core; million core problem solving environment; multicore cpu; turbulent combustion; computer bugs; graphics processing units; problem-solving; runtime; schedules; testing},
month = may,
pages = {75--83},
title = {Practical formal correctness checking of million-core problem solving environments for HPC},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2013.6615102}}
@article{DecykEtAl1997,
acmid = {1239847},
address = {Amsterdam, The Netherlands, The Netherlands},
author = {Viktor K. Decyk and Charles D. Norton and Bolesaw K. Szymanski},
doi = {10.1155/1997/570746},
issn = {1058-9244},
issue_date = {October 1997},
journal = {Sci. Program.},
month = oct,
number = {4},
numpages = {28},
pages = {363--390},
publisher = {IOS Press},
title = {How to Express C++ Concepts in Fortran90},
url = {http://dx.doi.org/10.1155/1997/570746},
volume = {6},
year = {1997},
bdsk-url-1 = {http://dx.doi.org/10.1155/1997/570746}}
@article{DeMilloEtAl1978,
author = {Richard A. DeMillo and Richard J. Lipton and Frederick G. Sayward},
doi = {10.1109/C-M.1978.218136},
issn = {0018-9162},
journal = {IEEE Computer},
keywords = {Computer bugs;Computer errors;Error analysis;Error correction;Process design;Programming profession;Software debugging;Software reliability;System testing},
month = apr,
number = {4},
pages = {34-41},
title = {Hints on Test Data Selection: Help for the Practicing Programmer},
volume = {11},
year = {1978},
bdsk-url-1 = {https://doi.org/10.1109/C-M.1978.218136}}
@mastersthesis{Deshpande2011,
author = {Shweta Deshpande},
school = {Ohio State University},
title = {A Study of Software Engineering Practices for Micro Teams},
year = {2011}}
@inproceedings{Parnas1975,
abstract = {This talk will describe some methods which have been used to produce a family of related software products using many relatively unskilled programmers. The primary topics of the talk will be: 1. An interpretation of the word ``structure'' with regard to software; 2. Criteria to be used in decomposing software into modules; 3. Problems and techniques with regard to software module specifications. },
address = {Berlin, Heidelberg},
author = {Parnas, D. L.},
booktitle = {Programming Methodology},
date-added = {2018-02-06 19:36:32 +0000},
date-modified = {2018-02-06 19:36:43 +0000},
editor = {Hackl, Clemens E.},
isbn = {978-3-540-37401-5},
pages = {225--235},
publisher = {Springer Berlin Heidelberg},
title = {Software engineering or methods for the multi-person construction of multi-version programs},
year = {1975},
bdsk-file-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAYLi4vLi4vcHViL1Bhcm5hczE5NzUucGRmTxEBRAAAAAABRAACAAAMTWFjaW50b3NoIEhEAAAAAAAAAAAAAAAAAAAAAAAAAEJEAAH/////DlBhcm5hczE5NzUucGRmAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAP////8AAAAAAAAAAAAAAAAAAgACAAAKIGN1AAAAAAAAAAAAAAAAAANwdWIAAAIAJy86VXNlcnM6c21pdGhzOlJlcG9zOnB1YjpQYXJuYXMxOTc1LnBkZgAADgAeAA4AUABhAHIAbgBhAHMAMQA5ADcANQAuAHAAZABmAA8AGgAMAE0AYQBjAGkAbgB0AG8AcwBoACAASABEABIAJVVzZXJzL3NtaXRocy9SZXBvcy9wdWIvUGFybmFzMTk3NS5wZGYAABMAAS8AABUAAgAN//8AAAAIAA0AGgAkAD8AAAAAAAACAQAAAAAAAAAFAAAAAAAAAAAAAAAAAAABhw==}}
@misc{Wilson2009,
author = {Greg Wilson},
date-added = {2018-02-05 04:40:07 +0000},
date-modified = {2018-02-05 04:41:09 +0000},
howpublished = {\url{https://www.slideshare.net/gvwilson/bits-of-evidence-2338367}},
month = oct,
title = {Bits of Evidence: {W}hat we actually know about software development, and why we believe it's true},
year = {2009}}
@article{StewartEtAl2017,
annote = {- report discusses important CS goals
- computer science problem of dealing with massive amounts of data
- improved efficiency, scalability and performance
- training
- explain and quantify how huge their problems is
- sustainability seems to mean a move to Python},
archiveprefix = {arXiv},
author = {Graeme Stewart and others},
date-added = {2018-02-04 22:24:37 +0000},
date-modified = {2018-02-04 22:54:56 +0000},
eprint = {1712.06982},
journal = {arXiv},
primaryclass = {physics.comp-ph},
reportnumber = {HSF-CWP-2017-001, HSF-CWP-2017-01, FERMILAB-PUB-17-607-CD},
slaccitation = {%%CITATION = ARXIV:1712.06982;%%},
title = {{A Roadmap for HEP Software and Computing R\&D for the 2020s}},
year = {2017},
bdsk-file-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAdLi4vLi4vcHViL1N0ZXdhcnRFdEFsMjAxNy5wZGZPEQFWAAAAAAFWAAIAAAxNYWNpbnRvc2ggSEQAAAAAAAAAAAAAAAAAAAAAAAAAQkQAAf////8TU3Rld2FydEV0QWwyMDE3LnBkZgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/////wAAAAAAAAAAAAAAAAACAAIAAAogY3UAAAAAAAAAAAAAAAAAA3B1YgAAAgAsLzpVc2VyczpzbWl0aHM6UmVwb3M6cHViOlN0ZXdhcnRFdEFsMjAxNy5wZGYADgAoABMAUwB0AGUAdwBhAHIAdABFAHQAQQBsADIAMAAxADcALgBwAGQAZgAPABoADABNAGEAYwBpAG4AdABvAHMAaAAgAEgARAASACpVc2Vycy9zbWl0aHMvUmVwb3MvcHViL1N0ZXdhcnRFdEFsMjAxNy5wZGYAEwABLwAAFQACAA3//wAAAAgADQAaACQARAAAAAAAAAIBAAAAAAAAAAUAAAAAAAAAAAAAAAAAAAGe}}
@article{Obreshkov2011,
abstract = {ATLAS is one of the largest collaborations in the physical sciences and involves 3000 scientists and engineers from 174 institutions in 38 countries. The geographically dispersed developer community has produced a large amount of software which is organized in 10 projects. In this presentation we discuss how the software is built on a variety of compiler and operating system combinations every night. File level and package level parallelism together with multi-core build servers are used to perform fast builds of the different platforms in several branches. We discuss the different tools involved during the software release build process and also the various mechanisms implemented to provide performance gains and error detection and retry mechanisms in order to counteract network and other instabilities that would otherwise degrade the robustness of the system. The goal is to provide high quality software built as fast as possible ready for final validation and deployment.},
author = {Emil Obreshkov and the ATLAS Collaboration},
date-added = {2018-02-04 17:01:54 +0000},
date-modified = {2018-02-04 17:02:04 +0000},
journal = {Journal of Physics: Conference Series},
number = {4},
pages = {042017},
title = {Software release build process and components in ATLAS offline},
url = {http://stacks.iop.org/1742-6596/331/i=4/a=042017},
volume = {331},
year = {2011},
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bdsk-url-1 = {http://stacks.iop.org/1742-6596/331/i=4/a=042017}}
@book{CarverEtAl2016,
date-added = {2018-02-03 13:29:31 +0000},
date-modified = {2018-02-03 13:34:52 +0000},
editor = {Jeffrey C. Carver and Neil P. Chue Hong and George K. Thiruvathukal},
publisher = {Chapman and Hall/{CRC}},
series = {Chapman \& Hall/{CRC} Computational Science},
title = {Software Engineering for Science},
year = {2016}}
@misc{JordanEtAl2017,
author = {Kari L. Jordan and Ben Marwick and Jonah Duckles and Naupaka Zimmerman and Erin Becker},
date-added = {2018-02-02 16:06:31 +0000},
date-modified = {2018-02-02 16:06:52 +0000},
doi = {10.5281/zenodo.1043533},
month = jul,
title = {Analysis of Software Carpentry's Post-Workshop Surveys},
url = {https://doi.org/10.5281/zenodo.1043533},
year = 2017,
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bdsk-url-1 = {https://doi.org/10.5281/zenodo.1043533}}
@article{SimperlerAndWilson2015,
archiveprefix = {arXiv},
author = {Alexandra Simperler and Greg Wilson},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.org/rec/bib/journals/corr/SimperlerW15},
date-added = {2018-02-02 16:02:51 +0000},
date-modified = {2018-02-02 16:03:11 +0000},
eprint = {1506.02575},
journal = {CoRR},
timestamp = {Wed, 07 Jun 2017 14:40:27 +0200},
title = {Software Carpentry get more done in less time},
url = {http://arxiv.org/abs/1506.02575},
volume = {abs/1506.02575},
year = {2015},
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bdsk-url-1 = {http://arxiv.org/abs/1506.02575}}
@misc{Libarkin2012,
author = {J. Libarkin},
date-added = {2018-02-02 15:57:50 +0000},
date-modified = {2018-02-02 15:59:03 +0000},
howpublished = {\url{https://software-carpentry.org/files/bib/libarkin-assessment-report-2012-06.pdf}},
month = jun,
title = {Software Carpentry Workshop Evaluation},
year = {2012},
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@misc{Aranda2012,
author = {Jorge Aranda},
date-added = {2018-02-02 15:44:48 +0000},
date-modified = {2018-02-02 15:48:50 +0000},
howpublished = {\url{https://software-carpentry.org/files/bib/aranda-assessment-2012-07.pdf}},
month = jul,
title = {Software Carpentry Assessment Report},
year = {2012},
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@inproceedings{SmithEtAl2018_ICSEPoster,
author = {W. Spencer Smith and Mojdeh Sayari Nejad and Alan Wassyng},
booktitle = {ICSE 2018 Proceedings of the 40th International Conference on Software Engineering},
date-added = {2018-01-24 02:49:20 +0000},
date-modified = {2018-03-20 04:38:16 +0000},
month = may,
note = {2 pp},
title = {Assurance Cases for Scientific Computing Software (poster)},
year = {2018},
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@article{SamoulyEtAl2018,
author = {Aly Al Samouly and Chanh Nien Luong and Zhong Li and Spencer Smith and Brian Baetz and Maysara Ghaith},
date-added = {2018-01-24 02:38:29 +0000},
date-modified = {2019-01-30 16:18:19 -0500},
doi = {https://doi.org/10.1007/s12665-018-7701-2},
journal = {Environmental Earth Sciences},
number = {524},
pages = {1--12},
title = {Performance of a Multi-Model Ensemble for the Simulation of Temperature Variability Over {O}ntario, {C}anada},
volume = {77},
year = {2018},
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@article{Veldhuizen2007,
abstract = {Software is a communication system. The usual topic of commu- nication is program behavior, as encoded by programs. Domain- specific libraries are codebooks, domain-specific languages are coding schemes, and so forth. To turn metaphor into method, we adapt tools from information theory---the study of efficient communication---to probe the efficiency with which languages and libraries let us communicate programs. In previous work we devel- oped an information-theoretic analysis of software reuse in prob- lem domains. This new paper uses information theory to analyze tradeoffs in the design of components, generators, and metalan- guages. We seek answers to two questions: (1) How can we judge whether a component is over- or under-generalized? Drawing on minimum description length principles, we propose that the best component yields the most succinct representation of the use cases. (2) If we view a programming language as an assemblage of met- alanguages, each providing a complementary style of abstraction, how can these metalanguages aid or hinder us in efficiently de- scribing software? We describe a complex triangle of interactions between the power of an abstraction mechanism, the amount of reuse it enables, and the cognitive difficulty of its use.},
annote = {- uses tools from information theory to probe the tradeoffs in the design of components, generators and metalanguages
- A fruitful viewpoint for understand- ing the role of abstractions in design is that of software as a com- munication system. The subject of the communication is program behaviors, as encoded in a programming language.
Definition of parsimony (from Marriam Webster's on-line)
parsimony - economy in the use of means to an end; especially : economy of explanation in conformity with Occam's razor - the scientific law of parsimony dictates that any example of animal behavior should be interpreted at its simplest, most immediate level ---Peter Gorner
(Occam's razor states that among competing hypotheses, the one with the fewest assumptions should be selected.) Wikipedia
parsimony is related to simplicity
shows running example of summation at various levels of abstraction - uses count of tokens to estimate code length. Sums tokens to write original component and then adds cost of adaption tokens to cover all use cases.
},
archiveprefix = {arXiv},
author = {Todd L. Veldhuizen},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.org/rec/bib/journals/corr/abs-0707-4166},
date-added = {2017-12-12 13:57:16 +0000},
date-modified = {2017-12-13 13:36:49 +0000},
eprint = {0707.4166},
journal = {CoRR},
timestamp = {Wed, 07 Jun 2017 14:42:18 +0200},
title = {Parsimony Principles for Software Components and Metalanguages},
url = {http://arxiv.org/abs/0707.4166},
volume = {abs/0707.4166},
year = {2007},
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bdsk-url-1 = {http://arxiv.org/abs/0707.4166}}
@article{ShampineAndThompson2000,
author = {L. F. Shampine and S. Thompson},
date-added = {2017-12-12 11:45:43 +0000},
date-modified = {2021-11-02 12:09:10 -0400},
journal = {Computers & Mathematics With Applications},
number = {5},
pages = {43--54},
title = {Event Location for Ordinary Differential Equations},
volume = {39},
year = {2000},
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bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0898122100000456}}
@techreport{Jackson2013,
annote = {``In the design of Alloy, our modeling language, we often ap- plied what we called the ``fork-in-the-road principle'', which holds that if (when exploring the design space) you reach a fork in the road, where both choices---turning to the le or turning to the right---seem equally plausible, you should turn back. If either choice seemed equally plausible to the designers at design time, they would surely seem equally plausible to users trying to guess how the language is designed (in the case of the language, how to form a construct or what its meaning would be), thus making the language error prone and hard to use. Such a fork in the road might be seen as evidence of a lack of integrity; when a design has a strong core, later decisions o en seem to follow almost inevitably, as a con- sequence of earlier and more fundamental decisions (and of the principles that they estab- lished, explicitly or implicitly).''
- concepts might apply to chunks in scientific knowledge - theory, data definition, general definition, instance model, assumption etc.
},
author = {Daniel Jackson},
date-added = {2017-11-29 21:33:48 +0000},
date-modified = {2017-11-29 21:33:48 +0000},
institution = {CSAIL, MIT},
month = aug,
number = {MIT-CSAIL-TR-2013-020},
title = {Conceptual Design of Software: A Research Agenda},
url_paper = {pubs/2013/conceptual-research-agenda-2013.pdf},
year = {2013},
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@misc{CummaudoEtAl2019,
abstract = {Background: Good API documentation facilities the development process, improving productivity and quality. While the topic of API documentation quality has been of interest for the last two decades, there have been few studies to map the specific constructs needed to create a good document. In effect, we still need a structured taxonomy against which to capture knowledge. Aims: This study reports emerging results of a systematic mapping study. We capture key conclusions from previous studies that assess API documentation quality, and synthesise the results into a single framework. Method: By conducting a systematic review of 21 key works, we have developed a five dimensional taxonomy based on 34 categorised weighted recommendations. Results: All studies utilise field study techniques to arrive at their recommendations, with seven studies employing some form of interview and questionnaire, and four conducting documentation analysis. The taxonomy we synthesise reinforces that usage description details (code snippets, tutorials, and reference documents) are generally highly weighted as helpful in API documentation, in addition to design rationale and presentation. Conclusions: We propose extensions to this study aligned to developer's utility for each of the taxonomy's categories.},
annote = {- building a taxonomy
- good documentation facilitates productivity and thus quality is better engineered
into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on this reference - it doesn't actually make the statement it is attributed to have made}},
author = {Alex Cummaudo and Rajesh Vasa and John Grundy},
date-added = {2017-11-23 16:38:57 +0000},
date-modified = {2020-06-03 15:37:56 -0400},
howpublished = {\url{https://arxiv.org/abs/1907.13260}},
month = July,
title = {What should I document? A preliminary systematic mapping study into API documentation knowledge},
year = {2019},
bdsk-url-1 = {https://arxiv.org/abs/1907.13260},
bdsk-url-2 = {https://arxiv.org/pdf/1907.13260.pdf}}
@article{Brooks1987,
acmid = {26441},
address = {Los Alamitos, CA, USA},
author = {Brooks, Jr., Frederick P.},
date-added = {2017-11-03 18:23:36 +0000},
date-modified = {2017-11-03 18:23:54 +0000},
doi = {10.1109/MC.1987.1663532},
issn = {0018-9162},
issue_date = {April 1987},
journal = {Computer},
month = apr,
number = {4},
numpages = {10},
pages = {10--19},
publisher = {IEEE Computer Society Press},
title = {No Silver Bullet Essence and Accidents of Software Engineering},
url = {http://dx.doi.org/10.1109/MC.1987.1663532},
volume = {20},
year = {1987},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MC.1987.1663532}}
@inproceedings{MeshAndHawker2013,
acmid = {2663376},
address = {Piscataway, NJ, USA},
author = {Mesh, Erika S. and Hawker, J. Scott},
booktitle = {Proceedings of the 5th International Workshop on Software Engineering for Computational Science and Engineering},
date-added = {2017-10-04 14:19:32 +0000},
date-modified = {2017-10-04 14:19:44 +0000},
isbn = {978-1-4673-6261-0},
location = {San Francisco, California},
numpages = {8},
pages = {32--39},
publisher = {IEEE Press},
series = {SE-CSE '13},
title = {Scientific Software Process Improvement Decisions: A Proposed Research Strategy},
url = {http://dl.acm.org/citation.cfm?id=2663370.2663376},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2663370.2663376}}
@incollection{CrookEtAl2013,
abstract = {Reproducible experiments are the cornerstone of science: only observations that can be independently confirmed enter the body of scientific knowledge. Computational science should excel in reproducibility, as simulations on digital computers avoid many of the small variations that are beyond the control of the experimental biologist or physicist. However, in reality, computational science has its own challenges for reproducibility: many computational scientists find it difficult to reproduce results published in the literature, and many authors have met problems replicating even the figures in their own papers. We present a distinction between different levels of replicability and reproducibility of findings in computational neuroscience. We also demonstrate that simulations of neural models can be highly sensitive to numerical details, and conclude that often it is futile to expect exact replicability of simulation results across simulator software packages. Thus, the computational neuroscience community needs to discuss how to define successful reproduction of simulation studies. Any investigation of failures to reproduce published results will benefit significantly from the ability to track the provenance of the original results. We present tools and best practices developed over the past 2 decades that facilitate provenance tracking and model sharing.},
address = {New York, NY},
author = {Crook S.M. and Davison A.P. and Plesser H.E.},
booktitle = {20 Years of Computational Neuroscience},
date-added = {2017-10-02 14:23:55 +0000},
date-modified = {2017-10-02 14:26:14 +0000},
editor = {Bower J.},
publisher = {Springer},
series = {Springer Series in Computational Neuroscience},
title = {Learning from the Past: Approaches for Reproducibility in Computational Neuroscience},
volume = {9},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1007/978-1-4614-1424-7_4}}
@inbook{CourtesAndWurmus2015,
abstract = {Support teams of high-performance computing (HPC) systems often find themselves between a rock and a hard place: on one hand, they understandably administrate these large systems in a conservative way, but on the other hand, they try to satisfy their users by deploying up-to-date tool chains as well as libraries and scientific software. HPC system users often have no guarantee that they will be able to reproduce results at a later point in time, even on the same system---software may have been upgraded, removed, or recompiled under their feet, and they have little hope of being able to reproduce the same software environment elsewhere. We present GNU Guix and the functional package management paradigm and show how it can improve reproducibility and sharing among researchers with representative use cases.},
address = {Cham},
author = {Court{\`e}s, Ludovic and Wurmus, Ricardo},
booktitle = {Euro-Par 2015: Parallel Processing Workshops: Euro-Par 2015 International Workshops, Vienna, Austria, August 24-25, 2015, Revised Selected Papers},
date-added = {2017-09-29 20:23:11 +0000},
date-modified = {2017-09-29 20:23:11 +0000},
doi = {10.1007/978-3-319-27308-2_47},
editor = {Hunold, Sascha and Costan, Alexandru and Gim{\'e}nez, Domingo and Iosup, Alexandru and Ricci, Laura and G{\'o}mez Requena, Mar{\'\i}a Engracia and Scarano, Vittorio and Varbanescu, Ana Lucia and Scott, Stephen L. and Lankes, Stefan and Weidendorfer, Josef and Alexander, Michael},
isbn = {978-3-319-27308-2},
pages = {579--591},
publisher = {Springer International Publishing},
title = {Reproducible and User-Controlled Software Environments in HPC with Guix},
url = {https://doi.org/10.1007/978-3-319-27308-2_47},
year = {2015},
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bdsk-url-1 = {https://doi.org/10.1007/978-3-319-27308-2_47},
bdsk-url-2 = {http://dx.doi.org/10.1007/978-3-319-27308-2_47}}
@article{CollbergAndProebsting2016,
abstract = {The article discusses the factors that affect the sharing of research artifacts relating to computer systems according to the authors. Topics covered include the importance of sharing research artifacts for repeatability and benefaction, the research studies the evaluated the willingness of computer science researchers in sharing code and data, and details relating to the three measures of weak repeatability determined by the authors.},
author = {COLLBERG, CHRISTIAN and PROEBSTING, TODD A.},
date-added = {2017-09-29 20:16:21 +0000},
date-modified = {2017-09-29 20:16:44 +0000},
issn = {00010782},
journal = {Communications of the ACM},
keywords = {Computer systems, Research, Computer science, Computer file sharing, Data},
number = {3},
pages = {62 - 69},
title = {Repeatability in Computer Systems Research.},
url = {http://libaccess.mcmaster.ca/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=bth&AN=113448638&site=ehost-live&scope=site},
volume = {59},
year = {2016},
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@article{Wilson1996,
acknowledgement = ack-nhfb,
author = {Gregory V. Wilson},
bibdate = {Sat Jan 9 08:57:23 MST 1999},
bibsource = {http://www.computer.org/cse/cs1998; http://www.math.utah.edu/pub/tex/bib/ieeecomputscieng.bib},
coden = {ISCEE4},
date-added = {2017-09-29 19:09:37 +0000},
date-modified = {2017-09-29 19:12:28 +0000},
doi = {http://dx.doi.org/10.1109/99.503313},
fjournal = {IEEE Computational Science \& Engineering},
issn = {1070-9924 (print), 1558-190X (electronic)},
issn-l = {1070-9924},
journal = {Computational Science and Engineering},
journal-url = {http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=99},
month = {Summer},
number = {2},
pages = {46--54},
title = {What Should Computer Scientists Teach to Physical Scientists and Engineers?},
url = {http://www.computer.org/cse/cs1998/c2046abs.htm},
volume = {3},
year = {1996},
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bdsk-url-1 = {http://dx.doi.org/10.1109/99.503313},
bdsk-url-2 = {http://www.computer.org/cse/cs1998/c2046abs.htm}}
@article{Wilson2016,
author = {Greg Wilson},
date-added = {2017-09-29 17:42:51 +0000},
date-modified = {2017-09-29 17:46:46 +0000},
journal = {F1000Research},
number = {62},
pages = {1--12},
title = {Software Carpentry: lessons learned [version 2; referees: 3 approved]},
volume = {3},
year = {2016},
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bdsk-url-1 = {http://dx.doi.org/10.12688/f1000research.3-62.v2}}
@article{LandwehrEtAl2017,
acmid = {3063218},
address = {New York, NY, USA},
author = {Landwehr, Carl and Ludewig, Jochen and Meersman, Robert and Parnas, David Lorge and Shoval, Peretz and Wand, Yair and Weiss, David and Weyuker, Elaine},
date-added = {2017-09-28 16:07:50 +0000},
date-modified = {2017-09-28 16:08:00 +0000},
doi = {10.1016/j.jss.2016.12.016},
issn = {0164-1212},
issue_date = {March 2017},
journal = {J. Syst. Softw.},
keywords = {Education, Engineering, Information systems, Software design, Software development, Software documentation, Software education},
month = mar,
number = {C},
numpages = {11},
pages = {354--364},
publisher = {Elsevier Science Inc.},
title = {Software Systems Engineering Programmes a Capability Approach},
url = {https://doi.org/10.1016/j.jss.2016.12.016},
volume = {125},
year = {2017},
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bdsk-url-1 = {https://doi.org/10.1016/j.jss.2016.12.016},
bdsk-url-2 = {http://dx.doi.org/10.1016/j.jss.2016.12.016}}
@electronic{Parnas2013_Slides,
annote = {- developers forget why they document - it is not for them!},
author = {David Lorge Parnas},
date-added = {2017-09-28 16:05:49 +0000},
date-modified = {2017-09-28 16:07:13 +0000},
title = {Software Engineering, Why And What},
urldate = {2013},
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@electronic{Parnas2009_Slides,
author = {David Lorge Parnas},
date-added = {2017-09-28 16:02:10 +0000},
date-modified = {2017-09-28 16:03:32 +0000},
title = {How Precise Documentation allows Information Hiding to Reduce Software Complexity and Increase its Agility},
url = {http://www.comp.hkbu.edu.hk/%7Epgday/2009/10th_PPT/HOSEI%20Making%20Information%20Hiding%20Work%20slides.pdf},
urldate = {2009},
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bdsk-url-1 = {http://www.comp.hkbu.edu.hk/%7Epgday/2009/10th_PPT/HOSEI%20Making%20Information%20Hiding%20Work%20slides.pdf}}
@electronic{Parnas2012_Slides,
author = {David Lorge Parnas},
date-added = {2017-09-28 15:54:48 +0000},
date-modified = {2017-09-28 15:56:36 +0000},
title = {Software Development: What is Still Missing?},
url = {https://www.research.ibm.com/haifa/Workshops/plse2012/papers/thumbs.pdf},
urldate = {2012},
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bdsk-url-1 = {https://www.research.ibm.com/haifa/Workshops/plse2012/papers/thumbs.pdf}}
@article{DeissenboeckEtAl2017,
annote = {- useful paper to look at if ever return to the exercise of measuring quality},
author = {Florian Deissenboeck and Stefan Wagner and Markus Pizka and Stefan Teuchert and Jean{-}Fran{\c{c}}ois Girard},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/corr/Deissenboeck0PT17},
date-added = {2017-09-28 14:39:03 +0000},
date-modified = {2017-09-28 14:40:47 +0000},
journal = {CoRR},
timestamp = {Sat, 05 Aug 2017 14:56:16 +0200},
title = {An Activity-Based Quality Model for Maintainability},
url = {http://arxiv.org/abs/1707.08341},
volume = {abs/1707.08341},
year = {2017},
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bdsk-url-1 = {http://arxiv.org/abs/1707.08341}}
@misc{FDA2014,
author = {{U.S. Food and Drug Administration}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {on-line},
month = dec,
title = {Infusion Pumps Total Product Life Cycle: Guidance for Industry and FDA Staff},
year = {2014},
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@mastersthesis{Nejad2017,
address = {Hamilton, ON, Canada},
author = {Mojdeh Sayari Nejad},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2019-07-12 13:56:54 -0400},
month = jul,
note = {\url{http://hdl.handle.net/11375/23075}},
school = {McMaster University},
title = {A Case Study in Assurance Case Development for Scientific Software},
year = {2017},
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@article{Wassyng2015,
author = {Alan Wassyng and Neeraj Kumar Singh and Mischa Geven and Nicholas Proscia and Hao Wang and Mark Lawford and Tom Maibaum},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/dt/WassyngSGPWLM15},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1109/MDAT.2015.2462720},
journal = {{IEEE} Design {\&} Test},
number = {5},
pages = {45--55},
timestamp = {Wed, 14 Jun 2017 01:00:00 +0200},
title = {Can Product-Specific Assurance Case Templates Be Used as Medical Device Standards?},
url = {https://doi.org/10.1109/MDAT.2015.2462720},
volume = {32},
year = {2015},
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@techreport{RinehartEtAl2015,
address = {Langley Research Centre, Hampton, Virginia},
author = {Rinehart, David J. and Knight, John C. and Rowanhill, Jonathan},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {National Aeronautics and Space Administration (NASA)},
month = jan,
number = {CR-2014-218678},
title = {Current Practices in Constructing and Evaluating Assurance Cases with Applications to Aviation},
year = {2015},
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@article{Smith2017_CISE,
author = {W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computing in Science \& Engineering},
title = {Beyond Software Carpentry},
year = {2017 (in preparation)}}
@article{SmithEtAl2017_SIAM,
author = {W. Spencer Smith and Alan Wassyng and Mojdeh Sayari Nejad},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {SIAM Journal of Scientific Computing},
title = {The Assurance Case Challenge for Scientific Computing Software},
year = {2017 (in preparation)}}
@inproceedings{SmithEtAl2017_SECSE,
author = {W. Spencer Smith and Mojdeh Sayari Nejad and Alan Wassyng},
booktitle = {Proceedings of 2017 International Workshop on Software Engineering for High Performance Computing in Computational and Data-Enabled Science and Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {1--8},
title = {Assurance Cases for Scientific Computing Software},
year = {2017 (in preparation)},
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@inproceedings{SzymczakEtAl2017,
author = {Daniel Szymczak and W. Spencer Smith and Jacques Carette and Steven Palmer},
booktitle = {Proceedings of 2017 International Workshop on Software Engineering for High Performance Computing in Computational and Data-Enabled Science and Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {1--8},
title = {Using {Drasil} for Maintainable and Reusable Scientific Software},
year = {2017 (in preparation)}}
@techreport{CDRH2002,
address = {York, England},
author = {{Center for Devices and Radiological Health, CDRH}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {{US} Department Of Health and Human Services Food and Drug Administration Center for Devices and Radiological Health Center for Biologics Evaluation and Research},
month = jan,
title = {General Principles of Software Validation; Final Guidance for Industry and {FDA} Staff},
year = {2002},
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@incollection{KanewalaAndLundgren2016,
author = {Upulee Kanewala and Anders Lundgren},
booktitle = {Software Engineering for Science},
chapter = {Examples of the Application of Traditional Software Engineering Practices to Science},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Jeffrey C. Carver and Neil Chue Hong and George Thiruvathukal},
pages = {151--174},
publisher = {Taylor \& Francis},
series = {Chapman \& Hall/{CRC} Computational Science},
title = {Automated Metamorphic Testing of Scientific Software},
year = {2016},
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@book{Knuth1992,
author = {Donald E. Knuth},
bibdate = {Tue Mar 03 12:24:41 1998},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0-937073-80-6 (paper), 0-937073-81-4 (cloth)},
isbn-13 = {978-0-937073-80-3 (paper), 978-0-937073-81-0 (cloth)},
keywords = {electronic digital computers --- programming},
lccn = {QA76.6.K644},
pages = {xv + 368},
publisher = {Center for the Study of Language and Information},
series = {CSLI Lecture Notes Number 27},
title = {Literate Programming},
url = {http://csli-www.stanford.edu/publications/literate.html},
year = {1992},
bdsk-url-1 = {http://csli-www.stanford.edu/publications/literate.html}}
@inproceedings{Smith2017Dal,
address = {Dalhousie University, Halifax, Nova Scotia, Canada},
author = {W. Spencer Smith},
booktitle = {Third Canadian Symposium in Numerical Analysis and Scientific Computing (CSNASC)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jul,
title = {A Literate Approach for Improving the Verifiability, Reusability and Reproducibility of Scientific Computing Software},
year = {2017}}
@inproceedings{Smith2017,
address = {Princeton University, New Jersey, United States},
author = {W. Spencer Smith},
booktitle = {2nd S2I2 HEP/CS Workshop},
date = {2},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = may,
title = {Generating All the Things: Using Code Generation to Transform Scientific Knowledge to Software Artifacts (Lightening Talk)},
year = {2017},
bdsk-url-1 = {https://indico.cern.ch/event/622920/contributions/2544090/subcontributions/227183/attachments/1452485/2240225/DrasilPoster.pdf}}
@inproceedings{Parnas1978,
address = {Piscataway, NJ, USA},
author = {David L. Parnas},
booktitle = {ICSE '78: Proceedings of the 3rd international conference on Software engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {none},
location = {Atlanta, Georgia, United States},
pages = {264--277},
publisher = {IEEE Press},
title = {Designing Software for Ease of Extension and Contraction},
year = {1978},
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@book{Spriggs2012,
address = {London},
author = {John Spriggs},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Springer-Verlag},
title = {{GSN} - The Goal Structuring Notation},
year = {2012},
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@techreport{CollbergEtAl2015,
address = {Tucson, AZ},
author = {Christian Collberg and Todd Proebsting and Alex M Warren},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Department of Computer Science, University of Arizona},
number = {TR 14-04},
title = {Repeatability and Benefaction in Computer Systems Research},
url = {http://repeatability.cs.arizona.edu/v2/RepeatabilityTR.pdf},
year = {2015},
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@inproceedings{HaveraaenEtAl1992,
author = {Haveraaen, Magne and Madsen, Victor and Munthe-Kaas, Hans},
booktitle = {Norsk Informatikk Konferanse},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {55--68},
title = {Algebraic programming technology for partial differential equations},
volume = {92},
year = {1992}}
@article{BientinesiEtAl2005,
acmid = {1055533},
address = {New York, NY, USA},
author = {Bientinesi, Paolo and Quintana-Ort\'{\i}, Enrique S. and {v}an~{d}e~{G}eijn, Robert A.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1055531.1055533},
issn = {0098-3500},
issue_date = {March 2005},
journal = {ACM Transactions on Mathematical Software},
keywords = {Application program interfaces, formal derivation, high-performance libraries, linear algebra},
month = mar,
number = {1},
numpages = {33},
pages = {27--59},
publisher = {ACM},
title = {Representing linear algebra algorithms in code: the {FLAME} application program interfaces},
url = {http://doi.acm.org/10.1145/1055531.1055533},
volume = {31},
year = {2005},
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bdsk-url-2 = {http://dx.doi.org/10.1145/1055531.105553},
bdsk-url-3 = {http://dx.doi.org/10.1145/1055531.1055533}}
@inproceedings{Smith2016CSE,
address = {McMaster University, Hamilton, Ontario},
author = {% Spencer Smith},
booktitle = {Computational Science and Engineering (CSE) Seminars},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = nov,
title = {The {Drasil} Framework for Literate Scientific Software},
year = {2016},
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@inproceedings{Wilson2013,
acmid = {2508189},
address = {New York, NY, USA},
author = {Wilson, Gregory V.},
booktitle = {Proceedings of the 2013 Companion Publication for Conference on Systems, Programming, \&\#38; Applications: Software for Humanity},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2508075.2508189},
isbn = {978-1-4503-1995-9},
keywords = {academic-industrial collaboration},
location = {Indianapolis, Indiana, USA},
numpages = {2},
pages = {3--4},
publisher = {ACM},
series = {SPLASH '13},
title = {Two Solitudes},
url = {http://doi.acm.org/10.1145/2508075.2508189},
year = {2013},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2508075.2508189},
bdsk-url-2 = {http://dx.doi.org/10.1145/2508075.2508189},
bdsk-url-3 = {http://www.slideshare.net/gvwilson/splash-2013}}
@mastersthesis{Jegatheesan2016,
address = {Hamilton, Ontario, Canada},
author = {Thulasi Jegatheesan},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jul,
school = {McMaster University},
title = {Case Studies in Document Driven Design of Scientific Computing Software},
year = {2016},
bdsk-file-1 = {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},
bdsk-url-1 = {https://macsphere.mcmaster.ca/handle/11375/20454}}
@article{LeVequeEtAl2012,
abstract = {{This article considers the obstacles involved in creating reproducible computational research as well as some efforts and approaches to overcome them.}},
author = {LeVeque, Randall and Mitchell, Ian and Stodden, Victoria},
citeulike-article-id = {10898423},
citeulike-linkout-0 = {http://doi.ieeecomputersociety.org/10.1109/MCSE.2012.38},
citeulike-linkout-1 = {http://dx.doi.org/10.1109/mcse.2012.38},
citeulike-linkout-2 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=6171147},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
day = {01},
doi = {10.1109/mcse.2012.38},
issn = {1521-9615},
journal = {Computing in Science and Engineering},
keywords = {reproducibility},
month = jul,
number = {4},
pages = {13--17},
posted-at = {2013-12-12 15:38:48},
priority = {2},
publisher = {IEEE CS and the AIP},
title = {{Reproducible research for scientific computing: Tools and strategies for changing the culture}},
url = {http://dx.doi.org/10.1109/mcse.2012.38},
volume = {14},
year = {2012},
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bdsk-url-1 = {http://dx.doi.org/10.1109/mcse.2012.38}}
@article{Palinscar1998,
abstract = {{Social constructivist perspectives focus on the interdependence of social and individual processes in the co-construction of knowledge. After the impetus for understanding the influence of social and cultural factors on cognition is reviewed, mechanisms hypothesized to account for learning from this perspective are identified, drawing from Piagetian and Vygotskian accounts. The empirical research reviewed illustrates (a) the application of institutional analyses to investigate schooling as a cultural process, (b) the application of interpersonal analyses to examine how interactions promote cognition and learning, and (c) discursive analyses examining and manipulating the patterns and opportunities in instructional conversation. The review concludes with a discussion of the application of this perspective to selected contemporary issues, including: acquiring expertise across domains, assessment, educational equity, and educational reform.}},
author = {Palincsar, Sullivan A.},
citeulike-article-id = {2487065},
citeulike-linkout-0 = {http://www.annualreviews.org/doi/abs/10.1146/annurev.psych.49.1.345},
citeulike-linkout-1 = {http://dx.doi.org/10.1146/annurev.psych.49.1.345},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1146/annurev.psych.49.1.345},
journal = {Annual Review of Psychology},
keywords = {constructivist, education, journal-annual-review-psychology, learning, social, teaching, theory},
number = {1},
pages = {345--375},
posted-at = {2008-08-12 01:49:13},
priority = {3},
title = {{Social Constructivist Perspectives on Teaching and Learning}},
url = {http://dx.doi.org/10.1146/annurev.psych.49.1.345},
volume = {49},
year = {1998},
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bdsk-url-1 = {http://dx.doi.org/10.1146/annurev.psych.49.1.345}}
@book{OpieAndSikes2004,
author = {Opie, C. and Sikes, P.J.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {9780761970026},
lccn = {2003109262},
publisher = {SAGE Publications},
title = {Doing Educational Research},
url = {https://books.google.ca/books?id=XjBJltyWTzAC},
year = {2004},
bdsk-url-1 = {https://books.google.ca/books?id=XjBJltyWTzAC}}
@article{ConnollyEtAl2012,
author = {Connolly, Thomas M and Boyle, Elizabeth A and MacArthur, Ewan and Hainey, Thomas and Boyle, James M},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computers \& Education},
number = {2},
pages = {661--686},
publisher = {Elsevier},
title = {A systematic literature review of empirical evidence on computer games and serious games},
volume = {59},
year = {2012},
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@article{WuEtAl2013,
author = {Wu, Hsin-Kai and Lee, Silvia Wen-Yu and Chang, Hsin-Yi and Liang, Jyh-Chong},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computers \& Education},
pages = {41--49},
publisher = {Elsevier},
title = {Current status, opportunities and challenges of augmented reality in education},
volume = {62},
year = {2013},
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@article{WoutersEtAl2013,
author = {Wouters, Pieter and Van Nimwegen, Christof and Van Oostendorp, Herre and Van Der Spek, Erik D},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Educational Psychology},
number = {2},
pages = {249},
publisher = {American Psychological Association},
title = {A meta-analysis of the cognitive and motivational effects of serious games.},
volume = {105},
year = {2013},
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@article{AnnettaEtAl2009,
author = {Annetta, Leonard A and Minogue, James and Holmes, Shawn Y and Cheng, Meng-Tzu},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computers \& Education},
number = {1},
pages = {74--85},
publisher = {Elsevier},
title = {Investigating the impact of video games on high school students' engagement and learning about genetics},
volume = {53},
year = {2009},
bdsk-file-1 = {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}}
@article{ChengAndTsai2013,
author = {Cheng, Kun-Hung and Tsai, Chin-Chung},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Science Education and Technology},
number = {4},
pages = {449--462},
publisher = {Springer},
title = {Affordances of augmented reality in science learning: Suggestions for future research},
volume = {22},
year = {2013},
bdsk-file-1 = {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}}
@article{RosenbaumEtAl2007,
author = {Rosenbaum, Eric and Klopfer, Eric and Perry, Judy},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Science Education and Technology},
number = {1},
pages = {31--45},
publisher = {Springer},
title = {On location learning: Authentic applied science with networked augmented realities},
volume = {16},
year = {2007},
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@inproceedings{Smith2016PASC,
address = {Lausanne Switzerland},
author = {%Spencer Smith},
booktitle = {{Platform for Advanced Scientific Computing Conference, PASC 2016, Minisymposium, Software Engineering Meets Scientific Computing: Generality, Reusablity and Performance for Scientific Software Platforms {I}: Engineering Methodologies and Development Processes}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jun,
title = {Literate Scientific Software},
year = {2016},
bdsk-file-1 = {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},
bdsk-url-1 = {http://www.pasc16.org/program/program/}}
@inproceedings{Mobius2010,
acmid = {2187629},
address = {Berlin, Heidelberg},
author = {M\"{o}bius, Jan and Kobbelt, Leif},
booktitle = {Proceedings of the 7th International Conference on Curves and Surfaces},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1007/978-3-642-27413-8_31},
isbn = {978-3-642-27412-1},
keywords = {geometry processing, open source, software framework},
location = {Avignon, France},
numpages = {13},
pages = {488--500},
publisher = {Springer-Verlag},
title = {OpenFlipper: An Open Source Geometry Processing and Rendering Framework},
url = {http://dx.doi.org/10.1007/978-3-642-27413-8_31},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-642-27413-8_31}}
@article{CrickAndHall2014,
author = {Tom Crick and Benjamin A. Hall and Samin Ishtiaq},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/corr/CrickHI14},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {CoRR},
timestamp = {Fri, 01 Aug 2014 13:50:01 +0200},
title = {``{C}an {I} Implement Your Algorithm?'': {A} Model for Reproducible Research Software},
url = {http://arxiv.org/abs/1407.5981},
volume = {abs/1407.5981},
year = {2014},
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bdsk-url-1 = {http://arxiv.org/abs/1407.5981}}
@book{Pilato2004,
address = {Sebastopol, CA, USA},
author = {Pilato, Michael},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0596004486},
publisher = {O'Reilly \& Associates, Inc.},
title = {Version Control With Subversion},
year = {2004}}
@article{BarabAndDede2007,
author = {Sasha Barab and Chris Dede},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1007/s10956-007-9043-9},
issn = {1059-0145},
journal = {Journal of Science Education and Technology},
month = feb,
number = {1},
pages = {1--3},
title = {Games and immersive participatory simulations for science education: An emerging type of curricula},
volume = {16},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1007/s10956-007-9043-9}}
@article{Dunleavy2009,
abstract = {{The purpose of this study was to document how teachers and students describe and comprehend the ways in which participating in an augmented reality (AR) simulation aids or hinders teaching and learning. Like the multi-user virtual environment (MUVE) interface that underlies Internet games, AR is a good medium for immersive collaborative simulation, but has different strengths and limitations than MUVEs. Within a design-based research project, the researchers conducted multiple qualitative case studies across two middle schools (6th and 7th grade) and one high school (10th grade) in the northeastern United States to document the affordances and limitations of AR simulations from the student and teacher perspective. The researchers collected data through formal and informal interviews, direct observations, web site posts, and site documents. Teachers and students reported that the technology-mediated narrative and the interactive, situated, collaborative problem solving affordances of the AR simulation were highly engaging, especially among students who had previously presented behavioral and academic challenges for the teachers. However, while the AR simulation provided potentially transformative added value, it simultaneously presented unique technological, managerial, and cognitive challenges to teaching and learning.}},
annote = {- Teachers and students reported that the technology-mediated narrative and the interactive, situated, collaborative problem solving affordances of the AR simulation were highly engaging, especially among students who had previously presented behavioral and academic challenges for the teachers. However, while the AR simulation provided potentially transformative added value, it simultaneously presented unique technological, managerial, and cognitive chal- lenges to teaching and learning.},
author = {Dunleavy, Matt and Dede, Chris and Mitchell, Rebecca},
booktitle = {Journal of Science Education and Technology},
citeulike-article-id = {3621421},
citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10956-008-9119-1},
citeulike-linkout-1 = {http://www.springerlink.com/content/f07855468080k253},
citeulike-linkout-2 = {http://link.springer.com/article/10.1007/s10956-008-9119-1},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
day = {1},
doi = {10.1007/s10956-008-9119-1},
issn = {1059-0145},
journal = {Journal of Science Education and Technology},
keywords = {education},
month = feb,
number = {1},
pages = {7--22},
posted-at = {2010-04-04 11:57:54},
priority = {3},
publisher = {Springer Netherlands},
title = {{Affordances and Limitations of Immersive Participatory Augmented Reality Simulations for Teaching and Learning}},
url = {http://dx.doi.org/10.1007/s10956-008-9119-1},
volume = {18},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1007/s10956-008-9119-1}}
@article{IEEE1998,
author = {IEEE},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1109/IEEESTD.1998.88286},
journal = {IEEE Std 830-1998},
keywords = {formal specification;IEEE Std 830-1998;IEEE recommended practice;IEEE/EIA Std 12207.1-1997;commercial software product selection;contracts;customers;guidelines;in-house software product selection;prototyping;software development;software requirements specification;standards compliance;suppliers;system requirements specifications;Software requirements and specifications;contract;customer;prototyping;software requirements specification;supplier;system requirements specifications},
month = oct,
pages = {1-40},
title = {Recommended Practice for Software Requirements Specifications},
year = {1998},
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bdsk-url-1 = {http://dx.doi.org/10.1109/IEEESTD.1998.88286}}
@article{JohnsonAndJohnson1997,
address = {{Houston, TX}},
author = {Johnson, Andrew and Johnson, Brad},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Linux Journal},
month = oct,
pages = {64--69},
publisher = {{Belltown Media}},
title = {Literate Programming Using {\tt Noweb}},
volume = {42},
year = 1997}
@incollection{Smith2016,
address = {Boca Raton, FL},
author = {W. Spencer Smith},
booktitle = {Software Engineering for Science},
chapter = {Examples of the Application of Traditional Software Engineering Practices to Science},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2020-09-05 11:07:03 -0400},
editor = {Jeffrey C. Carver and Neil Chue Hong and George Thiruvathukal},
pages = {33--63},
publisher = {Chapman and Hall/{CRC}},
series = {Chapman \& Hall/{CRC} Computational Science},
title = {A Rational Document Driven Design Process for Scientific Computing Software},
year = {2016},
bdsk-file-1 = {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}}
@mastersthesis{Sarafraz2014,
address = {Hamilton, ON, Canada},
author = {Padideh Sarafraz},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University},
title = {Thermal Optimization of Flat Plate {PCM} Capsules in Natural Convection Solar Water Heating Systems},
url = {http://hdl.handle.net/11375/14128},
year = {2014},
bdsk-file-1 = {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},
bdsk-url-1 = {http://hdl.handle.net/11375/14128}}
@techreport{Knuth1983WSS,
acknowledgement = ack-nhfb,
address = {Stanford, {CA}},
author = {Donald E. Knuth},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Stanford University},
month = sep,
number = {{CS}980},
title = {The {WEB{}} System of Structured Documentation},
type = {Stanford Computer Science Report},
year = {1983}}
@book{kernighan1999practice,
address = {Reading, MA},
author = {Kernighan, Brian W and Pike, Rob},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Addison-Wesley Professional},
title = {The Practice of Programming},
year = {1999}}
@inproceedings{fischer2001software,
author = {Fischer, Gerhard},
booktitle = {International Symposium on Future Software Technology},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {1--8},
title = {The software technology of the 21st century: From software reuse to collaborative software design},
year = {2001}}
@book{dawkins1996blind,
author = {Dawkins, Richard},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {WW Norton \& Company},
title = {The blind watchmaker: Why the evidence of evolution reveals a universe without design},
year = {1996}}
@misc{simon1996sciences,
author = {Simon, Herbert A},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {The MIT Press},
title = {The Sciences of the Artificial. 3rd},
year = {1996}}
@misc{GRASS,
author = {{GRASS Development Team}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://grass.osgeo.org/}},
title = {{GRASS} {GIS} Bringing Advanced Geospatial Technologies to the World},
url = {http://grass.osgeo.org/},
year = {2014},
bdsk-url-1 = {http://grass.osgeo.org/}}
@misc{craninstall,
author = {CRAN},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://cran.r-project.org/}},
lastchecked = {June 16, 2014},
title = {The Comprehensive R Archive Network},
url = {http://cran.r-project.org/},
year = {2014},
bdsk-url-1 = {http://cran.r-project.org/}}
@misc{Isti2013,
author = {Isti},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://www.earthwormcentral.org/documentation2/PROGRAMMER/SoftwareStandards.html}},
month = sep,
title = {Earthworm Software Standards},
year = {2013},
bdsk-url-1 = {http://www.earthwormcentral.org/documentation2/PROGRAMMER/SoftwareStandards.html}}
@misc{CIG2015,
author = {CIG},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://geodynamics.org/cig/software/mineos/}},
month = mar,
title = {Mineos},
year = {2015},
bdsk-url-1 = {http://geodynamics.org/cig/software/mineos/}}
@article{ParnasEtAl1990,
acmid = {78974},
address = {New York, NY, USA},
author = {Parnas, David L. and van Schouwen, A. John and Kwan, Shu Po},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/78973.78974},
issn = {0001-0782},
issue_date = {June 1990},
journal = {Commun. ACM},
month = jun,
number = {6},
numpages = {13},
pages = {636--648},
publisher = {ACM},
title = {Evaluation of Safety-critical Software},
url = {http://doi.acm.org/10.1145/78973.78974},
volume = {33},
year = {1990},
bdsk-url-1 = {http://doi.acm.org/10.1145/78973.78974},
bdsk-url-2 = {http://dx.doi.org/10.1145/78973.78974}}
@inproceedings{Smith2015,
address = {University of Toronto, Ontario, Canada},
author = {W. Spencer Smith},
booktitle = {2nd Graduate Attribute \& Curriculum Improvement Process (GACIP) Summit},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-08-01 14:36:17 -0400},
day = {10},
month = dec,
title = {{MEASURE}: A Prototype Accreditation Support Tool Using {Vena}},
year = {2015}}
@article{KanewalaAndBieman2014,
acmid = {2658307},
address = {Newton, MA, USA},
author = {Kanewala, Upulee and Bieman, James M.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1016/j.infsof.2014.05.006},
issn = {0950-5849},
issue_date = {October, 2014},
journal = {Inf. Softw. Technol.},
keywords = {Scientific software, Software quality, Software testing, Systematic literature review},
month = oct,
number = {10},
numpages = {14},
pages = {1219--1232},
publisher = {Butterworth-Heinemann},
title = {Testing Scientific Software: A Systematic Literature Review},
url = {http://dx.doi.org/10.1016/j.infsof.2014.05.006},
volume = {56},
year = {2014},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.infsof.2014.05.006}}
@article{HeatonAndCarver2015,
acmid = {2829726},
address = {Newton, MA, USA},
author = {Heaton, Dustin and Carver, Jeffrey C.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1016/j.infsof.2015.07.011},
issn = {0950-5849},
issue_date = {November 2015},
journal = {Inf. Softw. Technol.},
keywords = {Computational science, Scientific software, Systematic literature review},
month = nov,
number = {C},
numpages = {13},
pages = {207--219},
publisher = {Butterworth-Heinemann},
title = {Claims About the Use of Software Engineering Practices in Science},
url = {http://dx.doi.org/10.1016/j.infsof.2015.07.011},
volume = {67},
year = {2015},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.infsof.2015.07.011}}
@inproceedings{Pueschel2001,
author = {Markus P\"{u}schel and Bryan Singer and Manuela Veloso and Jos\'{e} M. F. Moura},
booktitle = {International Conference on Computational Science (ICCS)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {97--106},
publisher = {Springer},
series = {Lecture Notes In Computer Science},
title = {Fast Automatic Generation of {DSP} Algorithms},
volume = {2073},
year = {2001},
bdsk-file-1 = {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}}
@techreport{ISO2010,
author = {{ISO/IEC}},
citeulike-article-id = {10951538},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2021-09-16 17:05:00 -0400},
posted-at = {2012-07-27 13:14:40},
priority = {2},
publisher = {ISO/IEC},
title = {{ISO/IEC 25010 - Systems and software engineering - Systems and software Quality Requirements and Evaluation (SQuaRE) - System and software quality models}},
type = {Standard},
year = {2010},
bdsk-file-1 = {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}}
@techreport{ISO2007,
author = {{ISO/IEC}},
citeulike-article-id = {10951578},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
posted-at = {2012-07-27 14:20:32},
priority = {2},
publisher = {ISO/IEC},
title = {{ISO/IEC 25021:2007 - Software engineering - Software product Quality Requirements and Evaluation (SQuaRE) - Quality measure elements}},
year = {2007},
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@book{Adams2013,
address = {Thousand Oaks, CA, USA},
author = {Adams, Ernest},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {3rd},
isbn = {0321929675, 978-0321929679},
publisher = {New Riders Publishing},
title = {Fundamentals of Game Design},
year = {2013}}
@inproceedings{SampaioEtAl2013,
acmid = {2526985},
address = {New York, NY, USA},
author = {Sampaio, Bruno and Morgado, Carmen and Barbosa, Fernanda},
booktitle = {Proceedings of the 13th {Koli} Calling International Conference on Computing Education Research},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2526968.2526985},
isbn = {978-1-4503-2482-3},
keywords = {collaborative learning environments, educational games, quizzes},
location = {Koli, Finland},
numpages = {7},
pages = {153--159},
publisher = {ACM},
series = {Koli Calling '13},
title = {Building Collaborative Quizzes},
url = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2526968.2526985},
year = {2013},
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@article{Rajaravivarma2005,
acmid = {1113886},
address = {New York, NY, USA},
author = {Rajaravivarma, Rathika},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1113847.1113886},
issn = {0097-8418},
issue_date = {December 2005},
journal = {SIGCSE Bull.},
keywords = {CS1, active learning, game programming, games-based approach, pedagogy, word \& number games},
month = dec,
number = {4},
numpages = {5},
owner = {Samantha},
pages = {98--102},
publisher = {ACM},
timestamp = {2014.06.10},
title = {A Games-based Approach for Teaching the Introductory Programming Course},
volume = {37},
year = {2005},
bdsk-url-1 = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/1113847.1113886},
bdsk-url-2 = {http://dx.doi.org/10.1145/1113847.1113886}}
@inproceedings{PirkerEtAl2014,
acmid = {2591750},
address = {New York, NY, USA},
author = {Pirker, Johanna and Riffnaller-Schiefer, Maria and G\"{u}tl, Christian},
booktitle = {Proceedings of the 2014 Conference on Innovation \& Technology in Computer Science Education},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2591708.2591750},
isbn = {978-1-4503-2833-3},
keywords = {active learning, cs education, game-based learning, gamification, interactive learning, motivation, motivational active learning, motivational learning, pedagogy},
location = {Uppsala, Sweden},
numpages = {6},
pages = {297--302},
publisher = {ACM},
series = {ITiCSE '14},
title = {Motivational Active Learning: Engaging University Students in Computer Science Education},
year = {2014},
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@article{Perneger1998,
an = {PMC1112991},
author = {Perneger, Thomas V},
date = {1998/04/18},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
db = {PMC},
isbn = {0959-8138; 1468-5833},
j1 = {BMJ},
journal = {BMJ : British Medical Journal},
month = apr,
number = {7139},
pages = {1236--1238},
publisher = {British Medical Journal},
title = {What's wrong with {Bonferroni} adjustments},
ty = {JOUR},
u1 = {9553006{$[$}pmid{$]$}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1112991/},
volume = {316},
year = {1998},
year1 = {1998/01/16/accepted},
bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1112991/}}
@inproceedings{NickelAndBarnes2010,
acmid = {1822391},
address = {New York, NY, USA},
author = {Nickel, Andrea and Barnes, Tiffany},
booktitle = {Proceedings of the Fifth International Conference on the Foundations of Digital Games},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1822348.1822391},
isbn = {978-1-60558-937-4},
keywords = {computer-supported collaborative learning, multiplayer games, pair programming, serious games},
location = {Monterey, California},
numpages = {3},
pages = {274--276},
publisher = {ACM},
series = {FDG '10},
title = {Games for {CS} Education: Computer-supported Collaborative Learning and Multiplayer Games},
year = {2010},
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@article{Long2007,
author = {Long, Ju},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Information Technology Education},
owner = {Samantha},
pages = {279-290},
timestamp = {2014.06.10},
title = {Just For Fun: Using Programming Games in Software Programming Training and Education--A Field Study of {IBM} Robocode Community.},
volume = {6},
year = {2007}}
@inproceedings{Kahn1999,
author = {Ken Kahn},
booktitle = {National Educational Computing Conference: {NECC} '00: Spotlight on the Future: Technology for the New Millenium},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
owner = {Samantha},
timestamp = {2014.06.06},
title = {A Computer Game to Teach Programmming},
year = {1999}}
@inproceedings{Hicks2010,
acmid = {1822386},
address = {New York, NY, USA},
author = {Hicks, Andrew},
booktitle = {Proceedings of the Fifth International Conference on the Foundations of Digital Games},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1822348.1822386},
isbn = {978-1-60558-937-4},
keywords = {CS1, education, games, motivation, serious games, social gaming, social networking},
location = {Monterey, California},
numpages = {3},
pages = {259--261},
publisher = {ACM},
series = {FDG '10},
title = {Towards Social Gaming Methods for Improving Game-based Computer Science Education},
year = {2010},
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@inproceedings{Cockburn1998,
author = {Cockburn, Andy and Bryant, Andrew},
booktitle = {Computer Human Interaction, 1998. Proceedings. 3rd {Asia} {Pacific}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {IEEE},
owner = {Samantha},
pages = {189--194},
timestamp = {2014.06.10},
title = {Cleogo: collaborative and multi-metaphor programming for kids},
year = {1998}}
@inproceedings{ChaffinEtAl2009,
acmid = {1581086},
address = {New York, NY, USA},
author = {Chaffin, Amanda and Doran, Katelyn and Hicks, Drew and Barnes, Tiffany},
booktitle = {Proceedings of the 2009 {ACM SIGGRAPH} Symposium on Video Games},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1581073.1581086},
isbn = {978-1-60558-514-7},
keywords = {education, evaluation, game development, motivation},
location = {New Orleans, Louisiana},
numpages = {8},
pages = {79--86},
publisher = {ACM},
series = {Sandbox '09},
title = {Experimental Evaluation of Teaching Recursion in a Video Game},
year = {2009},
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bdsk-url-2 = {http://dx.doi.org/10.1145/1581073.1581086}}
@inproceedings{BoyceEtAl2011,
acmid = {2159384},
address = {New York, NY, USA},
author = {Boyce, Acey and Doran, Katelyn and Campbell, Antoine and Pickford, Shaun and Culler, Dustin and Barnes, Tiffany},
booktitle = {Proceedings of the 6th International Conference on Foundations of Digital Games},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2159365.2159384},
isbn = {978-1-4503-0804-5},
keywords = {education, evaluation, game development, motivation},
location = {Bordeaux, France},
numpages = {8},
pages = {139--146},
publisher = {ACM},
series = {FDG '11},
title = {BeadLoom Game: Adding Competitive, User Generated, and Social Features to Increase Motivation},
year = {2011},
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@article{BlandAndAltman1995,
an = {PMC2548561},
author = {Bland, J M and Altman, D G},
date = {1995/01/21},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
db = {PMC},
isbn = {0959-8138; 1468-5833},
j1 = {BMJ},
journal = {BMJ : British Medical Journal},
month = jan,
number = {6973},
pages = {170--170},
publisher = {BMJ Group},
title = {Multiple significance tests: the {Bonferroni} method.},
ty = {JOUR},
u1 = {7833759{$[$}pmid{$]$}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2548561/},
volume = {310},
year = {1995},
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@inproceedings{BarnesEtAl2008,
acmid = {1463674},
address = {New York, NY, USA},
author = {Barnes, Tiffany and Powell, Eve and Chaffin, Amanda and Lipford, Heather},
booktitle = {Proceedings of the 3rd International Conference on Game Development in Computer Science Education},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1463673.1463674},
isbn = {978-1-60558-057-9},
keywords = {education, evaluation, game development, motivation},
location = {Miami, Florida},
numpages = {5},
pages = {1--5},
publisher = {ACM},
series = {GDCSE '08},
title = {{Game2Learn}: Improving the Motivation of {CS1} Students},
url = {http://doi.acm.org/10.1145/1463673.1463674},
year = {2008},
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@inproceedings{BaloianEtAl2013,
acmid = {2535622},
address = {New York, NY, USA},
author = {Baloian, Nelson and Pino, Jos{\'e} A. and Vargas, Roberto},
booktitle = {Proceedings of the 2013 {Chilean} Conference on Human - Computer Interaction},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2535597.2535622},
isbn = {978-1-4503-2200-3},
keywords = {english as a foreign language education, gestures evaluation, iPad, natural user interfaces, tablet gestures},
location = {Temuco, Chile},
numpages = {6},
pages = {98--103},
publisher = {ACM},
series = {ChileCHI '13},
title = {Tablet Gestures As a Motivating Factor for Learning},
year = {2013},
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@inproceedings{Andersen2012,
author = {Andersen, Erik and O'Rourke, Eleanor and Liu, Yun-En and Snider, Rich and Lowdermilk, Jeff and Truong, David and Cooper, Seth and Popovic, Zoran},
booktitle = {Proceedings of the {SIGCHI} Conference on Human Factors in Computing Systems},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {ACM},
owner = {Samantha},
pages = {59--68},
timestamp = {2014.07.03},
title = {The impact of tutorials on games of varying complexity},
year = {2012}}
@article{WendelEtAl2013,
acmid = {2467151},
address = {Hingham, MA, USA},
author = {Wendel, Viktor and Gutjahr, Michael and G\"{o}bel, Stefan and Steinmetz, Ralf},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1007/s10639-012-9244-6},
issn = {1360-2357},
issue_date = {June 2013},
journal = {Education and Information Technologies},
keywords = {CSCL, Collaborative learning, Game-based learning, Serious games},
month = jun,
number = {2},
numpages = {22},
pages = {287--308},
publisher = {Kluwer Academic Publishers},
title = {Designing Collaborative Multiplayer Serious Games},
url = {http://dx.doi.org/10.1007/s10639-012-9244-6},
volume = {18},
year = {2013},
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@article{EagleAndBarnes2008,
acmid = {1384337},
address = {New York, NY, USA},
author = {Eagle, Michael and Barnes, Tiffany},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1597849.1384337},
issn = {0097-8418},
issue_date = {September 2008},
journal = {SIGCSE Bull.},
keywords = {CS1 education, Game2Learn, arrays, games, iteration},
month = jun,
number = {3},
numpages = {5},
pages = {245--249},
publisher = {ACM},
title = {Wu's Castle: Teaching Arrays and Loops in a Game},
url = {http://doi.acm.org/10.1145/1597849.1384337},
volume = {40},
year = {2008},
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bdsk-url-2 = {http://dx.doi.org/10.1145/1597849.1384337}}
@article{Tinto2000,
author = {Tinto, V.},
citeulike-article-id = {10452319},
citeulike-linkout-0 = {http://suedweb.syr.edu/Faculty/Vtinto/Files/AACRAOSpeech.pdf},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {NACADA Journal},
number = {2},
pages = {5--10},
posted-at = {2012-03-14 15:39:02},
priority = {2},
title = {{Taking Student Retention Seriously: Rethinking the First Year of College}},
url = {http://suedweb.syr.edu/Faculty/Vtinto/Files/AACRAOSpeech.pdf},
volume = {19},
year = {2000},
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@article{ProctorAndMarks2013,
acmid = {2442295},
address = {Oxford, UK, UK},
author = {Proctor, Michael D. and Marks, Yaela},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1016/j.compedu.2012.10.022},
issn = {0360-1315},
issue_date = {March, 2013},
journal = {Computers \& Education},
keywords = {Educational computer games, Human-computer interface, Improving classroom teaching, Interactive learning environments, Pedagogical issues, Perceived Ease of Use, Perceived Usefulness, Simulations},
month = mar,
numpages = {10},
pages = {171--180},
publisher = {Elsevier Science Ltd.},
title = {A Survey of Exemplar Teachers' Perceptions, Use, and Access of Computer-based Games and Technology for Classroom Instruction},
url = {http://dx.doi.org/10.1016/j.compedu.2012.10.022},
volume = {62},
year = {2013},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.compedu.2012.10.022}}
@article{KebritchiAndHirumi2008,
acmid = {1405478},
address = {Oxford, UK, UK},
author = {Kebritchi, Mansureh and Hirumi, Atsusi \"2c\"},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1016/j.compedu.2008.05.004},
issn = {0360-1315},
issue_date = {December, 2008},
journal = {Computers \& Education},
keywords = {Educational computer games, Interactive learning environments, Pedagogical issues, Simulations, Teaching/learning strategies},
month = dec,
number = {4},
numpages = {15},
pages = {1729--1743},
publisher = {Elsevier Science Ltd.},
title = {Examining the Pedagogical Foundations of Modern Educational Computer Games},
url = {http://dx.doi.org/10.1016/j.compedu.2008.05.004},
volume = {51},
year = {2008},
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@inproceedings{BastarricaAndHitschfeld-Kahler2004,
author = {Bastarrica, M Cecilia and Hitschfeld-Kahler, Nancy},
booktitle = {International Meshing Roundtable},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {Citeseer},
pages = {203--212},
title = {An Evolvable Meshing Tool Through a Flexible Object-Oriented Design.},
year = {2004},
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@article{deLeeuwAndMair2007,
accepted = {2007-05-01},
author = {Jan de Leeuw and Patrick Mair},
bibdate = {2007-05-01},
coden = {JSSOBK},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
day = {1},
issn = {1548-7660},
journal = {Journal of Statistical Software},
month = may,
number = {1},
pages = {1--5},
submitted = {2006-07-12},
title = {An Introduction to the Special Volume on Psychometrics in R},
url = {http://www.jstatsoft.org/v20/i01},
volume = {20},
year = {2007},
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bdsk-url-1 = {http://www.jstatsoft.org/v20/i01}}
@article{Rosseel2012,
accepted = {2012-02-06},
author = {Yves Rosseel},
bibdate = {2012-02-06},
coden = {JSSOBK},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
day = {24},
issn = {1548-7660},
journal = {Journal of Statistical Software},
month = may,
number = {2},
pages = {1--36},
submitted = {2011-09-23},
title = {lavaan: An R Package for Structural Equation Modeling},
url = {http://www.jstatsoft.org/v48/i02},
volume = {48},
year = {2012},
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bdsk-url-1 = {http://www.jstatsoft.org/v48/i02}}
@techreport{DOE2003,
author = {{United States Department of Energy}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Office of Environment, Health, Safety \& Security, Department of Energy, United States of America},
month = oct,
number = {CRAD - 4.2.4.1},
title = {Assessment Criteria and Guidelines for Determining the Adequacy of Software Used in the Safety Analysis and Design of Defense Nuclear Facilities},
year = {2003},
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@techreport{CNSC2000,
author = {{Canadian Nuclear Safety Commission (CNSC)}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Minister of Public Works and Government Services Canada},
month = oct,
number = {G-149},
title = {Computer Programs Used in Design and Safety Analyses of Nuclear Power Plants and Research Reactors},
year = {2000},
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@article{AntoniolEtAl2002,
acmid = {631291},
address = {Piscataway, NJ, USA},
author = {Antoniol, Giuliano and Canfora, Gerardo and Casazza, Gerardo and De Lucia, Andrea and Merlo, Ettore},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1109/TSE.2002.1041053},
issn = {0098-5589},
issue_date = {October 2002},
journal = {IEEE Trans. Softw. Eng.},
keywords = {Redocumentation, traceability, program comprehension, object orientation, information retrieval.},
month = oct,
number = {10},
numpages = {14},
pages = {970--983},
publisher = {IEEE Press},
title = {Recovering Traceability Links Between Code and Documentation},
url = {http://dx.doi.org/10.1109/TSE.2002.1041053},
volume = {28},
year = {2002},
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bdsk-url-1 = {http://dx.doi.org/10.1109/TSE.2002.1041053}}
@incollection{Nedialkov2011,
author = {Nedialkov, Nedialko S},
booktitle = {Modeling, Design, and Simulation of Systems with Uncertainties},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {3--19},
publisher = {Springer},
title = {Implementing a rigorous ODE solver through literate programming},
year = {2011}}
@misc{ATA2013,
author = {American Tinnitus Association},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://www.ata.org/sites/ata.org/files/pdf/Most_common_ServiceConnectedDisabilities_FY2012.pdf}},
title = {Actual and Projected Cost to Compensate Veterans for Tinnitus, Analysis of Department of Veterans Affairds Data by ATA},
year = {2013},
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@article{ShargorodskyEtAl2010,
author = {Josef Shargorodsky and Gary C. Curhan and Wildon R. Farwell},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {The American Journal of Medicine},
keywords = {anxiety, depression, epidemiology, hearing loss, tinnitus},
month = aug,
number = {8},
pages = {711--718},
title = {Prevalence and Characteristics of Tinnitus among {US} Adults},
volume = {123},
year = {2010},
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@article{Corliss1987,
abstract = {Integrals of a function of a single variable can be expressed as the sum of a numerical quadrature rule and a remainder term. The quadrature rule is a linear combination of function values and weights, or the integral of a Taylor polynomial, while the remainder term depends on some derivative of the integrand evaluated at an unknown point in the interval of integration. Numerical quadrature is made self validating by using interval computations to capture both the roundoff and truncation errors made when using a given formula. Necessary derivatives can be generated automatically by using well-known recurrence relations for Taylor coefficients. In order for quadrature methods of this type to be accurate (in the sense that small intervals are produced) and efficient (to obtain results of given accuracy in a reasonably short time), an accurate scalar product and an adaptive strategy are required. The necessary scalar product and support for interval arithmetic are provided in Pascal-SC (for microcomputers) and ACRITH (for IBM 370 computers). The adaptive strategy chooses the subintervals of integration and the order of the quadrature formula in each subinterval on the basis of guaranteed, rather than estimated, information about the error of numerical integration in each subinterval. The program described here implements standard Newton-Cotes, Gaussian and Taylor series formulas for numerical integration. The handling of singularities is discussed, and comparisons are given with a standard numerical integration method.},
author = {Corliss, George F. and Rall, L. B.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {01965204},
journal = {Society for Industrial and Applied Mathematics.SIAM Journal on Scientific and Statistical Computing},
keywords = {Mathematics},
language = {English},
month = sep,
note = {Copyright - Copyright] {\copyright} 1987 Society for Industrial and Applied Mathematics; Last updated - 2012-02-10},
number = {5},
pages = {831-17},
title = {Adaptive, Self-Validating Numerical Quadrature},
url = {http://search.proquest.com/docview/920880417?accountid=12347},
volume = {8},
year = {1987},
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bdsk-url-1 = {http://search.proquest.com/docview/920880417?accountid=12347}}
@inproceedings{PryceEtAl2008,
address = {Dagstuhl, Germany},
annote = {Keywords: Interval arithmetic, validated computation, floating point, standards, exceptions, not an interval},
author = {John D. Pryce and George C. Corliss and R. Baker Kearfott and Ned S. Nedialkov and W. Spencer Smith},
booktitle = {Numerical Validation in Current Hardware Architectures},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Annie Cuyt and Walter Kr{\"a}mer and Wolfram Luther and Peter Markstein},
issn = {1862-4405},
number = {08021},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"u}r Informatik (IBFI), Schloss Dagstuhl, Germany},
series = {Dagstuhl Seminar Proceedings},
title = {Second Note on Basic Interval Arithmetic for IEEE754R},
url = {http://drops.dagstuhl.de/opus/volltexte/2008/1451},
year = {2008},
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bdsk-url-1 = {http://drops.dagstuhl.de/opus/volltexte/2008/1451}}
@misc{Lipovaca2015,
author = {Miran Lipovaca},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://learnyouahaskell.com/}},
month = apr,
title = {Learn You a {H}askell for Great Good},
year = {2015}}
@article{Hickey2001,
acmid = {502106},
address = {New York, NY, USA},
author = {Hickey, Timothy and Ju, Qun and Van Emden, Maarten H.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/502102.502106},
issn = {0004-5411},
issue_date = {September 2001},
journal = {J. ACM},
month = sep,
number = {5},
numpages = {31},
pages = {1038--1068},
publisher = {ACM},
title = {Interval Arithmetic: From Principles to Implementation},
url = {http://doi.acm.org/10.1145/502102.502106},
volume = {48},
year = {2001},
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bdsk-url-1 = {http://doi.acm.org/10.1145/502102.502106},
bdsk-url-2 = {http://dx.doi.org/10.1145/502102.502106}}
@article{ZienkiewiczAndPhillips1971,
abstract = {A computer orientated method is presented which generates meshes of triangular elements in plane and curved surfaces. Depending on geometrical and material variations, the region to be discretized is divided into a number of four sided zones. By using curvi-linear co-ordinate systems, nodes within and on the boundary of each zone are automatically positioned and referenced to a global Cartesian co-ordinate system. Elements are automatically assembled from these nodes. Input data is required to specify the positions and material properties of each zone and how they are connected. Examples are given which illustrate the range of meshes that can be generated. Extension of the method to generate three-dimensional tetrahedral elements is indicated.},
author = {Zienkiewicz, O. C. and Phillips, D. V.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1002/nme.1620030407},
issn = {1097-0207},
journal = {International Journal for Numerical Methods in Engineering},
number = {4},
pages = {519--528},
publisher = {John Wiley & Sons, Ltd},
title = {An automatic mesh generation scheme for plane and curved surfaces by `isoparametric' co-ordinates},
url = {http://dx.doi.org/10.1002/nme.1620030407},
volume = {3},
year = {1971},
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bdsk-url-1 = {http://dx.doi.org/10.1002/nme.1620030407}}
@book{Thompson1997,
address = {Boston, MA, USA},
author = {Thompson, Simon},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0-201-40357-9},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
title = {Haskell: The Craft of Functional Programming},
year = {1997}}
@inproceedings{KiselyovEtAl2004,
acmid = {1017794},
address = {New York, NY, USA},
author = {Kiselyov, Oleg and Swadi, Kedar N. and Taha, Walid},
booktitle = {Proceedings of the 4th ACM International Conference on Embedded Software},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/1017753.1017794},
isbn = {1-58113-860-1},
keywords = {abstract interpretation, multi-stage programming},
location = {Pisa, Italy},
numpages = {10},
pages = {249--258},
publisher = {ACM},
series = {EMSOFT '04},
title = {A Methodology for Generating Verified Combinatorial Circuits},
url = {http://doi.acm.org/10.1145/1017753.1017794},
year = {2004},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1017753.1017794},
bdsk-url-2 = {http://dx.doi.org/10.1145/1017753.1017794}}
@inproceedings{Lee2013,
acmid = {2493424},
address = {New York, NY, USA},
annote = {- a research proposal, not completed work},
author = {Lee, Michael J.},
booktitle = {Proceedings of the Ninth Annual International ACM Conference on International Computing Education Research},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2493394.2493424},
isbn = {978-1-4503-2243-0},
keywords = {assessment, debugging, educational game, efficiency, engagement, programming, serious game},
location = {San Diego, San California, USA},
numpages = {2},
pages = {181--182},
publisher = {ACM},
series = {ICER '13},
title = {How Can a Social Debugging Game Effectively Teach Computer Programming Concepts?},
url = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2493394.2493424},
year = {2013},
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bdsk-url-1 = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2493394.2493424},
bdsk-url-2 = {http://dx.doi.org/10.1145/2493394.2493424}}
@inproceedings{XiaoAndMiller2014,
acmid = {2567858},
address = {New York, NY, USA},
annote = {- teaching through a multiplayer game
- description of a work in progress
- points out that many-player games allow student to learn from their peers},
author = {Xiao, David and Miller, Robert C.},
booktitle = {Proceedings of the First ACM Conference on Learning @ Scale Conference},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/2556325.2567858},
isbn = {978-1-4503-2669-8},
keywords = {educational games, moocs, software engineering education, team programming},
location = {Atlanta, Georgia, USA},
numpages = {2},
pages = {159--160},
publisher = {ACM},
series = {L@S '14},
title = {A Multiplayer Online Game for Teaching Software Engineering Practices},
url = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2556325.2567858},
year = {2014},
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bdsk-url-1 = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2556325.2567858},
bdsk-url-2 = {http://dx.doi.org/10.1145/2556325.2567858}}
@phdthesis{Taha:1999:PhD,
author = {Walid Taha},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {Oregon Graduate Institute of Science and Technology},
title = {Multi-stage programming: its theory and applications.},
year = 1999,
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@inproceedings{ThulasiEtAl2015,
author = {Thulasi Jegatheesan and W. Spencer Smith and Ned Nedialkov},
booktitle = {Current Research in Engineering, Science \& Technology},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = mar,
organization = {Women in Science and Engineering Initiative},
publisher = {McMaster University},
title = {A Case Study in Document-Driven Development for Scientific and Engineering Software},
year = {2015},
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@techreport{Hseih2007,
author = {{Henry (Shang-Rou)} Hsieh},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Lawrence Livermore National Laboratory},
month = dec,
number = {UCRL-TR-237205},
title = {Application of the PSUADE Tool for Sensitivity Analysis of an Engineering Simulation},
type = {Technical report},
year = {2007},
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@techreport{SmithEtAl2015-MG-TR,
author = {W. Spencer Smith and Adam Lazzarato and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University},
month = jan,
note = {45 pp},
number = {CAS-15-04-SS},
title = {State of the Practice for Mesh Generation Software},
type = {Technical Report},
year = {2015},
bdsk-file-1 = {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}}
@techreport{LazzaratoEtAl2015-RS-TR,
author = {Adam Lazzarato and W. Spencer Smith and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University},
month = jan,
note = {47 pp},
number = {CAS-15-03-SS},
title = {State of the Practice for Remote Sensing Software},
type = {Technical Report},
year = {2015},
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@techreport{SmithEtAl2015-OS-TR,
author = {W. Spencer Smith and Yue Sun and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University, Department of Computing and Software},
month = jan,
note = {49 pp},
number = {CAS-15-02-SS},
title = {State of the Practice for Developing Oceanographic Software},
type = {Technical Report},
year = {2015},
bdsk-file-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAhLi4vLi4vcHViL1NtaXRoRXRBbDIwMTUtT1MtVFIucGRmTxEBZgAAAAABZgACAAAMTWFjaW50b3NoIEhEAAAAAAAAAAAAAAAAAAAAAAAAAEJEAAH/////F1NtaXRoRXRBbDIwMTUtT1MtVFIucGRmAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAP////8AAAAAAAAAAAAAAAAAAgACAAAKIGN1AAAAAAAAAAAAAAAAAANwdWIAAAIAMC86VXNlcnM6c21pdGhzOlJlcG9zOnB1YjpTbWl0aEV0QWwyMDE1LU9TLVRSLnBkZgAOADAAFwBTAG0AaQB0AGgARQB0AEEAbAAyADAAMQA1AC0ATwBTAC0AVABSAC4AcABkAGYADwAaAAwATQBhAGMAaQBuAHQAbwBzAGgAIABIAEQAEgAuVXNlcnMvc21pdGhzL1JlcG9zL3B1Yi9TbWl0aEV0QWwyMDE1LU9TLVRSLnBkZgATAAEvAAAVAAIADf//AAAACAANABoAJABIAAAAAAAAAgEAAAAAAAAABQAAAAAAAAAAAAAAAAAAAbI=}}
@techreport{SmithEtAl2015-SS-TR,
author = {W. Spencer Smith and Yue Sun and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University},
month = jan,
note = {43 pp},
number = {CAS-15-01-SS},
title = {Comparing Psychometrics Software Development Between {CRAN} and Other Communities},
type = {Technical Report},
year = {2015},
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@article{HanksEtAl2011,
abstract = {This article provides a review of educational research literature focused on pair programming in the undergraduate computer science curriculum. Research suggests that the benefits of pair programming include increased success rates in introductory courses, increased retention in the major, higher quality software, higher student confidence in solutions, and improvement in learning outcomes. Moreover, there is some evidence that women, in particular, benefit from pair programming. The literature also provides evidence that the transition from paired to solo programming is easy for students. The greatest challenges for paired students appear to concern scheduling and partner compatibility. This review also considers practical issues such as assigning partners, teaching students to work in pairs, and assessing individual contributions, and concludes with a discussion of open research questions.},
author = {Hanks, Brian and Fitzgerald, Sue and McCauley, Ren{\'e}e and Murphy, Laurie and Zander, Carol},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1080/08993408.2011.579808},
eprint = {http://dx.doi.org/10.1080/08993408.2011.579808},
journal = {Computer Science Education},
number = {2},
pages = {135-173},
title = {Pair programming in education: a literature review},
url = {http://dx.doi.org/10.1080/08993408.2011.579808},
volume = {21},
year = {2011},
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bdsk-url-1 = {http://dx.doi.org/10.1080/08993408.2011.579808}}
@mastersthesis{Chan2014,
address = {Hamilton, ON, Canada},
author = {Samantha Chan},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = sep,
school = {McMaster University},
title = {The Educational Effectiveness of a Cooperative and Competitive Video Game for Teaching Introductory Programming},
year = {2014},
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@inproceedings{CzarneckiEtAl2004,
author = {Krzysztof Czarnecki and John O'Donnell and J{\"u}rg Striegnitz and Walid Taha},
booktitle = {Domain-Specific Program Generation, LNCS},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {51--72},
publisher = {Springer-Verlag},
title = {DSL implementation in MetaOCaml, Template Haskell, and C},
volume = {3016},
year = {2004},
bdsk-file-1 = {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}}
@inproceedings{Czarnecki2004,
abstract = {System family engineering seeks to exploit the commonalities among systems from a given problem domain while managing the variabilities among them in a systematic way. In system family engineering, new system variants can be rapidly created based on a set of reusable assets (such as a common architecture, components, models, etc.). Generative software development aims at modeling and implementing system families in such a way that a given system can be automatically generated from a specification written in one or more textual or graphical domain-specific languages. This paper gives an overview of the basic concepts and ideas of generative software development including DSLs, domain and application engineering, generative domain models, networks of domains, and technology projections. The paper also discusses the relationship of generative software development to other emerging areas such as Model Driven Development and Aspect-Oriented Software Development.},
annote = {- current research and practical experience suggest that achieving significant progress with respect to software reuse requires a paradigm shift towards modelling and developing software system families rather than individual systems.
- exploit commonalities and manage variabilities in a systematic way
- The traditional approach to providing domain-specific abstractions in pro- gramming languages is through libraries of user-defined functions, classes, and data structures. We consider the application programming interfaces (APIs) ex- posed by such libraries as a possible implementation form for DSLs.
- At the same time, while satisfying the first benefit in the list above, traditional libraries and APIs usually come short on the other items, such as domain-specific notation (beyond operator overloading, which may be available in the host language), error checking, and optimizations. Achieving the latter goals usually requires some form of metaprogramming.
- The problem space with its common and variable features and con- straints in the configuration view defines a domain-specific language, and the components in the solution space can also be viewed as an implementation lan- guage. {\ldots} Thus, the configuration view can also be interpreted as a mapping between languages.
{where is the idea of refinement? abstract to more concrete - relates to chaining of mappings, but isn't made explicit}
{more examples would be nice}
{Drasil should take more explicit account of a family approach. What are the commonalities and what are the variabilities? Might be a good student project to reverse engineer our family documentation.}
- Perhaps the closest related area to generative software development is model- driven development (MDD), which aims at capturing every important aspect of a software system through appropriate models.
- There has been a trend in MDD towards representing models using appro- priate DSLs, which makes MDD and generative software development closely related. Perhaps the main difference between MDD and generative software de- velopment is the focus of the latter on system families. While system families can be of interest to MDD, they are not regarded as a necessity.
{says ``Aspect-oriented development provides better separation of concerns and composition mechanisms.'' but connection to aspect oriented is not made clear}
NOTES FROM CAS 761 DISCUSSION
- some said it was boring - thought the vocabulary was obvious
- JC - he was right to focus on the problem space - the interesting things are in the problem space
- some seemed to think that usability was the only quality that program families solved},
author = {Krzysztof Czarnecki},
booktitle = {In Proceedings of Unconventional Programming Paradigms (UPP) 2004, 15-17 September, Mont Saint-Michel, France, Revised Papers},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-09-10 13:29:13 -0400},
pages = {313--328},
publisher = {Springer-Verlag},
title = {Overview of generative software development},
year = {2004},
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@misc{SageDevTeam2014,
author = {{Sage Development Team}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {Sage Computer Algebra System},
url = {http://sagemath.org/index.html},
year = {2014},
bdsk-url-1 = {http://sagemath.org/index.html}}
@misc{SymPyDevTeam2013,
author = {{SymPy Development Team}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {{SymPy} Python Symbolic Mathematics Library},
url = {http://www.sympy.org/en/index.html},
year = {2013},
bdsk-url-1 = {http://www.sympy.org/en/index.html}}
@misc{ValgrindDevTeam2014,
author = {{Valgrind Development Team}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {Valgrind Diagnostic Tool},
url = {http://valgrind.org/},
year = {2014},
bdsk-url-1 = {http://valgrind.org/}}
@book{Fischer1998,
author = {Fischer, Ian},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {9780849391156},
publisher = {Taylor \& Francis},
title = {Dual-Number Methods in Kinematics, Statics and Dynamics},
url = {http://books.google.com.tr/books?id=hfinyCUHDW0C},
year = {1998},
bdsk-url-1 = {http://books.google.com.tr/books?id=hfinyCUHDW0C}}
@misc{StauningAndBendtsen2003,
author = {Ole Stauning and Claus Bendtsen},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {{FADBAD++} Flexible Automatic differentiation using templates and operator oveloading in {ANSI} {C++}},
url = {http://www.imm.dtu.dk/~kajm/FADBAD/},
year = {2003},
bdsk-url-1 = {http://www.imm.dtu.dk/~kajm/FADBAD/}}
@mastersthesis{Sanchez2010,
address = {Hamilton, ON, Canada},
author = {Gonzalo Sanchez},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = apr,
school = {School of Computational Science and Engineering, McMaster University},
title = {Virtual Material Testing Laboratory (Version 1.1)},
year = {2010},
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@book{Bird98:Introduction,
author = {Richard S. Bird},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0134843460},
publisher = {Prentice-Hall},
title = {Introduction to Functional Programming Using {H}askell},
url = {http://www.cs.ox.ac.uk/publications/books/functional/},
year = {1998},
bdsk-file-1 = {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},
bdsk-url-1 = {http://www.cs.ox.ac.uk/publications/books/functional/}}
@book{Millington2007,
author = {Ian Millington},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {9780123694713},
lccn = {2006023852},
publisher = {Taylor \& Francis},
series = {Game Physics Engine Development},
title = {Game Physics Engine Development},
url = {http://books.google.ca/books?id=OsJ-8IRkRWgC},
year = {2007},
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@inproceedings{Owen1998,
author = {Steven J. Owen},
booktitle = {INTERNATIONAL MESHING ROUNDTABLE},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {239--267},
title = {A Survey of Unstructured Mesh Generation Technology},
year = {1998},
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@article{saaty-ahp,
author = {Thomas L. Saaty},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {European Journal of Operational Research},
keywords = {ahp},
number = {1},
pages = {9-26},
title = {How to make a decision: The Analytic Hierarchy Process},
volume = {48},
year = {1990},
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@book{PharrAndHumphreys2004,
address = {San Francisco, CA, USA},
author = {Pharr, Matt and Humphreys, Greg},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Morgan Kaufmann Publishers Inc.},
title = {Physically Based Rendering: From Theory to Implementation},
year = 2004}
@unpublished{ZengEtAl2014RA,
author = {Zheng Zeng and W. Spencer Smith and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-09-25 13:16:28 -0400},
note = {Part of MEng Report},
title = {Radio Astronomy Software: State of Practice},
year = {2014},
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@article{SmithEtAl2018,
author = {W. Spencer Smith and Zheng Zeng and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-05-20 13:41:32 +0000},
journal = {Journal of Seismology},
keywords = {seismology, scientific computing, software quality model, analytic hierarchy process, software engineering},
month = {May},
number = {3},
pages = {755--788},
title = {Seismology Software: State of the Practice},
volume = {22},
year = {2018},
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@article{KapilEtAl2014SA,
author = {Vasudha Kapil and W. Spencer Smith and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Applied Spatial Analysis and Policy},
title = {State of the Practice for Software Tools in Spatial Analysis},
year = {Submitted 2014?},
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@article{KapilEtAl2014MI,
author = {Vasudha Kapil and W. Spencer Smith and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Digital Imaging},
title = {State of the Practice for Software Tools in Medical Imaging},
year = {Submitted 2014?},
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@article{LazzaratoEtAl2017GIS,
author = {Adam Lazzarato and W. Spencer Smith and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computers \& Geosciences},
note = {43 pp},
title = {State of the Practice for Geographic Information Systems},
year = {2017 (in preparation)},
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@inproceedings{Smith2014,
address = {Department of Electrical and Computer Engineering, Marquette University, Milwaukee, Wisconsin, USA},
author = {%Spencer Smith},
booktitle = {{GasDay} Seminar (presented over webex)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {Verifiable, Maintainable and Understandable Scientific Computing Code},
year = {2014},
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@article{SmithEtAl2014JOS,
author = {W. Spencer Smith and Yue Sun and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Oceanography Software?},
title = {State of the Practice for Developing Oceanographic Software},
year = {Submitted 2014?},
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@misc{SmithEtAl2018_StatSoft,
author = {W. Spencer Smith and Yue Sun and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-02-22 05:20:15 +0000},
howpublished = {\url{https://arxiv.org/abs/1802.07362}},
journal = {arXiv},
note = {33 pp.},
title = {Statistical Software for Psychology: Comparing Development Practices Between {CRAN} and Other Communities},
year = {2018},
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@article{Wickham2011,
author = {Hadley Wickham},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {The R Journal},
pages = {5--10},
title = {{testthat}: Get Started with Testing},
url = {http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf},
volume = {3},
year = {2011},
bdsk-url-1 = {http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf}}
@techreport{Knuth1983,
acknowledgement = ack-hk,
author = {Donald E. Knuth},
bibdate = {Fri Sep 23 02:22:30 1994},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = inst-STAN-CS,
number = {STAN-CS-83-981},
title = {Literate Programming},
type = {Technical report},
year = {1983}}
@url{RCoreTeam2014,
author = {{R Core Team}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
lastchecked = {2014},
title = {Writing {R} Extensions},
url = {http://cran.r-project.org/doc/manuals/r-release/R-exts.html},
urldate = {2014},
year = {2014},
bdsk-url-1 = {http://cran.r-project.org/doc/manuals/r-release/R-exts.html}}
@manual{WickhamEtAl2014,
author = {Hadley Wickham and Peter Danenberg and Manual Eugster and RStudio},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = sep,
organization = {CRAN repository},
title = {roxygen2: In-source documentation for {R}},
url = {http://cran.r-project.org/web/packages/roxygen2/index.html},
year = {2014},
bdsk-url-1 = {http://cran.r-project.org/web/packages/roxygen2/index.html}}
@inproceedings{Leisch2002,
author = {Friedrich Leisch},
booktitle = {Compstat 2002 --- Proceedings in Computational Statistics},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Wolfgang H{\"a}rdle and Bernd R{\"o}nz},
note = {ISBN 3-7908-1517-9},
pages = {575--580},
publisher = {Physica Verlag, Heidelberg},
title = {Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis},
url = {http://www.stat.uni-muenchen.de/~leisch/Sweave},
year = 2002,
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bdsk-url-1 = {http://www.stat.uni-muenchen.de/~leisch/Sweave}}
@article{NorrisEtAl2014,
author = {Boyana Norris and Sa{-}Lin Bernstein and Ramya Nair and Elizabeth R. Jessup},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/corr/NorrisBNJ14},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {CoRR},
timestamp = {Tue, 21 Oct 2014 22:52:49 +0200},
title = {Lighthouse: {A} User-Centered Web Service for Linear Algebra Software},
url = {http://arxiv.org/abs/1408.1363},
volume = {abs/1408.1363},
year = {2014},
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bdsk-url-1 = {http://arxiv.org/abs/1408.1363}}
@article{SarrabAndRehman2014,
author = {Mohamed Sarrab and Osama M. Hussain Rehman},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Advances in Engineering Software},
pages = {1--11},
title = {Empirical study of open source software selection for adoption, based on software quality characteristics},
url = {http://dx.doi.org/10.1016/j.advengsoft.2013.12.001},
volume = {69},
year = {2014},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.advengsoft.2013.12.001}}
@article{Barnes2010,
author = {Nick Barnes},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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month = oct,
pages = {753},
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volume = {467},
year = {2010},
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bdsk-url-1 = {doi:10.1038/467753a}}
@techreport{Nedialkov2006,
address = {{1280 Main Street West, Hamilton, Ontario, L8S 4K1}},
author = {Nedialko S. Nedialkov},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Department of Computing and Software, McMaster University},
number = {CAS-06-06-NN},
title = {{VNODE-LP} --- A Validated Solver for Initial Value Problems in Ordinary Differential Equations},
year = {2006}}
@techreport{Nedialkov2010,
author = {Nedialko S. Nedialkov},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Department of Computing and Software, McMaster University},
number = {{CAS-10-02-NN}},
title = {{Implementing a Rigorous {ODE} Solver through Literate Programming}},
year = {2010},
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@inproceedings{GuanaAndStroulia2014,
author = {Victor Guana and Eleni Stroulia},
booktitle = {IEEE Games, Entertainment, and Media Conference (IEEE GEM'14)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {PhyDSL: A Code-generation Environment for 2D Physics-based Games},
year = {2014},
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@incollection{Dijkstra1972,
acmid = {1243381},
address = {London, UK, UK},
author = {Dijkstra, Edsger W.},
booktitle = {Structure Programming},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Dahl, O. J. and Dijkstra, E. W. and Hoare, C. A. R.},
isbn = {0-12-200550-3},
numpages = {82},
pages = {1--82},
publisher = {Academic Press Ltd.},
title = {Notes on Structured Programming},
url = {http://dl.acm.org/citation.cfm?id=1243380.1243381},
year = {1972},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=1243380.1243381}}
@book{DahlEtAl1972,
address = {London, UK, UK},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Dahl, O. J. and Dijkstra, E. W. and Hoare, C. A. R.},
isbn = {0-12-200550-3},
publisher = {Academic Press Ltd.},
source = {Library of Congress Catalog Card Number: 72-84452},
title = {Structured Programming},
year = {1972},
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@article{SchulteEtAl2012,
accepted = {2011-10-03},
author = {Eric Schulte and Dan Davison and Thomas Dye and Carsten Dominik},
bibdate = {2011-10-03},
coden = {JSSOBK},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
day = {25},
issn = {1548-7660},
journal = {Journal of Statistical Software},
month = jan,
number = {3},
pages = {1--24},
submitted = {2010-12-22},
title = {A Multi-Language Computing Environment for Literate Programming and Reproducible Research},
url = {http://www.jstatsoft.org/v46/i03},
volume = {46},
year = {2012},
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bdsk-url-1 = {http://www.jstatsoft.org/v46/i03}}
@article{HatcliffEtAl2009,
abstract = {In August of 2007 and December of 2007, North American academic researchers,
industry representatives and regulators were invited to meetings
in Washington and Minneapolis, respectively, with the goal of forming
a Software Certification Consortium (SCC). At the first meeting,
objectives were established for the consortium and a certification
grand challenge was issued. At the second meeting, all participants
were asked to complete the statement: ``Software certification is
hard because . . .''. The group then synthesized the results into
a ``Top 9'' list by means of discussion and voting. In this article,
we describe the goals that we believe should be the goals of SCC,
via details of these Top 9 hurdles that are preventing us from making
software certification part of the mainstream},
author = {Hatcliff, John and Heimdahl, Mats and Lawford, Mark and Maibaum, Tom and Wassyng, Alan and Wurden, Fred},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1016/j.entcs.2009.09.002},
file = {:Users/gonzalo/McSCert/scc/ref/McSCert/A Software Certification Consortium and its Top 9 Hurdles (safecert08).pdf:pdf},
issn = {1571-0661},
journal = {Electronic Notes in Theoretical Computer Science},
keywords = {formal methods,objectives,projects,scc,software certification consortium},
number = {4},
pages = {11--17},
publisher = {Elsevier},
title = {A Software Certification Consortium and its Top 9 Hurdles},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1571066109003570},
volume = {238},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.entcs.2009.09.002},
bdsk-url-2 = {http://linkinghub.elsevier.com/retrieve/pii/S1571066109003570}}
@article{SmithCaretteAndElSheikh2014,
author = {W. Spencer Smith and Jacques Carette and Mustafa ElSheikh},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Advances in Engineering Software},
title = {Code Generation for Improving the Quality of Scientific Computing Software},
year = {2014?}}
@article{SmithAndYu2014,
author = {W. Spencer Smith and Wen Yu},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Advances in Engineering Software},
title = {A Family Approach for Scientific Computing Software},
year = {2014?}}
@article{SmithAndChan2017,
abstract = {This study measures the success of using a collaborative and competitive video game, named Space Race, to teach computing to first year engineering students. Space Race is played by teams of four, each with their own tablet, collaborating to compete against the other teams in the class. The impact of the game on student learning was studied through measurements using 485 students, over one term. Surveys were used to gauge student reception of the game. Pre and post-tests, and in-course examinations were used to quantify student performance. The game was well received with at least 82{\%} of the students that played it recommending it to others. In some cases, game participants outperformed non-participants on course exams. On the final course exam, all of the statistically significant (p<0.05) comparisons (42{\%} of the relevant questions) showed a performance improvement of game participants on the questions, with a maximum grade improvement of 41{\%}. The findings also suggest that some students retain the knowledge obtained from Space Race for at least 7 weeks. The results of this study provide strong evidence that a collaborative and competitive video game can be an effective tool for teaching computing in post-secondary education.},
author = {W. Spencer Smith and Samantha Chan},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1007/s10956-017-9690-4},
journal = {Journal of Science Education and Technology},
month = aug,
number = {4},
pages = {438--457},
title = {Collaborative and Competitive Video Games for Teaching Computing in Higher Education},
volume = {26},
year = {2017},
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bdsk-url-1 = {https://doi.org/10.1007/s10956-017-9690-4}}
@techreport{MastragostinoAndSmith2014,
author = {Robert Mastragostino and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University, Engineering 1},
keywords = {automatic differentiation, constitutive model, material testing},
month = jan,
note = {22 pp},
title = {Using Automatic Differentiation to Implement a Family of Material Models},
type = {Technical Report},
url = {http://hdl.handle.net/11375/16648},
year = {2015},
bdsk-file-1 = {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},
bdsk-url-1 = {http://hdl.handle.net/11375/16648}}
@techreport{GabardoAndSmith2014,
author = {Philip Gabardo and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University, Engineering 1},
number = {??},
title = {Teaching Assistant Scheduling with Binary Integer Programming},
type = {Technical Report},
year = {2014?},
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@techreport{SmithMcCutchanAndCarette2017,
author = {W. Spencer Smith and John McCutchan and Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University, Department of Computing and Software},
number = {CAS-17-01-SS},
title = {Commonality Analysis for a Family of Material Models},
type = {Technical Report},
year = {2017},
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@inproceedings{ChanAndSmith2014,
author = {Samantha Chan and W. Spencer Smith},
booktitle = {International Conference on Engineering Education and Research iCEER2014},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
note = {4 pp.},
title = {A Cooperative Competitive Video Game for Teaching Introductory Computer Programming},
year = {2014},
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@misc{UConn2014,
author = {University of Connecticut},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
howpublished = {\url{http://assessment.uconn.edu/primer/goals1.html}},
month = may,
title = {How to Write Program Objectives/Outcomes},
year = {2014}}
@article{McCue2012,
author = {T. J. McCue},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {\href{http://www.forbes.com/sites/tjmccue/2012/05/02/additive-manufacturing-will-change-in-the-next-5-10-years/}{http://www.forbes.com/sites/tjmccue/2012/05/02/additive-manufacturing-will-change-in-the-next-5-10-years/}},
lastchecked = {April 10, 2014},
title = {Additive Manufacturing Will Change in the Next 5-10 Years},
urldate = {May 5, 2012},
year = {2012},
bdsk-url-1 = {http://www.forbes.com/sites/tjmccue/2012/05/02/additive-manufacturing-will-change-in-the-next-5-10-years/}}
@inproceedings{ChanAndSmith_CREST_2014,
author = {Samantha Chan and W. Spencer Smith},
booktitle = {Current Research in Engineering, Science \& Technology},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = mar,
organization = {Women in Science and Engineering Initiative},
publisher = {McMaster University},
title = {Video Games as a Pedagogical Tool for Teaching Computer Programming},
year = {2014}}
@inproceedings{KellerEtAl2008,
added-at = {2008-01-04T00:00:00.000+0100},
author = {Keller, Gabriele and Chaffey-Millar, Hugh and Chakravarty, Manuel M. T. and Stewart, Don and Barner-Kowollik, Christopher},
biburl = {http://www.bibsonomy.org/bibtex/2fe5a034fc1b3f64cb42f12ec8c6b0aa9/dblp},
booktitle = {PADL},
crossref = {conf/padl/2008},
date = {2008-01-04},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
description = {dblp},
editor = {Hudak, Paul and Warren, David Scott},
ee = {http://dx.doi.org/10.1007/978-3-540-77442-6_9},
interhash = {2851fe860c8a36401b85276311f53177},
intrahash = {fe5a034fc1b3f64cb42f12ec8c6b0aa9},
isbn = {978-3-540-77441-9},
keywords = {dblp},
pages = {116-132},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
timestamp = {2008-01-04T00:00:00.000+0100},
title = {Specialising Simulator Generators for High-Performance Monte-Carlo Methods.},
url = {http://dblp.uni-trier.de/db/conf/padl/padl2008.html#KellerCCSB08},
volume = 4902,
year = 2008,
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bdsk-url-1 = {http://dblp.uni-trier.de/db/conf/padl/padl2008.html#KellerCCSB08}}
@inproceedings{Korelc2001,
acmid = {384130},
address = {New York, NY, USA},
author = {Korelc, Joze},
booktitle = {Proceedings of the 2001 International Symposium on Symbolic and Algebraic Computation},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1145/384101.384130},
isbn = {1-58113-417-7},
keywords = {code generation, finite element environments, symbolic approach},
location = {London, Ontario, Canada},
numpages = {8},
pages = {209--216},
publisher = {ACM},
series = {ISSAC '01},
title = {Hybrid System for Multi-language and Multi-environment Generation of Numerical Codes},
url = {http://doi.acm.org/10.1145/384101.384130},
year = {2001},
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bdsk-url-1 = {http://doi.acm.org/10.1145/384101.384130},
bdsk-url-2 = {http://dx.doi.org/10.1145/384101.384130}}
@article{McCafferty,
author = {Dennis McCafferty},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Communications of the ACM},
month = oct,
number = {10},
pages = {16--17},
title = {Should Code by Released?},
volume = {53},
year = {2010},
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@book{Wriggers2008,
annote = {- has information on automatic code generation for FEM},
author = {Wriggers, P.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {9783540710004},
lccn = {2008933297},
publisher = {Springer},
title = {Nonlinear Finite Element Methods},
url = {http://books.google.ca/books?id=IaV0wgG2jacC},
year = {2008},
bdsk-file-1 = {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},
bdsk-url-1 = {http://books.google.ca/books?id=IaV0wgG2jacC}}
@inproceedings{Taha2004,
abstract = {Multi-stage programming (MSP) is a paradigm for developing generic software that does not pay a runtime penalty for this generality. This is achieved through concise, carefully-designed language ex- tensions that support runtime code generation and program execution. Additionally, type systems for MSP languages are designed to statically ensure that dynamically generated programs are type-safe, and therefore require no type checking after they are generated.
This hands-on tutorial is aimed at the reader interested in learning the basics of MSP practice. The tutorial uses a freely available MSP extension of OCaml called MetaOCaml, and presents a detailed analysis of the issues that arise in staging an interpreter for a small programming language. The tutorial concludes with pointers to various resources that can be used to probe further into related topics.},
author = {Walid Taha},
booktitle = {Domain-specific Program Generation, LNCS},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-09-13 23:13:37 -0400},
pages = {30--50},
publisher = {Springer-Verlag},
title = {A gentle introduction to multi-stage programming},
year = {2004},
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@article{GabardoEtAl2015,
annote = {- originally submitted to ASEE Advances in Engineering Education - rejected
- previous versions were also submitted},
author = {Philip Gabardo and Thomas E. Doyle and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Learning and Instruction},
note = {18 pp},
title = {Intelligent Prediction Modelling for Determining Students at Risk of Failure},
volume = {Submitted},
year = {2015},
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@book{Voelter2013,
author = {Markus Voelter},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Donationware},
title = {DSL Engineering Desiging, Implementing and Using Domain-Specific Languages},
year = {2013}}
@inproceedings{CzarneckiEtAl2000,
address = {London, UK},
author = {Czarnecki, Krzysztof and Eisenecker, Ulrich W. and Gluck, Robert and Vandevoorde, David and Veldhuizen, Todd L.},
booktitle = {Selected Papers from the International Seminar on Generic Programming},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {3-540-41090-2},
pages = {25--39},
publisher = {Springer-Verlag},
title = {Generative Programming and Active Libraries},
year = {2000}}
@book{CzarneckiEtAl2000book,
address = {New York, NY, USA},
author = {Czarnecki, Krzysztof and Eisenecker, Ulrich W.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0-201-30977-7},
publisher = {ACM Press/Addison-Wesley Publishing Co.},
title = {Generative programming: methods, tools, and applications},
year = {2000}}
@article{Carette2008,
author = {Jacques Carette and Oleg Kiselyov},
bibsource = {DBLP, http://dblp.uni-trier.de},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
ee = {http://dx.doi.org/10.1016/j.scico.2008.09.008},
journal = {Sci. Comput. Program.},
number = {5},
pages = {349-375},
title = {Multi-stage programming with {F}unctors and {M}onads: {E}liminating abstraction overhead from generic code},
volume = {76},
year = {2011},
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@inproceedings{Smith2013,
author = {W. Spencer Smith},
booktitle = {Engineering 1 Summer Seminar Series},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {learning outcomes, graduate attributes, engineering computation},
month = jun,
title = {Do Learning Outcomes Lead to the Outcome of Learning?},
year = {2013}}
@periodical{Economist2012,
author = {{Staff writer}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {The Economist},
title = {When code can kill or cure},
volume = {\url{http://www.economist.com/node/21556098}},
year = {2012}}
@inproceedings{DoyleEtAl2013,
author = {Thomas E. Doyle and W. Spencer Smith and Philip Gabardo},
booktitle = {Proceedings of the 4th Annual Conference of the Canadian Engineering Education Association},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jun,
title = {Machine Learning Methodology for the Analysis of Engineering Student Retention Data},
year = {2013}}
@book{Epstein2010,
author = {Epstein, M.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {9780521198554},
lccn = {2010019217},
publisher = {Cambridge University Press},
series = {The Geometrical Language of Continuum Mechanics},
title = {The Geometrical Language of Continuum Mechanics},
url = {http://books.google.ca/books?id=u3Gyjc1ufDoC},
year = {2010},
bdsk-url-1 = {http://books.google.ca/books?id=u3Gyjc1ufDoC}}
@inproceedings{SmithAndCurwin2012,
author = {Michael D. Curwin and W. Spencer Smith},
booktitle = {Centre for Leadership and Learning - Learning Technology Symposium, McMaster Univeristy},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = apr,
title = {An Elliptical Shaped Classroom: A Room with a View},
year = {2012},
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@article{Merali2010,
annote = {doi:10.1038/467775a
article and comments at: http://www.nature.com/news/2010/101013/full/467775a.html},
author = {Zeeya Merali},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Nature},
pages = {775--777},
title = {Computational science: ...Error},
volume = {467},
year = {2010},
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@techreport{SanchezEtAl2011,
abstract = {This document provides the authors' view on certification
of scientific computing software (SCS). Initially, the relevance of SCS is
underlined, which sets the motivation for attempting the certification of
SCS products. Following this, the semantics of terminology commonly
used in the context of software certification is clarified, given the ambiguous and even contradictory uses in the literature. In particular, the key
concepts of software verification and validation are presented and their
relationship to certification is discussed in the context of SCS. Thereafter,
this report describes approaches to software verification and validation
the authors believe are most promising for SCS - formal specification,
literate programming, document-driven development, code reviews, the
method of manufactured solutions, software mutation, fault injection,
and uncertainty quantification. The product-based approach for certifying software qualities is then presented, alongside the rationale for advocating it.},
author = {Gonzalo Sanchez and W. Spencer Smith and Ned Nedialkov},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McSCert},
month = jul,
note = {26 pp},
number = {2},
title = {{C}ertification of {S}cientific {C}omputing {S}oftware},
type = {Technical Report},
year = {2011},
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@article{Prince2004,
author = {Michael Prince},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {J. Engr. Education},
month = jul,
pages = {223--231},
title = {Does active learning work? A review of the research},
year = {2004},
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@article{PrinceAndFelder2006,
author = {Michael J. Prince and Richard M. Felder},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Engineering Education},
pages = {123--138},
title = {Inductive teaching and learning methods: Definitions, comparisons, and research bases},
volume = {95},
year = {2006},
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@mastersthesis{ElSheikh2010,
address = {Hamilton, ON, Canada},
author = {Mustafa ElSheikh},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University, Open Access Dissertations and Theses. Paper 4992., \url{http://digitalcommons.mcmaster.ca/opendissertations/4992}},
title = {A Generative Approach to Meshing Geometry},
year = {2010},
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@mastersthesis{Yu2007,
author = {Wen Yu},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University},
title = {A Document Driven Methodology for Improving the Quality of a Parallel Mesh Generation Toolbox},
year = {2007}}
@inproceedings{PantelicEtAl2011,
author = {Jacques Carette and Chris George and Zarrin Langari and Mark Lawford and Tom Maibaum and Ned Nedialkov and Vera Pantelic and W. Spencer Smith and Ali Taleghani and Alan Wassyng and Jonathan Ostroff},
booktitle = {Progress on the Certification of Critical Software-Intensive Systems, Certification of Safety-Critical Software-Intensive Systems First Public Workshop},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = nov,
title = {Analysis of Critical Scientific Software},
year = {2011},
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@inproceedings{SmithAndYu2011,
author = {W. Spencer Smith and Wen Yu},
booktitle = {Applied Mathematics, Modeling and Computational Science conference (AMMCS-2011), Minisymposium: Progress and Prospects in Model-Based Scientific Software Development},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jul,
title = {A Family Approach for Scientific Computing Software},
year = {2011},
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@inproceedings{Smith2011,
author = {W. Spencer Smith},
booktitle = {Canadian Engineering Education Association (CEEA 2011) The Evolution of Engineering Education},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jun,
note = {6 pp},
title = {Strategic Planning in an Academic Context},
year = {2011},
bdsk-file-1 = {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}}
@inproceedings{CurwinEtAl2011,
author = {Michael D. Curwin and Thomas E. Doyle and W. Spencer Smith},
booktitle = {The Canadian Higher Education IT Conference CANHEIT 2011, The Nature of Technology},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jun,
title = {Virtual Desktop Computing for Graphically and Computationally Resource Intensive Applications},
year = {2011}}
@inproceedings{DoyleEtAl2011,
annote = {Acknowledgement: MapleSoft},
author = {Thomas E. Doyle and W. Spencer Smith and Adrian Ieta},
booktitle = {Conference Proceedings of $118^{th}$ ASEE Annual Conference \& Exposition},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jun,
note = {9 pp},
organization = {American Society for Engineering Education},
title = {Closing the Design Loop in Freshman Engineering},
year = {2011},
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@techreport{ElSheikhEtAl2011,
author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University, Department of Computing and Software},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/2011/ElSheikhEtAl_CAS_TR_2011/ElSheikhEtAl_CAS_TR_2011.pdf},
note = {19 pp},
number = {CAS-11-06-SS},
title = {Assessment of two a posteriori error estimators for steady-state flow problems},
type = {Technical Report},
year = {2011},
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@article{IEEE2003,
author = {IEEE},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1109/IEEESTD.2003.94394},
journal = {IEEE Std 181-2003},
pages = {54},
title = {{IEEE} Standard on Transitions, Pulses, and Related Waveforms},
year = {2003},
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bdsk-url-1 = {http://dx.doi.org/10.1109/IEEESTD.2003.94394}}
@book{Zelle2004,
annote = { ISBN 13: 978-1887902991},
author = {J. Zelle},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {1st},
publisher = {Franklin, Beedle \& Associates},
title = {{Python Programming: An Introduction to Computer Science}},
year = {2004}}
@techreport{McMasterFacultyOfEng2009,
address = {http:// www.eng.mcmaster.ca/ strategicplan/ index.html},
author = {{Faculty of Engineering}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {McMaster University},
title = {Engineering a Sustainable Society},
type = {Strategic Plan},
year = {2009},
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@techreport{AppliedGeographics2006,
address = {{www.nsgic.org/hottopics/strategic\_plan\_template.pdf}},
author = {{Applied Geographics}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {National States Geographic Information Council (NSGIC)},
month = mar,
number = {05HQCN0034},
title = {Strategic Plan Template},
type = {Contract},
year = {2006},
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@techreport{ParkerGates2010,
author = {Linda {Parker Gates}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Software Engineering Institute, Carnegie-Mellon University},
month = nov,
number = {CMU/SEI-2010-TR-037},
title = {Strategic Planning with Critical Success Factors and Future Scenarios: An Integrated Strategic Planning Framework},
year = {2010},
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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pages = {22--29},
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volume = {86},
year = {2006},
bdsk-file-1 = {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}}
@misc{McCaffrey2005,
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date-added = {2017-09-28 14:24:37 +0000},
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year = {2005},
bdsk-url-1 = {http://msdn.microsoft.com/en-us/magazine/cc163785.aspx}}
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author = {Thomas L. Saaty},
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year = {1995}}
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date-modified = {2017-09-28 14:24:37 +0000},
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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year = {2000}}
@misc{Blitz2010,
author = {Blitz},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
node = {Version 1.2},
title = {Blitz++, Object-Oriented Scientific Computing},
url = {http://www.oonumerics.org/blitz/},
year = {Last Accessed in December 2001},
bdsk-url-1 = {http://www.oonumerics.org/blitz/}}
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.future.2003.09.002}}
@misc{Indiana2010,
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bdsk-url-1 = {http://www.generic-programming.org/}}
@book{Plauger2000,
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year = {2000}}
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isbn = {1-58113-842-3},
location = {Lancaster, UK},
numpages = {10},
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publisher = {ACM},
series = {AOSD '04},
title = {Using AspectJ to separate concerns in parallel scientific Java code},
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bdsk-url-1 = {http://doi.acm.org/10.1145/976270.976286}}
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date-added = {2017-09-28 14:24:37 +0000},
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publisher = {Springer-Verlag},
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institution = {Carnegie-Mellon University Software Engineering Institute},
interhash = {7d9a7ab3a80077c31cfd2a83150d5b3f},
intrahash = {1910de1c3156c3a5821385760069cc52},
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date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.ieeecomputersociety.org/10.1109/TSE.2010.30},
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pages = {309-322},
publisher = {IEEE Computer Society},
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booktitle = {International Conference on Software Testing (ICST)},
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@misc{Mellon2010,
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year = {2002}}
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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publisher = {Institute of Physics Publishing},
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year = {2005}}
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date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1007/s00778-007-0044-3},
issn = {1066-8888},
journal = {The VLDB Journal},
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pages = {389--415},
publisher = {Springer-Verlag New York, Inc.},
title = {Service oriented architectures: approaches, technologies and research issues},
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year = {2007},
bdsk-url-1 = {http://dx.doi.org/10.1007/s00778-007-0044-3}}
@book{Heineman2001,
address = {Boston, MA, USA},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Heineman, George T. and Councill, William T.},
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year = {2001}}
@inproceedings{Crabtree2009,
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booktitle = {SECSE '09: Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1109/SECSE.2009.5069158},
isbn = {978-1-4244-3737-5},
pages = {22--27},
publisher = {IEEE Computer Society},
title = {An empirical characterization of scientific software development projects according to the {B}oehm and {T}urner model: A progress report},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1109/SECSE.2009.5069158}}
@article{William2003,
address = {Los Alamitos, CA, USA},
author = {Wood, William A. and Kleb, William L.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1109/MS.2003.1196317},
issn = {0740-7459},
journal = {IEEE Softw.},
number = {3},
pages = {30--36},
publisher = {IEEE Computer Society Press},
title = {Exploring XP for Scientific Research},
volume = {20},
year = {2003},
bdsk-url-1 = {http://dx.doi.org/10.1109/MS.2003.1196317}}
@article{Kane2006,
author = {Kane, David and Hohman, Moses and Cerami, Ethan and McCormick, Michael and Kuhlmman, Karl and Byrd, Jeff},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1186/1471-2105-7-273},
journal = {BMC Bioinformatics},
number = {1},
pages = {273},
title = {Agile methods in biomedical software development: a multi-site experience report},
url = {http://www.biomedcentral.com/1471-2105/7/273},
volume = {7},
year = {2006},
bdsk-url-1 = {http://www.biomedcentral.com/1471-2105/7/273},
bdsk-url-2 = {http://dx.doi.org/10.1186/1471-2105-7-273}}
@article{EasterbrookAndJohns2009,
address = {Los Alamitos, CA, USA},
author = {Easterbrook, Steve M. and Johns, Timothy C.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1109/MCSE.2009.193},
issn = {0740-7475},
journal = {Comuting in Science \& Engineering},
month = {November/December},
number = {6},
pages = {65--74},
publisher = {IEEE Computer Society Press},
title = {Engineering the Software for Understanding Climate Change},
volume = {11},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.193}}
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address = {Piscataway, NJ, USA},
author = {Di Felice, P.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1109/32.238586},
issn = {0098-5589},
journal = {IEEE Trans. Softw. Eng.},
number = {8},
pages = {835--843},
publisher = {IEEE Press},
title = {Reusability of Mathematical Software: A Contribution},
volume = {19},
year = {1993},
bdsk-url-1 = {http://dx.doi.org/10.1109/32.238586}}
@article{Patzak2001,
address = {Oxford, UK, UK},
author = {Patz\'{a}k, B. and Bittnar, Z.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1016/S0965-9978(01)00027-8},
issn = {0965-9978},
journal = {Adv. Eng. Softw.},
number = {10-11},
pages = {759--767},
publisher = {Elsevier Science Ltd.},
title = {Design of object oriented finite element code},
volume = {32},
year = {2001},
bdsk-url-1 = {http://dx.doi.org/10.1016/S0965-9978(01)00027-8}}
@book{Meyer1988,
address = {Upper Saddle River, NJ, USA},
author = {Meyer, Bertrand},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0136290493},
publisher = {Prentice-Hall, Inc.},
title = {Object-Oriented Software Construction},
year = {1988}}
@article{Miller2006,
author = {Miller, Greg},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {10.1126/science.314.5807.1856},
eprint = {http://www.sciencemag.org/cgi/reprint/314/5807/1856.pdf},
journal = {Science},
number = {5807},
pages = {1856-1857},
title = {{SCIENTIFIC PUBLISHING: A Scientist's Nightmare: Software Problem Leads to Five Retractions}},
url = {http://www.sciencemag.org},
volume = {314},
year = {2006},
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bdsk-url-1 = {http://www.sciencemag.org},
bdsk-url-2 = {http://dx.doi.org/10.1126/science.314.5807.1856}}
@inproceedings{SmithEtAl2010,
author = {W. Spencer Smith and Thomas E. Doyle and Michael D. Curwin},
booktitle = {Canadian Engineering Education Association (CEEA) Inaugural Conference},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = jun,
note = {5 pp},
title = {Undergraduate Engineering Computing Virtualisation},
year = {2010},
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@article{TverskyandKahneman1974,
author = {Amos Tversky and Daniel Kahneman},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Science},
month = sep,
number = {4157},
pages = {1124--1131},
title = {Judgement under Uncertainty: Heuristics and Biases},
volume = {185},
year = {1974}}
@url{YoungAndMacPhedran2011,
author = {Roger Young and Ian MacPhedran},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
lastchecked = {January 28, 2011},
title = {Internet Finite Element Resources, \verb|http://homepage.usask.ca/| \verb|~ijm451/finite/fe_resources/|},
url = {http://homepage.usask.ca/~ijm451/finite/fe_resources/},
urldate = {2011},
bdsk-url-1 = {http://homepage.usask.ca/~ijm451/finite/fe_resources/}}
@inproceedings{YuAndSmith2009_WISE,
address = {McMaster University, Hamilton, Ontario},
author = {Wen Yu and W. Spencer Smith},
booktitle = {International Women's Day Conference},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/GradStudents/WenYuPhD/PhD/Papers/WISE/Presentation.pdf},
month = mar,
organization = {Women in Science and Engineering Initiative},
title = {Reusability of {FEM} Software: A Program Family Approach},
year = {2009},
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@book{KnuppAndSalari2003,
author = {Patrick Knupp and Kambiz Salari},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {K. H. Rosen},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/KnuppAndSalari_2003_Verification%20of%20computer%20codes%20in%20computational%20science%20and%20engineering.pdf},
publisher = {Chapman and Hall/CRC},
title = {Verification of Computer Codes in Computational Science and Engineering},
year = {2003},
bdsk-file-1 = {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}}
@inbook{Korelc2008,
author = {J. Korelc},
chapter = {Automation of the Finite Element Method},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Peter Wriggers},
pages = {483--508},
publisher = {Springer},
title = {Nonlinear Finite Element Methods},
year = {2008}}
@article{PolakAndLutchen2003,
author = {Adam G. Polak and Kenneth R. Lutchen},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Annals of Biomedical Engineering},
keywords = {forced expiration, bronchial tree asymmetry, heterogeneous lung emptying, regional flow interdependence},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/BronchialThermoplastyAndRelated/Polak 2003 -modelling flow.pdf},
month = sep,
number = {8},
pages = {891--907},
title = {Computational Model for Forced Expiration from Asymmetric Normal Lungs},
url = {http://www.springerlink.com/content/k037x12p3164j215/},
volume = {31},
year = {2003},
bdsk-file-1 = {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},
bdsk-url-1 = {http://www.springerlink.com/content/k037x12p3164j215/}}
@techreport{Logg2006,
author = {Anders Logg},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Finite Element Centre},
number = {Preprint 2006-01},
title = {Automating the Finite Element Method},
url = {http://www.femcenter.org/preprints/},
year = {2006},
bdsk-url-1 = {http://www.femcenter.org/preprints/}}
@article{BuiEtAl2008,
abstract = {Simulation of large deformation and post-failure of geomaterial in the framework of smoothed particle hydrodynamics (SPH) are presented in this study. The Drucker-Prager model with associated and non-associated plastic flow rules is implemented into the SPH code to describe elastic-plastic soil behavior. In contrast to previous work on SPH for solids, where the hydrostatic pressure is often estimated from density by an equation of state, this study proposes to calculate the hydrostatic pressure of soil directly from constitutive models. Results obtained in this paper show that the original SPH method, which has been successfully applied to a vast range of problems, is unable to directly solve elastic-plastic flows of soil because of the so-called SPH tensile instability. This numerical instability may result in unrealistic fracture and particles clustering in SPH simulation. For non-cohesive soil, the instability is not serious and can be completely removed by using a tension cracking treatment from soil constitutive model and thereby give realistic soil behavior. However, the serious tensile instability that is found in SPH application for cohesive soil requires a special treatment to overcome this problem. In this paper, an artificial stress method is applied to remove the SPH numerical instability in cohesive soil. A number of numerical tests are carried out to check the capability of SPH in the current application. Numerical results are then compared with experimental and finite element method solutions. The good agreement obtained from these comparisons suggests that SPH can be extended to general geotechnical problems. Copyright 2008 John Wiley \& Sons, Ltd.},
author = {Ha H. Bui and Ryoichi Fukagawa and Kazunari Sako and Shintaro Ohno},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal for Numerical and Analytical Methods in Geomechanics},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MaterialPointMethod/MPM-Journal.pdf},
number = {12},
pages = {1537-1570},
title = {Lagrangian meshfree particles method (SPH) for large deformation and failure flows of geomaterial using elastic-plastic soil constitutive model},
volume = {32},
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@article{McLeishAndLarson1998,
author = {T. C. B. McLeish and R. G. Larson},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Rheology},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/FilmCastingRelated/McLeishAndLarson1998.pdf},
month = jan,
number = {1},
pages = {81--110},
title = {Molecular constitutive equaitons for a class of branched polymers: The pom-pom polymer},
volume = {42},
year = {1998},
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@article{HisahiroEtAl2003,
author = {Hisahiro Ito and Masao Doi and Takeharu Isaki and Masaaki Takeo},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of the Society of Rheology, Japan},
number = {3},
pages = {157--163},
title = {A Model of Neck-in Phenomenon in Film Casting Process},
volume = {31},
year = {2003}}
@inproceedings{FerrezAndLieblin2001,
address = {London, UK},
author = {J.-A. Ferrez and Th. M. Liebling},
booktitle = {HPCN Europe 2001: Proceedings of the 9th International Conference on High-Performance Computing and Networking},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {3-540-42293-5},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/DEM/FerrezAndLieblin2001.pdf},
pages = {211--220},
publisher = {Springer-Verlag},
title = {Parallel DEM Simulations of Granular Materials},
year = {2001},
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@article{MoyseyAndThompson2008,
author = {P. A. Moysey and M. R. Thompson},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Polymer Engineering and Science},
local-url = {/Users/smiths/LongTermArchives/Work/Research/Other\ Students/PaulMoysey/PaulMoyseyWritingUserGuideCode/PolymEngSci_48_1_p62-73_2008.pdf},
number = {1},
pages = {62--73},
title = {Discrete Particle Simulations of Solids Compaction and Conveying in a Single-Screw Extruder},
url = {http://www3.interscience.wiley.com/journal/117357205/abstract?CRETRY=1&SRETRY=0},
volume = {48},
year = {2008},
bdsk-url-1 = {http://www3.interscience.wiley.com/journal/117357205/abstract?CRETRY=1&SRETRY=0}}
@inproceedings{Smith2008_Kingston,
address = {Kingston, Ontario, Canada},
author = {W. Spencer Smith},
booktitle = {Ontario SECSE (Software Engineering for Computational Science and Engineering) Workshop},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {/Users/smiths/Work/Research/Papers/Ontario_SECSE_WorkshopRMC2008/Ont_SECSE_Workshop_Smith.pdf},
month = aug,
title = {Combining Software Engineering and Scientific Computing: Some Potential Research Directions},
year = {2008},
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@techreport{WorthAndGreenough2007,
author = {D. J. Worth and C. Greenough},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Science and Technology Facilities Council},
keywords = {software development, best practice, software tools, quality assurance, FORTRAN programming},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/SoftwareDevelopmentPractices-v3.pdf},
title = {Software Development Best Practice for CSED},
url = {http://www.cse.scitech.ac.uk/seg/html/wrap_pubs.shtml},
year = {2007},
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@book{Boehm1981,
address = {Englewood Cliffs, New Jersey},
author = {Barry Boehm},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Prentice Hall},
title = {Software Engineering Economics},
year = {1981}}
@article{VigderEtAl2008,
author = {Mark Vigder and Norman G. Vinson and Janice Singer and Darlene Stewart and Keith Mews},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Software},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/VigderEtAl2008.pdf},
month = {July/August},
number = {4},
pages = {52--58},
title = {Supporting Scientists' Everyday Work: Automating Scientific Workflows},
volume = {25},
year = {2008},
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@book{OliveiraAndStewart2006,
address = {New York, NY, USA},
author = {Suely Oliveira and David E. Stewart},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0521858968},
publisher = {Cambridge University Press},
title = {Writing Scientific Software: A Guide to Good Style},
year = {2006}}
@article{WollardEtAl2008,
author = {David Wollard and Chris A. Mattmann and Nenad Medvidovic and Yolanda Gil},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Software},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/WoollardEtAl2008.pdf},
month = {July/August},
number = {4},
pages = {37--43},
title = {Scientific Software as Workflows: From Discovery to Distribution},
volume = {25},
year = {2008},
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@article{BasiliEtAl2008,
author = {Victor R. Basili and Daniela Cruzes and Jeffrey C. Carver and Lorin M. Hochstein and Keffrey K. Hollingsworth and Marvin V. Zelkowitz and Forrest Shull},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Software},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/BasiliEtAl2008.pdf},
month = {July/August},
number = {4},
pages = {29--36},
title = {Understanding the High-Performance-Computing Community: A Software Engineer's Perspective},
volume = {25},
year = {2008},
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@article{Kelly2007,
address = {Los Alamitos, CA, USA},
author = {Diane F. Kelly},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1109/MS.2007.155},
issn = {0740-7459},
journal = {IEEE Software},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Kelly2007.pdf},
number = {6},
pages = {120--119},
publisher = {IEEE Computer Society Press},
title = {A Software Chasm: Software Engineering and Scientific Computing},
volume = {24},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MS.2007.155}}
@inbook{BoisvertEtAl2005,
address = {Philadelphia, PA},
author = {Ronald F. Boisvert and Ronald Cools and Bo Einarsson},
chapter = {Assessment of Accuracy and Reliability},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Bo Einarsson},
pages = {13 -- 32},
publisher = {SIAM},
series = {Software-Environments-Tools},
title = {Accuracy and Reliability in Scientific Computing},
year = {2005}}
@inproceedings{CarverEtAl2007,
address = {Washington, DC, USA},
author = {Jeffrey C. Carver and Richard P. Kendall and Susan E. Squires and Douglass E. Post},
booktitle = {ICSE '07: Proceedings of the 29th International Conference on Software Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1109/ICSE.2007.77},
isbn = {0-7695-2828-7},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/CarverEtAl2007.pdf},
pages = {550--559},
publisher = {IEEE Computer Society},
title = {Software Development Environments for Scientific and Engineering Software: A Series of Case Studies},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1109/ICSE.2007.77}}
@article{Glass2004,
address = {New York, NY, USA},
author = {Robert L. Glass},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.acm.org/10.1145/986213.986228},
issn = {0001-0782},
journal = {Commun. ACM},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Glass2004.pdf},
number = {5},
pages = {19--21},
publisher = {ACM},
title = {Matching methodology to problem domain},
volume = {47},
year = {2004},
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bdsk-url-1 = {http://doi.acm.org/10.1145/986213.986228}}
@techreport{KangEtAl1990,
author = {K.C. Kang and S. G. Cohen and J. A. Hess and W. E. Novak and A. S. Peterson},
date-added = {2017-09-28 14:24:37 +0000},
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institution = {Software Engineering Institute},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ProgramFamilies/foda.pdf},
number = {CMU/SEI-90-TR-21},
title = {Feature-Oriented Domain Analysis (FODA). Feasibility Study},
year = {1990},
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://dx.doi.org/10.1016/j.jss.2005.06.046},
issn = {0164-1212},
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number = {7},
pages = {926--938},
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title = {Goal and scenario based domain requirements analysis environment},
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year = {2006},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.jss.2005.06.046}}
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date-modified = {2017-09-28 14:24:37 +0000},
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publisher = {IEEE, Piscataway, NJ},
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {CT Watch Quarterly},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/SquiresEtAl2006.pdf},
month = nov,
pages = {52--61},
title = {Software Productivity Research in High Performance Computing},
url = {http://www.ctwatch.org/quarterly/articles/2006/11/software-productivity-research-in-high-performance-computing/},
year = {2006},
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title = {The Role of Data and Program Code Archives in the Future of Economic Research},
type = {Working Paper 2005-014C},
year = {2005}}
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month = sep,
title = {An Open and Reproducible Paper on Openness and Reproducibility of Papers in Computational Science},
year = {2014}}
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author = {W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Software, Special Issue on Developing Scientific Software},
keywords = {scientific computing, software engineering, requirements/specification, requirements{\newline}template},
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pages = {1--15},
title = {The Danger of Hidden Assumptions and the Need for Requirements in Scientific Computing},
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author = {Hans van Vliet},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {0-471-97508-7},
publisher = {John Wiley \& Sons, Inc.},
title = {Software Engineering (2nd ed.): Principles and Practice},
year = {2000},
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@book{Kreyszig1988,
author = {Erwin Kreyszig},
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date-modified = {2017-09-28 14:24:37 +0000},
edition = {6th},
publisher = {John Wiley \& Sons, Inc.},
title = {Advanced Engineering Mathematics},
year = {1988}}
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author = {Yasuyuki Kato},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {JSME International Journal Series A},
keywords = {finite deformation theory, numerical analysis, nonlinear problem, natural strain, angular strain, rate of deformation tensor, plasticity, deformation history},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ComputationalMechanics/Kato2006.pdf},
number = {3},
pages = {436--443},
title = {Finite Deformation Analysis Using Natural Strain (On Comparison with Other STrain Expression under Three Different Types of Deformation Paths and the Rationality of Natural Strain},
url = {http://www.jstage.jst.go.jp/article/jsmea/49/3/49_436/_article},
volume = {49},
year = {2006},
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@inproceedings{AnandEtAl2004,
author = {C. Anand and J. Carette and A. Korobkine},
booktitle = {{M}aple {S}ummer {W}orkshop 2004},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/GenerativeProgramming/VisualTracking.pdf},
title = {Visual Tracking Employing {M}aple Code Generation},
year = {2004},
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@techreport{CaretteEtAl2007_TR,
annote = {Acknowledgment: NSERC},
author = {Jacques Carette and W. Spencer Smith and John McCutchan and Christopher Anand and Alexandre Korobkine},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Software Quality Research Laboratory, McMaster University},
month = dec,
note = {41 pp},
number = {48},
title = {Model manipulation as part of a better development process for scientific computing code},
year = {2007},
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@inproceedings{AnandEtAl2005,
author = {Christopher K.~Anand and Jacques Carette and Andrew Curtis and David Miller},
booktitle = {Maple Conference 2005 Proceedings},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/GenerativeProgramming/AnandCaretteCurtisMiller.pdf},
pages = {198--212},
publisher = {Maplesoft},
title = {{COG-PETS}: Code Generation for Parameter Estimation in Time Series},
year = {2005},
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@techreport{AnandEtAl2005_SQRL,
author = {Christopher K.~Anand and Jacques Carette and Andrew Curtis and David Miller},
date = jun,
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Software Quality Research Laboratory, McMaster University},
note = {Long version of~\cite{AnCaCuMi}},
number = {31},
pages = {[17 p.]},
title = {{COG-PETS}: Code Generation for Parameter Estimation in Time Series},
type = {SQRL Report},
year = {2005}}
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bibdate = {Mon Nov 16 14:36:22 1998},
coden = {BITTEL, NBITAB},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
issn = {0006-3835},
journal = {BIT},
number = {1},
pages = {10--48},
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volume = {15},
year = {1975}}
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address = {Toronto, Canada},
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booktitle = {CAIMS-MITACS 2006 Joint Annual Conference},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {A Variational Multiscale Element Residual Method},
url = {http://www.mitacs.math.ca/AC06/sessions_events},
year = {2006},
bdsk-url-1 = {http://www.mitacs.math.ca/AC06/sessions_events}}
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author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Canadian Journal of Civil Engineering},
keywords = {adaptive finite elements, a posteriori error estimates, advection diffusion equations, error norm},
local-url = {/Users/smiths/Work/Research/Papers/CJCE_PartII_2007/FinalPublishedVersion.pdf},
month = nov,
pages = {1239--1250},
title = {Assessment of Two A Posteriori Error Estimators for Elasticity Problems},
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volume = {35},
year = {2008},
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@article{ElSheikhEtAl2008_CNM,
author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Communications in Numerical Methods in Engineering},
keywords = {adaptivity, a posteriori error estimation, element residual method, finite element method, steady-state flow, Zienkiewicz-Zhu patch recovery},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/ElSheikhEtAl_Submit2008_CNM_Rejected/ElSheikhEtAl_Submitted2008_CNM.pdf},
title = {Assessment of Two A Posteriori Error Estimators for Steady-State Flow Problems},
year = {Sumbitted 2008 Rejected 2009},
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@mastersthesis{McCutchan2007,
address = {Hamilton, ON, Canada},
author = {John McCutchan},
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date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/GradStudents/JohnMcCutchan/thesis/thesis/build/Thesis.pdf},
month = sep,
school = {McMaster University},
title = {A generative approach to a virtual material testing laboratory},
year = {2007},
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@article{ElSheikhEtAl2008,
author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computer Methods in Applied Mechanics and Engineering},
keywords = {a posteriori error estimation, adaptive meshing, finite element method, variational multiscale method},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/CMAME_ElSheikhEtAl2008_AcceptedRevision/ElSheikhEtAl2008_PublishedVersion.pdf},
month = aug,
pages = {3637--3656},
title = {A posteriori error estimation based on numerical realization of the variational multiscale method},
volume = {197},
year = {2008},
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@inproceedings{CohenEtAl2006,
address = {New York, NY, USA},
author = {Myra B. Cohen and Matthew B. Dwyer and Jiangfan Shi},
booktitle = {ROSATEA '06: Proceedings of the ISSTA 2006 workshop on Role of software architecture for testing and analysis},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.acm.org/10.1145/1147249.1147257},
isbn = {1-59593-459-6},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ProgramFamilies/CohenEtAl2006.pdf},
location = {Portland, Maine},
pages = {53--63},
publisher = {ACM Press},
title = {Coverage and adequacy in software product line testing},
year = {2006},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1147249.1147257}}
@article{Moore1992,
author = {Raymond Moore},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Mathematics and Computers in Simulation},
pages = {113--119},
title = {Parameter sets for bounded-error data},
volume = {34},
year = {1992}}
@book{Pietruszczak1996,
author = {S. Pietruszczak},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Course notes for Civil Engineering 746, McMaster University, Canada},
title = {Theory of Plasticity in Geomechanics},
year = {1996}}
@inbook{CaretteEtAl2008,
address = {Birmingham, UK},
author = {Jacques Carette and W. Spencer Smith and John McCutchan and Christopher Anand and Alexandre Korobkine},
chapter = {Case Studies in Model Manipulation for Scientific Computing},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {/Users/smiths/Work/Research/Papers/mmsc/aisc08/CaretteEtAl2008_AsPublished.pdf},
pages = {24--37},
publisher = {Springer Berlin / Heidelberg},
series = {Lecture Notes in Computer Science},
title = {Intelligent Computer Mathematics, 9th International Conference, AISC 2008},
url = {{http://dx.doi.org/10.1007/978-3-540-85110-3_4}},
year = {2008},
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@inproceedings{ChinEtAl2002,
author = {George Chin Jr. and Ruby Leung and Karen Schuchardt and Debbie Gracio},
booktitle = {Proceedings of the 7th International Conference on Intelligent User Interfaces},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/Problem_Solving_Environments/ChinEtAl2002.pdf},
location = {San Francisco, California, USA},
pages = {39--46},
publisher = {ACM Press},
title = {New Paradigms in Problem Solving Environments for Scientific Computing},
year = {2002},
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@article{VizCore2002,
author = {Y.M.A. Hashash and D. Wotring and J.I.-C. Yao and J.-S. Lee and Q. Fu},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {Visual Framework for Development and use of Constitutive Models. International Journal for Numerical and Analytical Methods in Geomechanics},
year = {2002}}
@article{BorjaAndLee1991,
author = {R. I. Borja and S. R. Lee},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computer Methods in Applied Mechanics and Engineering},
number = {78},
pages = {48--72},
title = {Cam-Clay Plasticity, Part {I}: Implicit Integration of Elasto-Plastic Constitutive Relations},
year = {1991}}
@article{ArnoldAndTan1989,
author = {S. Arnold and H. Tan},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computational Mechanics},
pages = {237--246},
title = {Symbolic derivation of potential based constitutive equations},
year = {1989}}
@article{DeursenEtAl2000,
author = {A.\~ van Deursen and P.\~Klint and J.\~Visser},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {ACM SIGPLAN Notice},
month = jun,
number = {6},
pages = {26--36},
title = {Domain-specific Languages: An Annotated Bibliography},
volume = {35},
year = {2000}}
@article{Einstein1916,
author = {A. Einsten},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Annalen der Physik},
title = {The foundation of the General Theory of Relativity},
year = {1916}}
@book{Joseph1990,
address = {New York},
author = {D. D. Joseph},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Springer Verlag},
title = {Fluid dynamics of viscoelastic liquids},
year = {1990}}
@article{Carette2006,
author = {Jacques Carette},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Science of Computer Programming},
keywords = {MetaOCaml, linear algebra, genericity, generative, staging},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ScientificComputing/Carette2006.pdf},
number = {1},
pages = {3--24},
title = {Gaussian Elimination: A case study in efficient genericity with {M}eta{OC}aml},
volume = {62},
year = {2006},
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@book{Long1961,
address = {Englewood Cliffs, New Jersey},
author = {Robert R. Long},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Prentice Hall},
title = {Mechanics of Solids and Fluids},
year = {1961}}
@book{BeerAndJohnston1985,
author = {F. P. Beer and E. R. Johnston},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {McGraw-Hill},
title = {Mechanics of Materials},
year = {1985}}
@book{ZienkiewiczEtAl2005b,
author = {O. C. Zienkiewicz and R. L. Taylor},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {6th},
publisher = {Elsevier Butterworth-Heinemann},
title = {The Finite Element Method For Solid and Structural Mechanics},
year = {2005}}
@inproceedings{Veldhuizen1998,
author = {Todd. L. Veldhuizen},
booktitle = {Proceedings of the 2nd International Scientific Computing in Object-Oriented Parallel Environments ({ISCOPE}'98), Lecture Notes in Computer Science},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/GenerativeProgramming/Veldhuizen98.pdf},
publisher = {Springer-Verlag},
title = {Arrays in {Blitz++}},
year = {1998},
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@book{McCallEtAl1977,
author = {J. McCall and P. Richards and G. Walters},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = nov,
publisher = {NTIS AD-A049-014, 015, 055},
title = {Factors in Software Quality},
year = {1977}}
@article{WhaleyEtAl2001,
author = {R. C. Whaley and A. Petitet and J. J. Dongarra},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Parallel Computing},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/GenerativeProgramming/WhaleyEtAl2001.pdf},
number = {1--2},
pages = {3--35},
title = {Automated empirical optimization of software and the {ATLAS} project},
volume = {27},
year = {2001},
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@article{RiceAndBoisvert1996,
annote = {Some extra citation information.
@article{Rice1996,
Address = {Los Alamitos, CA, USA},
Author = {Rice, John R. and Boisvert, Ronald F.},
Date-Added = {2011-01-29 01:13:39 -0500},
Date-Modified = {2011-01-29 01:13:39 -0500},
Doi = {http://dx.doi.org/10.1109/99.537091},
Issn = {1070-9924},
Journal = {IEEE Comput. Sci. Eng.},
Number = {3},
Pages = {44--53},
Publisher = {IEEE Computer Society Press},
Title = {From Scientific Software Libraries to Problem-Solving Environments},
Volume = {3},
Year = {1996},
Bdsk-Url-1 = {http://dx.doi.org/10.1109/99.537091}}
},
author = {John R. Rice and Ronald F. Boisvert},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Computational Science \& Engineering},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/Problem_Solving_Environments/RiceAndBoisvert1996.pdf},
month = {Fall},
number = {3},
pages = {44--53},
title = {From Scientific Software Libraries to Problem-Solving Environments},
volume = {3},
year = {1996},
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@article{Stolle1991,
author = {Dieter F. E. Stolle},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal for Numerical and Analytical Methods in Geomechanics},
pages = {399--416},
title = {An Interpretation of Initial Stress and Strain Methods and Numerical Stability},
volume = {15},
year = {1991}}
@inproceedings{TilleyEtAl2007,
address = {Dublin, Ireland},
author = {Scott Tilley and Kenny Wong and W. Spencer Smith},
booktitle = {Twentieth Conference on Software Engineering Education \& Training (CSEE\&T 2007)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {H. Edwards and R. Narayanan},
local-url = {/Users/smiths/Work/Research/Papers/CSEE&T2007/CSEE&T_2007_(02Apr07)_CameraReadyCopy.pdf},
month = jul,
organization = {%The %Institute %of %Electrical %and %Electronics %Engineers, %Inc.},
pages = {237--244},
publisher = {% IEEE %Computer %Society %Conference %Publishing %Services %(CPS)},
title = {Report from the 3rd International Symposium on Software Engineering Course Projects ({SWECP} 2006)},
year = {2007},
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@article{Perzyna1966,
author = {P. Perzyna},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Advances in Applied Mechanics},
pages = {243--377},
title = {Fundamental problems in viscoplasticity},
year = {1966}}
@inproceedings{McCutchanAndSmith2007,
address = {London, Ontario, Canada},
author = {John McCutchan and W. Spencer Smith},
booktitle = {Proceedings of SNC 2007},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/SNC2007/Version3/snc/McCutchanAndSmith_AsSubmitted.pdf},
title = {A Virtual Material Testing Laboratory Using Symbolic Processing and Code Generation},
year = {rejected},
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@article{HullEtAl1972,
author = {T.E. Hull and W.H. Enright and B.M. Fellen and A. E. Seddwick},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {SIAM Journal of Numerical Analysis},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ScientificComputing/HullEtAl1972.pdf},
title = {Comparing numerical methods for ordinary differential equations},
year = {1972},
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@article{Rivara1997,
author = {Rivara, Maria-Celilia},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal for Numerical Methods in Engineering},
pages = {3313--3324},
publisher = {Wiley},
title = {New Longest-Edge Algorithms for the Refinement and/or Improvement of Unstructured Triangulation.},
volume = {40},
year = {1997}}
@book{Blicq1987,
author = {Ron Blicq},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Prentice Hall},
title = {Technically-Write!},
year = {1987}}
@unpublished{OpenMesh2006,
author = {OpenMesh},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {OpenMesh, {C}omputer {G}raphics \& {M}ultimedia {G}roup, {R}heinisch-{W}estf\"{a}lische {T}echnische {H}ochschule {A}achen, http://www.openmesh.org/},
url = {http://www.openmesh.org/},
urldate = {January 12, 2007},
year = {2006},
bdsk-url-1 = {http://www.openmesh.org/}}
@book{Pressman1999,
author = {Roger S. Pressman},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {McGraw-Hill},
title = {Software Engineering, A Practitioner's Approach, fourth Edition},
year = {1999}}
@article{ElSheikhEtAl2006_NME,
author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal for Numerical Methods in Engineering},
title = {A posteriori error estimation based on numerical realization of the variational multiscale method},
year = {rejected}}
@mastersthesis{Cao2006,
author = {Fang Cao},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
month = apr,
school = {McMaster University},
title = {A Program Family Approach to Developing Mesh Generators},
year = {2006}}
@inproceedings{Owen1998_old_link,
address = {Dearborn, MI},
author = {Owen, Steven J.},
booktitle = {Proceedings 7th International Meshing Roundtable},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {www.andrew.cmu.edu/user/sowen/survey},
month = oct,
title = {A Survey of Unstructured Mesh Generation Technology},
year = {1998},
bdsk-url-1 = {http://dx.doi.org/www.andrew.cmu.edu/user/sowen/survey}}
@misc{OwenWeb2006,
author = {Owen, Steven J.},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://www.andrew.cmu.edu/user/sowen/mesh.html},
title = {Meshing Research Corner},
year = {2006},
bdsk-url-1 = {http://www.andrew.cmu.edu/user/sowen/mesh.html}}
@book{ZienkiewiczEtAl2005,
author = {O. C. Zienkiewicz and R. L. Taylor and J. Z. Zhu},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {6th},
publisher = {Elsevier Butterworth-Heinemann},
title = {The Finite Element Method Its Basis and Fundamentals},
year = {2005}}
@book{VanAlstyne2005,
address = {Upper Saddle River, New Jersey},
author = {Judith S.\ VanAlstyne},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {Sixth},
publisher = {Pearson Prentice Hall},
title = {Professional and Technical Writing Strategies},
year = {2005}}
@inproceedings{SiegelEtAl2006,
address = {Portland, ME},
author = {Stephen F.\ Siegel and Anastasia Mironova and George S.\ Avrunin and Lori A.\ Clarke},
booktitle = {International Symposium on Software Testing and Analysis (ISSTA)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/SiegelEtAl2006.pdf},
title = {Using Model Checking with Symbolic Execution to Verify Parallel Numerical Programs},
year = {2006},
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@book{Heath2002,
address = {New York, NY, USA},
author = {Michael Heath},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {2nd},
keywords = {scientific computing},
publisher = {McGraw-Hill Publishing Company},
title = {Scientific Computing: An Introductory Survey},
year = {2002}}
@book{EinarssonEtAl2005,
address = {Philadelphia, PA},
author = {Bo Einarsson and Ronald Boisvert and Fran\c{c}oise Chaitin-Chatelin and Ronald Cools and Craig Douglas and Kenneth Dritz and Wayne Enright and William Gropp and Sven Hammarling and Hans Petter Langtangen and Roldan Pozo and Siegfried Rump and Van Snyder and Elisabeth Traviesas-Cassan and Mladen Vouk and William Walster and Brian Wichmann},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {accuracy, numerical software, reliability},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/EinarssonEtAl2005_Accuracy_Reliability.pdf},
number = {0-89871-584-9},
publisher = {SIAM},
series = {Software-Environments-Tools},
title = {Accuracy and Reliability in Scientific Computing},
url = {http://ec-securehost.com/SIAM/SE18.html},
year = {2005},
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@book{ClementsAndNorthrop2001,
address = {Boston, MA, USA},
author = {Paul Clements and Linda M. Northrop},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
title = {Software product lines: practices and patterns},
year = {2002}}
@article{ElSheikhEtAl2008_CNME,
author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Communications in Numerical Methods in Engineering},
keywords = {adaptive finite elements, a posteriori error estimates, advection diffusion equations, error norm},
local-url = {/Users/smiths/Work/Research/Papers/ElSheikhEtAl2008_CommNumMethEng/ElSheikhEtAl2008_PublishedVersion.pdf},
month = sep,
pages = {711--726},
title = {Numerical investigation of the reliability of a posteriori error estimation for advection-diffusion equations},
volume = {24},
year = {2008},
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@article{Wilkinson1971,
author = {J. H. Wilkinson},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {{SIAM} Review},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ScientificComputing/Wilkinson1971.pdf},
pages = {548--568},
title = {Modern Error Analysis},
volume = {13},
year = {1971},
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@book{PohlEtAl2005,
author = {K. Pohl and G. B\"{o}ckle and F. van der Linden},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Springer-Verlag},
title = {Software Product Line Engineering: Foundations, Principles, and Techniques},
year = {2005}}
@incollection{Heitmeyer2002,
author = {Constance Heitmeyer},
booktitle = {Encyclopedia of Software Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {2nd},
editor = {J. J. Marciniak},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Heitmeyer2002.pdf},
publisher = {John Wiley \& Sons, Inc.},
title = {Software Cost Reduction},
year = {2002},
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@inproceedings{CorlissEtAl2008,
author = {George F. Corliss and R. Baker Kearfott and Ned Nedialkov and John D. Pryce and W. Spencer Smith},
booktitle = {Reliable Implementation of Real Number Algorithms: Theory and Practice, International Seminar Dagstuhl Castle, Germany, January 8--13, 2006},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {P. Hertling and C. M. Hoffmann and W. Luther and N. Revol},
month = sep,
organization = {Lecture Notes in Computer Science},
pages = {28--43},
publisher = {Springer Verlag},
title = {Interval Subroutine Library Mission},
url = {http:// drops.dagstuhl.de/ portals/ 06021/ (original draft)},
year = {2008},
bdsk-url-1 = {http://%20drops.dagstuhl.de/%20portals/%2006021/%20(original%20draft)}}
@inproceedings{CorlissEtAl2006_DROPS,
author = {George F. Corliss and R. Baker Kearfott and Ned Nedialkov and John D. Pryce and W. Spencer Smith},
booktitle = {Proceedings of Dagstuhl Seminar 06021 Reliable Implementation of Real Number Algorithms:{\newline}Theory and Practice},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
note = {[date of citation: 2005-02-01]},
number = {06021},
optannote = {Keywords: Dagstuhl Seminar 06021},
pages = {[15 p.]},
publisher = {Schloss Dagstuhl, Germany},
title = {Interval Subroutine Library Mission},
url = {http://drops.dagstuhl.de/portals/06021/},
year = {2006},
bdsk-url-1 = {http://drops.dagstuhl.de/portals/06021/}}
@inproceedings{Smith2006_UL,
address = {University of Limerick, Ireland},
author = {%W. Spencer Smith},
booktitle = {Software Quality Research Laboratory},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/LimerickPresent2006/LimerickPresent2006.pdf},
title = {Is Computer Science to Software Engineering as Physics is to Civil Engineering?},
year = {2006},
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@book{Saaty1980,
address = {New York, New York},
author = {T. L. Saaty},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {McGraw-Hill Publishing Company},
title = {The Analytic Hierarchy Process: Planning, Priority Setting, Resource Allocation},
year = {1980}}
@inproceedings{Smith2006_AIMS,
address = {Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario},
author = {%W. Spencer Smith},
booktitle = {Applied, Industrial and Financial Mathematics Seminar},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/AIMS2006/SmithAbstract.txt},
title = {Improving the Quality of Scientific Computing Software Through Requirements Analysis},
year = {2006},
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@article{Parnas1997,
address = {New York, NY, USA},
author = {David Lorge Parnas},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.acm.org/10.1145/260750.260784},
issn = {0001-0782},
journal = {Commun. ACM},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Parnas1997.pdf},
number = {9},
pages = {128},
publisher = {ACM Press},
title = {Software engineering: an unconsummated marriage},
volume = {40},
year = {1997},
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bdsk-url-1 = {http://doi.acm.org/10.1145/260750.260784}}
@inproceedings{Smith2006_Dag,
booktitle = {Reliable Implementation of Real Number Algorithms: Theory and Practice},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/Dagstuhl2006/Dagstuhl2006.pdf},
publisher = {Schlo\ss\ Dagstuhl, Germany, Seminar 06021},
title = {Quality Assurance in Developing an Interval Subroutine Library},
url = {http://www.dagstuhl.de/06021/index.en.phtml},
year = {2006},
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@techreport{Pryce2005,
address = {Dept of Information Systems, Shrivenham Campus, Swindon SN6 8LA, UK},
author = {J. D. Pryce},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Cranfield University},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/IntervalMethods/Pryce2005.pdf},
number = {DolS/TR01/05},
title = {An introduction to containment sets},
year = {2005},
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@misc{ElSheikhEtAl2005,
address = {Montreal Scientific Computing Days},
author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {Centre de recherches mathmatiques, Universit de Montreal, Montreal, Quebec},
title = {On Reliable Error Estimation for Advection-Diffusion Equations (Poster Presentation), {C}entre de {R}echerches {M}ath\'{e}matiques, {U}niversit\'{e} de {M}ontr\'{e}al, {M}ontr\'{e}al, {Q}u\'{e}bec},
year = {2005}}
@article{SpectorAndGifford1986,
address = {New York, NY, USA},
author = {Alfred Spector and David Gifford},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.acm.org/10.1145/5684.6327},
issn = {0001-0782},
journal = {Commun.\ ACM},
number = {4},
pages = {267--283},
publisher = {ACM Press},
title = {A computer science perspective of bridge design},
volume = {29},
year = {1986},
bdsk-url-1 = {http://doi.acm.org/10.1145/5684.6327}}
@mastersthesis{Kwan2005,
author = {Irwin Kwan},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Irwin_Kwan_-_Masters_Thesis_-_2005.final.pdf},
school = {Waterloo},
title = {On the Maintenance Costs of Formal Software Requirements Specifications Written in the Software Cost Reduction and in the Real-time Unified Modeling Language Notations},
year = {2005},
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@inproceedings{Clavet-2005-PVFS,
author = {Simon Clavet and Philippe Beaudoin and Pierre Poulin},
booktitle = {Symposium on Computer Animation 2005},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {computer graphics, computational geometry and object modelling - physically based modelling, three-dimensional graphics and realims - animation and virtual reality},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ComputerAnimation/ClavetEtAl2005.pdf},
pages = {219--228},
title = {Particle-based Viscoelastic Fluid Simulation},
url = {http://www.iro.umontreal.ca/labs/infographie/papers/Clavet-2005-PVFS/index.html},
year = {2005},
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@inproceedings{TilleyEtAl2006,
address = {Turtle Bay, Hawaii},
author = {Scott Tilley and Shihong Huang and Kenny Wong and W. Spencer Smith},
booktitle = {Proceedings of the 19th Conference on Software Engineering Education \& Training (CSEE\&T 2006)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {D. Martin},
pages = {87--94},
title = {Report from the 2nd International Workshop on Software Engineering Course Projects ({SECP} 2005)},
url = {http://db-itm.cba.hawaii.edu/cseet2006/papers.htm (Last Accessed Nov. 28. 2005)},
year = {2006},
bdsk-url-1 = {http://db-itm.cba.hawaii.edu/cseet2006/papers.htm%20(Last%20Accessed%20Nov.%2028.%202005)}}
@article{ElSheikhEtAl2006_ASCE2,
address = {{\par}},
author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {ASCE Journal of Engineering Mechanics},
local-url = {/Users/smiths/Work/Research/Papers/ASCEJournal_2005_PartII/ASCE_Part_2_May06_v1.pdf},
title = {Assessment of Two A Posteriori Error Estimators for {FEM}, Part {II}: Elasticity},
year = {rejected}}
@techreport{BabuskaAndOden2005,
author = {Ivo Babuska and J. Tinsley Oden},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {The Institute for Computational Engineering and Sciences, University of Texas},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ReliableComputing/BabuskaAndOden2005.pdf},
number = {ICES Report 05-10},
title = {The Reliability of Computer Predictions: Can they be trusted?},
url = {http://www.ices.utexas.edu/research/reports/2005.php},
year = {2005},
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@inproceedings{NuseibehAndEasterbrook2000,
address = {New York, NY, USA},
author = {Bashar Nuseibeh and Steve Easterbrook},
booktitle = {ICSE '00: Proceedings of the Conference on The Future of Software Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.acm.org/10.1145/336512.336523},
isbn = {1-58113-253-0},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ReqAnalysis/NuseibehAndEasterbrook2000.pdf},
location = {Limerick, Ireland},
pages = {35--46},
publisher = {ACM Press},
title = {Requirements engineering: a roadmap},
year = {2000},
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bdsk-url-1 = {http://doi.acm.org/10.1145/336512.336523}}
@article{BernEtAl1999,
author = {Marshall W. Bern and David Eppstein and Shang-Hua Teng},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal of Computational Geometry and Applications},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/BernEtAl1999.pdf},
number = {6},
pages = {517--532},
title = {Parallel Construction of Quadtrees and Quality Triangulations},
volume = {9},
year = {1999},
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@inbook{Baber1998,
author = {Robert Baber},
chapter = {The Prolonged Metamorphosis of a Software Engineer},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Baber1998.pdf},
pages = {174--208},
publisher = {IEEE Computer Society Press},
title = {In the Beginning: Recollections of Software Pioneers},
year = {1998},
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@inproceedings{SchleeAndVanderdonckt2004,
address = {New York, NY, USA},
author = {Max Schlee and Jean Vanderdonckt},
booktitle = {AVI '04: Proceedings of the working conference on Advanced visual interfaces},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
doi = {http://doi.acm.org/10.1145/989863.989936},
isbn = {1-58113-867-9},
keywords = {ABA. AI, ANGIE, DSL, FODA, GP, JANUS, OO, OOA/D, Qt, XML, UML},
location = {Gallipoli, Italy},
pages = {403--406},
publisher = {ACM Press},
title = {Generative Programming of graphical user interfaces},
year = {2004},
bdsk-url-1 = {http://doi.acm.org/10.1145/989863.989936}}
@inproceedings{JungEtAl2005,
author = {Thomas Jung and Horst Hadler and Michael Kellner},
booktitle = {Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics, WMSCI 2005},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/JungEtAl2005.pdf},
title = {ORCAN: An Open Component Framework, and its Application to the Development of Complex Simulation Software},
year = {2005},
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@inproceedings{Smith2005,
address = {Markham, Ontario},
author = {W. Spencer Smith},
booktitle = {Proceedings of the CASCON Workshops, Second International Workshop on Software Engineering Course Projects (SECP 2005)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {Teaching Capstone Software Design Project Courses: Issues and Challenges},
url = {https://www-927.ibm.com/ibm/cas/cascon/index.shtml (last accesed November 28, 2005)},
year = {2005},
bdsk-url-1 = {https://www-927.ibm.com/ibm/cas/cascon/index.shtml%20(last%20accesed%20November%2028,%202005)}}
@misc{FederlAndPrusinkiewicz?,
author = {Pavol Federl and Przemyslaw Prusinkiewicz},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {interactive graphics environment, software design, graphical browser, object, inheritance, hyperobject, link, modelling, simulation},
title = {Virtual Laboratory: an Interactive Software Environment for Computer Graphics},
url = {http://www.cpsu.ucalgary.ca/Redirect/bmv/vlab.orig/vlab.html},
year = {?},
bdsk-url-1 = {http://www.cpsu.ucalgary.ca/Redirect/bmv/vlab.orig/vlab.html}}
@inproceedings{Berti2003,
address = {Forschungszentrum J{\"u}lich},
author = {Guntram Berti},
booktitle = {Proceedings of the Workshop on Parallel/High-Performance Object-Oriented Scientific Computing (POOSC'03)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {J{\"o}rg Striegnitz and Kei Davis},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Berti2003.pdf},
month = jul,
organization = {number IB-2003-09 in NIC series},
pages = {15--30},
title = {Generic programming support for mesh partitioning based parallelization},
url = {http://www.kfa-juelich.de/zam/files/docs/ib/ib-03/ib-2003-09.pdf},
year = {2003},
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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title = {Decoupling Change From Design},
year = {1996}}
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date-modified = {2017-09-28 14:24:37 +0000},
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Telecommunications Research Institute of Ontario (TRIO), McMaster University},
number = {CRL Report 260},
title = {Tabular Representation of Relations},
year = {1992}}
@article{Fowler2002,
author = {Martin Fowler},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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title = {Public versus Published Interfaces},
year = {2002}}
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {J. Wiley \& Sons},
title = {Automatic Mesh Generation: Applications to Finite Methods},
year = {1991}}
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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year = {1999}}
@techreport{IEEE1996,
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Institute of Electronic and Electrical Engineers},
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year = {1996}}
@book{Liseiki1999,
author = {Vladimir D. Liseikin},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Springer-Verlag},
title = {Grid Generation Methods},
year = {1999}}
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author = {Martin Fowler},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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title = {To be Explicit},
year = {November 2001}}
@inproceedings{Bastarrica2002,
author = {Mar\'{i}a Cecilia Bastarrica},
booktitle = {Proceedings of the XXVIII Latin American Conference of Informatics, {CLEI'2002}, Montevideo, Uruguay},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {119},
title = {Base Architecture in a Software Product Line},
year = {2002}}
@misc{Owen2005,
author = {Steve Owen},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {Department of Civl and Environmental Engineering and Ansys Inc.},
title = {A Survey of Unstructured Mesh Generation Technology},
url = {http://www.andrew.cmu.edu/user/sowen/survey/index.html#intro},
urldate = {2005},
year = {2005},
bdsk-url-1 = {http://www.andrew.cmu.edu/user/sowen/survey/index.html#intro}}
@inproceedings{MobleyEtAl2001,
author = {Anton V. Mobley and Joseph R. Tristano and Christopher M. Hawkings},
booktitle = {Proceedings of the 10th Annual International Meshing Roundtable, {N}ewport {B}each, {C}alifornia, {USA}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {7--10},
title = {An object-oriented design for mesh generation and operation algorithms},
year = {2001}}
@inproceedings{ElSheikhEtAl2005_CanCam,
address = {Montr\'{e}al, Qu\'{e}bec},
author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
booktitle = {Proceedings of the 20th Canadian Congress of Applied Mechanics, CANCAM 2005},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {M. Ostoja-Starzewski},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/CanCam2005/CANCAM2005_v2.pdf},
pages = {492--493},
title = {A comparative analysis of two posteriori error estimators for the finite element method},
year = {2005},
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@book{Mase1970,
author = {George E. Mase},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {McGraw-Hill Publishing Company},
title = {Schaum's Outline of Theory and Problems of Continuum Mechanics},
year = {1970}}
@inproceedings{Tautges2000,
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booktitle = {Proceedings of the 9th Annual International Meshing Roundtable, October 2--5},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {337--347},
title = {The common geometry module ({CGM}): A generic, extensible, geometry interface},
year = {2000}}
@inproceedings{Sheard2001,
address = {London, UK},
author = {Tim Sheard},
booktitle = {SAIG 2001: Proceedings of the Second International Workshop on Semantics, Applications, and Implementation of Program Generation},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
isbn = {3-540-42558-6},
pages = {2--44},
publisher = {Springer-Verlag},
title = {Accomplishments and Research Challenges in Meta-programming},
year = {2001}}
@mastersthesis{Gao2004,
author = {Huanchun Gao},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University},
title = {A Framework for a Virtual Material Testing Laboratory},
year = {2004}}
@book{Rogerson1997,
author = {Dale Rogerson},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Microsoft Press},
title = {Inside {COM}},
year = {1997}}
@article{RemacleAndShephard2003,
author = {Jean-Fancois Remacle and Mark S. Shephard},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal for Numerical methods in Engineering},
keywords = {mesh database, mesh representation, C++STL},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/AOMD/RemacleAndShephard2003.pdf},
pages = {349--374},
title = {An Algorithm Oriented Mesh Database},
volume = {58},
year = {2003},
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@inproceedings{ErwigAndFu2004,
author = {Martin Erwig and Zhe Fu},
booktitle = {6th International Symposium on Practical Aspects of Declarative Languages (PADL'04)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {Fortran, Generic Programming, Program Generation, Haskell},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/ErwigAndFu2000%3F.pdf},
month = jun,
pages = {209--223},
publisher = {Springer Verlag, LNCS 3057},
title = {Parametric Fortran - A Program Generator for Customized Generic Fortran Extensions},
url = {http://web.engr.oregonstate.edu/~erwig/papers/abstracts.html},
year = {2004},
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bdsk-url-1 = {http://web.engr.oregonstate.edu/~erwig/papers/abstracts.html}}
@techreport{Han2001,
author = {Delian Han},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Software Engineering Research Group, McMaster University},
number = {SERG Report 398},
title = {Using Tabular Expression Input to Specify and Generate Program Family Members},
year = {2001}}
@techreport{FischerAndVisser2004,
author = {Bernd Fischer and Eelco Visser},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Institute of Information and Computing Sciences},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/GenerativeProgramming/RetrofittingAutobayes.pdf},
title = {Retrofitting the AutoBayes Program Synthesis System with Concrete Syntax},
year = {2004},
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@inproceedings{MerazziEtAl2000,
address = {New Orleans, U.S.A.},
author = {Silvio Merazzi and Edgar Gerteisen and Andrey Mezentsev},
booktitle = {Proceedings of the 9th Annual International Meshing Roundtable, October 2--5},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/MerazziEtAl2000.pdf},
pages = {361--370},
title = {A generic {CAD}-mesh interface},
year = {2000},
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@article{PenumaduEtAl2000,
author = {D. Penumadu and R. Zhao and J.D. Frost},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal of Numerical and Analytical Methods in Geomechanics},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/VirtualLab/PenumaduEtAl2000.pdf},
pages = {439--451},
title = {Virtual geotechnical laboratory experiement using a simulator},
volume = {24},
year = {2000},
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@book{PotterEtAl1996,
author = {Ben Potter and Jane Sinclair and David Till},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {2nd},
editor = {C.A.R. Hoare Series},
publisher = {Prentice Hall},
title = {An Introduction to Formal Specification and Z},
year = {1996}}
@article{FabriEtAl2000,
author = {Andreas Fabri and Geert--Jan Giezeman and Lutz Kettner and Stefan Schirra and Sven Schonherr},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Software -- Practice and Experience},
keywords = {computational geometry, software library, C++, generic programming},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/FabriEtAl2000.pdf},
pages = {1167--1202},
title = {On the Design of {CGAL} a computational geometry algorithms library},
volume = {30},
year = {2000},
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@article{RuizEtAl2000,
author = {Irene Luque Ruiz and Enrique L\'{o}pez Espinosa and Gonzalo Cerruela Garc\'{i}a and Miguel \'{A}ngel G\'{o}mez-Nieto},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Chemical Information and Computer Sciences},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/VirtualLab/RuizEtAl2000.pdf},
number = {3},
pages = {744--752},
title = {Design and development of computer aided chemical systems: representation and balance of inorganice chemical reactions},
volume = {40},
year = {2000},
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@inproceedings{ElSheikhEtAl2005_USNCCM,
address = {Austin, Texas},
author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
booktitle = {Proceedings of the Eighth United States National Congress on Computational Mechanics, USNCCM8, A Posteriori Error Estimation and Adaptive Procedures from 1976 to 2005, Symposium in Honor of Professor Ivo Babuska},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/USNCCM8/abstract_v2.pdf},
title = {On the Choice of An Error Norm for Advection Diffusion Equations},
year = {2005},
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@misc{BruasetAndLangtangen1996,
author = {A. Bruaset and H. Langtangen},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/BruasetAndLangtangen1996.pdf},
title = {A comprehensive set of tools for solving partial differential equations; Diffpack},
url = {citeseer.nj.nec.com/bruaset96comprehensive.html},
year = {1996},
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@article{KhannaEtAl2002,
author = {S. K. Khanna and C. H. Jenkins and D. Roylance},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Proceedings of the institution of mechanical engineers part L -- Journal of Materials-Design and Applications},
keywords = {mechanics, engineering materials, multimedia courseware, virtual laboratory, structure-propery relationship},
pages = {49--53},
title = {A new approach to integrated instruction in mechanics and material science},
volume = {216 (L1)},
year = {2002}}
@book{IEEE2000_ThayerAndDorfman,
author = {{The Institute of Electrical and Electronics Engineers, Inc.}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {2nd},
editor = {Richard H. Thayer and Merlin Dorfman},
publisher = {{IEEE} Computer Society Press},
title = {Software Requirements Engineering},
year = {2000}}
@article{GiakoumakisAndXylomenos1996,
author = {E.A. Giakoumakis and G. Xylomenos},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Software Engineering Journal},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/GiakoumakisAndXylomenos1996.pdf},
month = sep,
number = {5},
pages = {307-319},
title = {Evaluation and selection criteria for software requirements specification standards},
volume = {11},
year = {1996},
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@article{ElSheikhEtAl2006_ASCE1,
author = {Ahmed H. ElSheikh and Samir E. Chidiac and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {ASCE Journal of Engineering Mechanics},
local-url = {/Users/smiths/Work/Research/Papers/ASCEJournal_2005_PartI/ASCE_Part_1_May06_v1.pdf},
title = {Assessment of Two A Posteriori Error Estimators for {FEM}, Part {I}: Steady-State Flow},
year = {rejected}}
@book{Davis1990,
author = {Alan M. Davis},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {Revision},
keywords = {software engineering, requirements},
publisher = {Prentice Hall},
title = {Software requirements objects, functions, and states},
year = {1990}}
@misc{TautgesEtAl1995,
author = {T. Tautges and T. Blacker and S. Mitchell},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
text = {Tautges, T. J., Blacker, T., and Mitchell, S. A. `The Whisker Weaving Algorithm: A Connectivity-Based Method for Constructing All-Hexahedral Finite Element Meshes' submitted to Int. J. Num. Meth. Eng. (1995)},
title = {The Whisker Weaving Algorithm: A Connectivity-Based Method for Constructing All-Hexahedral Finite Element Meshes},
url = {citeseer.ist.psu.edu/tautges95whisker.html},
year = {1995},
bdsk-url-1 = {citeseer.ist.psu.edu/tautges95whisker.html}}
@book{Perry2000,
author = {William Perry},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {2nd ed.},
publisher = {John Wiley & Sons, Inc.},
title = {Effective methods for software testing},
year = {2000}}
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author = {Lawrence Bodin and Eddie Epstein},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computers & Operations Research},
number = {3},
pages = {205--215},
title = {Who's on first with probability 0.4},
volume = {27},
year = {2000}}
@article{AikenAndMartin1995,
author = {Milam Aiken and Jeanette Martin},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
issn = {0730-8639},
journal = {Math. Comput. Educ.},
number = {3},
pages = {232--235},
publisher = {Mathematics and Computer Education},
title = {Using a group decision support system for mathematics problem solving},
volume = {29},
year = {1995}}
@misc{Mirza1990,
author = {F. Mirza},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {Civil Engineering Department, McMaster University},
title = {Finite Element Course Notes},
year = {1990}}
@techreport{BlackerEtAl1994,
author = {T. D. Blacker and Robert A. Kerr and Patrick Knupp and Robert W. Leland and Darryl J. Melander and Scott A. Mitchell and Steven J. Owen and Jason F. Sheperd and Timoshy J. Tautges and David R. White and Steve Benzley and Michael J. Borden and Steven R. Jankovich and Jason Kraftcheck and Yong Lu and Ray J. Meyers and Michael Stephenson and Steve Storm and Eric Nielsen and Rammagy Yoeu},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Sandia National Laboratories, Albuquerque, New Mexico},
number = {SAND94-1100},
title = {CUBIT Mesh Generation Environment, Volume 1: User's Manual},
year = {May 1994}}
@article{Jones1975,
author = {Rondall E. Jones},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Association for Computing Machinery SIGNUM Newsletter, vol. 10, no. 4, pp. 31-34},
title = {The {QMESH} Mesh Generation Package},
year = {December 1975}}
@article{DesharnaisEtAl2004,
author = {Jules Desharnais and Ridha Khedri and Ali Mili},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Formal Methods in System Design},
note = {To appear},
pages = {40},
title = {Representation, Validation and Integration of Scenarios Using Tabular Expressions},
year = {2004}}
@techreport{vanSchouwen1992,
author = {A. John van Schouwen},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {Communications Research Laboratory, McMaster University},
title = {The {A}-7 Requirements Model: Re-Examination for Real-Time Systems and An Application to Monitoring Systems},
year = {1992}}
@article{GaoAndSmith2004,
author = {Huanchun Gao and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal of Software Engineering and Knowledge Engineering},
title = {Design of a Virtual Material Testing Laboratory using Software Engineering Methodologies},
volume = {rejected},
year = {2004}}
@misc{GaoAndSmith2002,
address = {Toronto, Ontario, Canada},
author = {Huanchun Gao and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
organization = {MMO Partnerships},
title = {A Virtual Laboratory (Poster Presentation), {M}aterials and {M}anufacturing ({MMO}) {P}artnerships, {T}oronto, {O}ntario},
year = {2002}}
@book{LeeAndVaraiya2003,
author = {Edward A. Lee and Pravin Varaiya},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Addison-Wesley},
title = {Structure and Interpretation of Signals and Systems},
year = {2003}}
@inproceedings{FowlerEtAl1999,
author = {Danielle Fowler and Brian Henderson-Sellers and Paul Swatman},
booktitle = {Proceedings of the 10th Australian Conference on Information Systems},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/PaperFowler-109.pdf},
title = {A Requirements Engineering Process for OPEN Development},
year = {1999},
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@inproceedings{SmithAndGao2005,
address = {Orlando, Florida},
author = {W. Spencer Smith and Huanchun Gao},
booktitle = {WMSCI 2005, The 9th World Multi-Conference on Systemics, Cybernetics and Informatics, Volume {VI}},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {N. Callaos and R. H. Chavez and S. Franger and R. Raut and Z. He},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/WMSCI2005/SmithAndHuanFullPaper2005_AsSubmitted.pdf},
pages = {273--278},
title = {A Virtual Laboratory for Material Testing},
year = {2005},
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@article{PetersAndParnas2002,
author = {Dennis K.~Peters and David Lorge Parnas},
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date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Transactions on Software Engineering},
pages = {146--158},
title = {Requirements-based Monitors for Real-Time Systems},
year = {2002}}
@techreport{ESA1991,
author = {ESA},
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institution = {European Space Agency},
title = {{ESA} Software Engineering Standards, {PSS-05-0} Issue 2},
year = {February 1991},
bdsk-url-1 = {http://microelectronics.esa.int/vhdl/pss/PSS-05-0.pdf}}
@inproceedings{vonMohrenschildtAndPeters1998,
author = {M.~von Mohrenschildt and D.~K.~Peters},
booktitle = {FIE '98. 28th Annual Frontiers in Education Conference. Moving from 'Teacher-Centered' to 'Learner-Centered' Education. Conference Proceedings (Cat. No.98CH36214)},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2020-01-03 08:48:15 -0500},
doi = {10.1109/FIE.1998.738548},
keywords = {software engineering;computer science education;teaching;educational courses;project engineering;control engineering education;robots;software engineering teaching project;draw-bot;software design principles;computer engineering students;students;enthusiasm;education course;Education;Software engineering;Software safety;Robots;Programming;Software testing;Concrete;Software design;Engineering students;Design engineering},
month = {Nov},
pages = {1022-1027},
title = {The {Draw-Bot}: A Project for Teaching Software Engineering},
volume = {3},
year = {1998},
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@article{CraigenEtAl1995,
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date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Transactions on Software Engineering},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/FormalMethodRealityCheck.pdf},
pages = {90--98},
title = {Formal Methods Reality Check: Industrial Usage},
year = {1995},
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@unpublished{Maibaum2004,
author = {T. S. E Maibaum},
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local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Roadmap-tsem.pdf},
title = {Mathematical Foundations of Software Engineering: a roadmap},
year = {2004},
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@unpublished{HaebererAndMaibaum2004,
author = {A. M. Haeberer and T. S. E. Maibaum},
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date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Haeberer_Maibaum.pdf},
title = {Scientific Rigour, and Answer to a Pragmatic Question: A Linguistic Framework for Software Engineering},
year = {2004},
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@book{CheneyAndKincaid2004,
author = {Ward Cheney and David Kincaid},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {5},
publisher = {Thomson Brooks/Cole},
title = {Numerical Mathematics and Computing},
year = {2004}}
@inproceedings{SmithAndStolle2003b,
address = {Albuquerque, New Mexico},
author = {W. Spencer Smith and Dieter F. E. Stolle},
booktitle = {Conference Proceedings for the 7th United States Congress on Computational Mechanics},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {{E}ulerian Versus Updated {L}agrangian Algorithms for Film Casting},
year = {2003}}
@inproceedings{StolleEtAl2001,
address = {Winnipeg, Manitoba},
author = {Dieter F. E. Stolle and M. Matt Pringle and W. Spencer Smith},
booktitle = {2nd Canadian Speciality Conference on Computing in Geotechnique},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {83--88},
title = {Use of Average Strain Elements in Geomechanics Problems},
year = {2001}}
@article{StolleAndSmith2004,
author = {Dieter F. E. Stolle and W. Spencer Smith},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Finite Elements in Analysis and Design},
keywords = {finite element, average strain, convergence},
local-url = {/Users/smiths/Work/Research/Papers/AvgStrain/Avg_strain6/AvgStrain_FEMinAD_1128.pdf},
number = {13--14},
pages = {2011--2024},
title = {Average Strain Strategy for Finite Elements},
url = {http://portal.acm.org/citation.cfm?id=1031924&coll=GUIDE&dl=GUIDE&CFID=://www.google.ca/search?hl=en&CFTOKEN=www.google.ca/search?hl=en},
volume = {40},
year = {2004},
bdsk-url-1 = {http://portal.acm.org/citation.cfm?id=1031924&coll=GUIDE&dl=GUIDE&CFID=://www.google.ca/search?hl=en&CFTOKEN=www.google.ca/search?hl=en}}
@article{SmithAndStolle2003,
author = {W. Spencer Smith and Dieter F. E. Stolle},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Polymer Engineering and Science},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/NumSimOfFilmCastUsingULAlgo/NumSimOfFilmCastUsingULAlgo.pdf},
number = {5},
pages = {1105--1122},
title = {Numerical Simulation of Film Casting Using an Updated {L}agrangian Finite Element Algorithm},
volume = {43},
year = {2003},
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@inproceedings{SmithAndStolle1999,
address = {Hamilton, Ontario},
author = {W. Spencer Smith and Dieter F. E. Stolle},
booktitle = {Proceedings of the 17th Canadian Congress of Applied Mechanics},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {S. Ziada and D. S. Weaver},
pages = {55--56},
title = {An Updated {L}agrangian Formulation for Film Casting},
year = {1999}}
@inproceedings{SmithAndStolle1999b,
address = {New York, New York},
author = {W. Spencer Smith and Dieter F. E. Stolle},
booktitle = {Conference Proceedings at ANTEC},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {255--258},
title = {Simulation of Draw Resonance in Film Casting Using a Material Description of Motion},
year = {1999}}
@book{TimoshenkoAndYoung1968,
author = {Stephen Timoshenko and D.~H.~ Young},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {5th},
publisher = {D.\ Van Nostrand Company, Inc.\},
title = {Elements of Strength of Materials},
year = {1968}}
@article{SmithAndStolle2002,
author = {W. Spencer Smith and Dieter F. E. Stolle},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Finite Elements in Analysis and Design},
number = {5},
pages = {401--415},
title = {A Comparison of Updated {L}agrangian and {E}ulerian Finite Element Algorithms for the Simulation of Film Casting},
volume = {38},
year = {2002},
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@inproceedings{SmithEtAl1998,
address = {Toronto, Ontario},
author = {W. Spencer Smith and Dieter F. E. Stolle and Brad Koziey},
booktitle = {Program and Abstracts, Polymer Processing Society, North American Meeting},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {134--135},
title = {Cast Film Modelling},
year = {1998}}
@inproceedings{SmithEtAl1998b,
address = {Atlanta, Georgia},
author = {W. Spencer Smith and Dieter F. E. Stolle and Brad Koziey},
booktitle = {ANTEC 1998 Conference Preprint},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {3512--3516},
title = {Nonisothermal Film Casting of a Viscous Polymer},
year = {1998}}
@book{DaughertyEtAl1985,
author = {Robert L. Daugherty and Joseph B. Franzini and E. John Finnermore},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {8},
publisher = {McGraw-Hill Publishing Company},
title = {Fluid mechanics with engineering applications},
year = {1985}}
@inproceedings{HallEtAl1994,
address = {Vermont South, Australia},
author = {Fred L. Hall and W. Spencer Smith and Frank Montgomery and W. Brilon},
booktitle = {Proceedings of the Second International Symposium on Highway Capacity},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {R. Akelik},
pages = {243--264},
title = {Comparison of Speed-Flow Relationships Based on Data From {N}orth {A}merica, the {U}nited {K}ingdom and {G}ermany},
year = {1994}}
@inproceedings{Leveson1992,
author = {Nancy G.\ Levenson},
booktitle = {Proceedings of the International Conference on Sotware Engineering, Melbourne, Australia},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {High-pressure steam engines and computer software},
year = {1992}}
@inproceedings{WassyngEtAl2003,
address = {McMaster University, Hamilton, Ontario},
author = {Alan Wassyng and W. Spencer Smith and Ridha Khedri and Konstantin Kreyman},
booktitle = {Canadian Software Requirements Symposium},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
title = {Software Requirements Research in {SQRL}},
year = {2003}}
@article{SmithAndStolle2000,
author = {W. Spencer Smith and Dieter F. E. Stolle},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Journal of Plastic Film \& Sheeting},
pages = {1--13},
title = {Draw Resonance in Film Casting as a Response Problem Using a Material Description of Motion},
volume = {16},
year = {2000}}
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University},
title = {Simulating the Cast Film Process Using an Updated {L}agrangian Finite Element Algorithm},
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date-added = {2017-09-28 14:24:37 +0000},
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year = {1997}}
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date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University},
title = {Nonisothermal Film Casting of a Viscous Fluid},
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year = {2004}}
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address = {Washington, D.C.},
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year = {2000}}
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title = {Software Requirements for the {A}-7{E} Aircraft},
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author = {Lei Lai},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
school = {McMaster University, Hamilton, Ontario, Canada},
title = {Requirements Documentation for Engineering Mechanics Software: Guidelines, Template and a Case Study},
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@misc{Fujio2000,
author = {Hidehiro Fujio},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
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title = {FEEL Environment A PSE prototype for the FEM},
year = {2000?},
bdsk-file-1 = {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}}
@article{OehsenEtAl2002,
author = {J. Barr von Oehsen and Richard C. Jenkins and Christopher L. Cox and Brian A. Malloy},
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pages = {1 - 5},
title = {Exploiting XML to Provide a Uniform Interface for Graphical Representation of Data},
year = {?},
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@inproceedings{DavisEtAl1993,
author = {A. Davis and et al.},
booktitle = {Proceedings of the 1st International Software Metrics Symposium},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {141-152},
publisher = {IEEE},
title = {Identifying and measuring quality in a software requirements specification},
year = {1993}}
@phdthesis{Gerlach2002,
author = {Jens Gerlach},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/gerlach_jens.pdf},
school = {Von der Fakult\"{a}t IV - Elektrotechnik und Informatik der Technischen Universit\"{a}t Berlin},
title = {Domain Engineering and Generic Programming for Parallel Scientific Computing},
year = {2002},
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@book{IEEE2000,
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
edition = {2nd},
editor = {R. H. Thayer and M. Dorfman},
publisher = {IEEE Computer Society, Washington, DC, USA},
title = {IEEE Recommended Practice for Software Requirements Specifications},
year = {2000}}
@book{ThompsonEtAl1985,
author = {Joe F. Thompson and Z. U. A. Warsi and C. Wayne Mastin},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {mesh generation},
publisher = {Elsevier Science Publishing Co., Inc.},
title = {Mesh Generation},
url = {http://www.erc.msstate.edu/publications/gridbook/index.html},
year = {1985},
bdsk-url-1 = {http://www.erc.msstate.edu/publications/gridbook/index.html}}
@inproceedings{Lamsweerde2001,
author = {Axel van Lamsweerde},
booktitle = {Proceedings of the 5th IEEE International Symposium on Requirements Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/ReqAnalysis/Lamsweerde2001.pdf},
month = aug,
organization = {IEEE},
pages = {249-263},
publisher = {IEEE Computer Society, Washington, DC, USA},
title = {Goal-oriented requirements engineering: a guided tour},
year = {2001},
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@book{Zienkiewicz1977,
author = {O.C. Zienkiewicz},
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date-modified = {2017-09-28 14:24:37 +0000},
keywords = {finite element method},
publisher = {McGraw-Hill Publishing Company},
title = {The Finite Element Method},
year = {1977}}
@article{ElSheikhEtAl2004,
author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Advances in Engineering Software},
keywords = {mesh generation, software engineering, modular decomposition, formal methods, software quality},
local-url = {/Users/smiths/Work/Research/Papers/SemiFormalDesMeshGen/OnLineVersionOfPaper.pdf},
number = {12},
pages = {827--841},
title = {Semi-formal design of reliable mesh generation systems},
volume = {35},
year = {2004},
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@article{Parnas1984,
author = {David L. Parnas},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {INFOR, Canadian Journal of Operations Research and Information Processing, vol. 22, no. 4, pp. 303-316},
keywords = {aspect ratio},
title = {Some Software Engineering Principles},
year = {November 1984}}
@book{Berti2000a,
author = {Guntram Berti},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Berti2000a.pdf},
publisher = {PhD Dissertation, TU Cottbus},
title = {Generic Software Components for Scientific Computing},
year = {2000},
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@techreport{Parnas1992,
author = {D. L. Parnas},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
institution = {CRL, McMaster University, Canada},
number = {241.1},
title = {Predicate logic for software engineering},
year = {1992}}
@article{ParnasAndClements1986,
author = {David L. Parnas and P.C. Clements},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Transactions on Software Engineering},
month = feb,
number = {2},
pages = {251--257},
title = {A Rational Design Process: How and Why to Fake it},
volume = {12},
year = {1986},
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@article{ParnasEtAl1981,
author = {David L. Parnas and S. Hester and D. Utter},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {The Bell System Technical Journal, vol. 60, no. 8, pp. 1941-1977},
title = {Using Documentation as a Software Design Medium},
year = {October 1981}}
@article{Heninger1980,
author = {Kathryn L. Heninger},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Transactions on Software Engineering},
number = {1},
pages = {2--13},
title = {Specifying Software Requirement for Complex System: New Techniques and Their Application},
volume = {6},
year = {1980}}
@article{ParnasAndSiewiorek1975,
author = {D. L. Parnas and D. P. Siewiorek},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Communications of the ACM},
title = {Use of the Concept of Transparency in the Design of Hierarchically Structured Systems, vol. 18, no. 7, pp. 401-408},
year = {July 1975}}
@book{vonMohrenschildtEtAl2000,
author = {M.~von Mohrenschildt and M. Directo and K. Kowalska},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {McMaster University Custom Courseware Production Services},
title = {Introduction to Software Engineering: A Collection of Formal Sofware Specification},
year = {August 2000}}
@article{TengAndWong2000,
author = {Shang-Hua Teng and Chi Wai Wong},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {International Journal of Computational Geometry and Applications},
keywords = {unstructured mesh generation, delaunay triangulation, octree, aspect ratio, computational geometry, radius-edge ratio, mesh generation, numerical methods, randomized algorithnms, weighted Delaunay triangulations, well-spaced points},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/TengAndWong2000.pdf},
month = jun,
number = {3},
pages = {227--266},
title = {Unstructured mesh generation: theory, practice and perspectives},
url = {http://www-sal.cs.uiuc.edu/~steng/mesh97_changed.ps},
volume = {10},
year = {2000},
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@article{Berti2001,
author = {Guntram Berti},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Proceedings of the 17th GaMM-Seminar Leipzig on ``Construction of Grid Generation Algorithms'', pp. 1-28},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Berti2001.pdf},
pages = {1--28},
title = {A Generic Toolbox for the Grid Craftsman},
url = {http://www.math.tu-cottbus.de/NMWR/papers/leipzig01.pdf},
year = {2001},
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@inproceedings{BernAndEppstein1992,
author = {Marshall Bern and David Eppstein},
booktitle = {Computing in Euclidean Geometry},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {D.-Z. Du and F.K. Hwang},
publisher = {World Scientific},
title = {Mesh Generation and Optimal Triangulation},
year = {1992}}
@inproceedings{Parnas1994,
address = {Amsterdam, The Netherlands},
author = {D. L. Parnas},
booktitle = {Proceedings of the {IFIP} 13th World Computer Congress. Volume 1 : Technology and Foundations},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {Bj{\o}rn Pehrson and Imre Simon},
isbn = {0-444-81989-4},
month = {August--September},
pages = {354--359},
publisher = {Elsevier Science Publishers},
title = {Mathematical Description and Specification of Software},
year = {1994}}
@inproceedings{Parnas1969,
author = {D. L. Parnas},
booktitle = {Proceedings of the 1969 National ACM Conference},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
key = {parnas},
organization = {Association for Computing Machinery},
pages = {739--743},
title = {On the Use of Transition Diagrams in the Design of a User Interface},
year = {1969}}
@inproceedings{AlfonsecaEtAl2001,
author = {Manual Alfonseca and Juan de Lara and Hans Vangheluwe},
booktitle = {Proceedings of the 2001 Winter Simulation Conference},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {B.A. Peters and J. S. Smith and D. J. Medeiros and M. W. Rohrer},
keywords = {simulation, partial differential equation},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/VirtualLab/AlfonsecaEtAl2001.pdf},
pages = {629-636},
title = {Web-based simulation of systems described by partial differential equations},
year = {2001},
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@incollection{Parnas1996,
author = {David L. Parnas},
booktitle = {Teaching and Learning Formal Methods, Academic Press, 1996},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {C. Neville Dean and Michael G. Hinchey},
title = {Education for Computing Professionals},
year = {1996}}
@inbook{deLaraAndAlfonseca2001,
author = {Juan de Lara and Manual Alfonseca},
chapter = {Using simulation and virtual reality for distance education},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {M. Ortega and J. Bravo},
keywords = {continuous simulation, web-based simulation, virtual reality, distance education},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/VirtualLab/deLaraAndAlfonseca2001.pdf},
publisher = {Kluwer Academic Publishers},
title = {Computers in Education: Towards an Interconnected Society},
year = {2001},
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@article{Parnas1979,
abstract = {Designing software to be extensible and easily contracted is discussed as a special case of design for change. A number of ways that extension and contraction problems manifest themselves in current software are explained. Four steps in the design of software that is more flexible are then discussed. The most critical step is the design of a software structure called the " uses" relation. Some criteria for design decisions are given and illustrated using a small example. It is shown that the identification of minimal subsets and minimal extensions can lead to software that can be tailored to the needs of a broad variety of users.},
author = {David L. Parnas},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2018-02-06 19:12:27 +0000},
journal = {IEEE Transactions on Software Engineering},
keywords = {Contractibility;extensibility;modularity;software engineering;subsets;supersets;Computer industry;Computer science;Data structures;Information systems;Job shop scheduling;Processor scheduling;Programming profession;Software design;Software engineering;Software systems;Contractibility;extensibility;modularity;software engineering;subsets;supersets},
month = mar,
number = {2},
pages = {128-138},
title = {Designing Software for Ease of Extension and Contraction},
volume = {SE-5},
year = {1979},
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@book{BernAndPlassmann2000,
author = {Marshall Bern and Paul Plassmann},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
publisher = {Handbook of Computational Geometry, Elsevier Science},
title = {Mesh Generation},
year = {2000}}
@article{Lee2000,
author = {M. H. Lee},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Software-Concepts and Tools},
keywords = {software modelling, qualitative reasoning, model-based systems},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/Lee2000.pdf},
month = apr,
pages = {179-189},
title = {Model-Based Reasoning: A principled approach to software engineering},
volume = {19},
year = {2000},
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@article{HullEtAl2000,
author = {M. Elizabeth C. Hull and Peter N. Nicholl and Philip Houston and Niall Rooney},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Software-Concepts and Tools},
keywords = {component-based software development, object technology, distributed objects, software frames, reuse, visual programming, development environments, software methodologies, client/server, legacy code},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/HullEtAl2000.pdf},
pages = {154-160},
title = {Towards a visual approach for component-based software development},
volume = {19},
year = {2000},
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@inproceedings{CoppitEtAl2000,
author = {David Coppit and Kevin J. Sullivan and Joanne Bechta Dugan},
booktitle = {Proceedings of the International Symposium on Software Reliability Engineering},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {formal methods, Z language, dynamic fault trees},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/5_Formal_Sem_of_Mod_for_Comp_Eng.pdf},
month = oct,
organization = {San Jose, California},
pages = {270-282},
publisher = {IEEEE},
title = {Formal Semantics of Models for Computational Engineering: A Case Study on Dynamic Fault Trees},
url = {www.cs.virginia.edu/~ftree/2003-redesign/pages/Research/ papers/FormalSemanticsOfModelsForCompEng.pdf},
year = {2000},
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bdsk-url-1 = {www.cs.virginia.edu/~ftree/2003-redesign/pages/Research/%20papers/FormalSemanticsOfModelsForCompEng.pdf}}
@article{Berti2000,
author = {Guntram Berti},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {submitted to First C++ Template Programming Workshop},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Berti2000.pdf},
title = {Generic Components for Grid Data Structures and Algorithms with C++},
url = {http://www.math.tu-cottbus.de/INSTITUT/lsnmwr/papers/},
year = {2000},
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bdsk-url-1 = {http://www.math.tu-cottbus.de/INSTITUT/lsnmwr/papers/}}
@article{BertiAndBader1998,
author = {Guntram Berti and Georg Bader},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {presented at the the 14th GAMM-Seminar Kiel on Concepts of Numerical Software},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/BaderAndBerti1998.pdf},
month = jan,
title = {Design Principles of Reusable Software Components for the Numerical Solution of {PDE} Problems},
url = {http://citeseer.ist.psu.edu/bader98design.html},
year = {1998},
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bdsk-url-1 = {http://citeseer.ist.psu.edu/bader98design.html}}
@article{Baber1997,
author = {Robert L. Baber},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Annals of the History of Computing},
keywords = {software engineering history},
number = {4},
pages = {5 - 17},
title = {Comparison of Electrical ``Engineering'' of Heaviside's Times and Software ``Engineering'' of Our Times},
volume = {19},
year = {1997}}
@inproceedings{BryantEtAl2002,
author = {Barret R. Bryant and Carol C. Burt and Mikhail Auguston and Rajeev R. Rale and Andrew M. Olson},
booktitle = {Proceedings of Software Engineering and Knowledge Engineering 2002},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/GenerativeProgramming/FormalSpecGenCompAssembly.pdf},
pages = {209-212},
title = {Formal Specification of Generative Component Assembly Using Two-Level Grammar},
year = {2002},
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@inproceedings{Glinz2000,
author = {Martin Glinz},
booktitle = {Proceedings of the 10th International Workshop on Software Specification and Design (IWSSD-10), San Diego},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {UML, requirements specification, model, use case, decomposition},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/UML/MartinGlinz2000.pdf},
month = nov,
pages = {11-22},
title = {Problems and Deficiencies of UML as a Requirements Specification Language},
year = {2000},
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@inproceedings{Berti2002,
address = {http://www.ccrl-nece.de/~berti/publications/},
author = {Guntram Berti},
booktitle = {Proceedings of ICCS 2002, Lecture Notes in Computer Science 2002},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
editor = {P.M.A. Sloot et al.},
keywords = {grid generation, generic programming, design},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/BertiGrAL_LectNotesCompSci.pdf},
pages = {745 - 754},
publisher = {Springer-Verlag Berlin Heidelberg},
title = {GrAL - The grid algorithms library},
year = {2002},
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@inproceedings{Parnas1974,
author = {David L. Parnas},
booktitle = {IFIP Congress 74},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
pages = {336-339},
publisher = {North Holland Publishing Company},
title = {On a 'Buzzword': Hierarchical Structure},
year = {1974}}
@article{Parnas1976,
author = {David Parnas},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {IEEE Transactions on Software Engineering},
keywords = {program families, step-wise refinement, modules},
number = {1},
pages = {1-9},
title = {On the design and development of program families},
volume = {SE-2},
year = {1976}}
@article{BrassardAndBodurtha2000,
author = {Pierre Brassard and Paul Bodurtha},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computers & Geosciences},
keywords = {chemical-equilibrium, algorithm, convergence, optimization, simplex},
pages = {277-291},
title = {A feasible set for chemical speciation problems},
volume = {26},
year = {2000}}
@book{Jacky1997,
author = {Jonathan Jacky},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {formal methods, software engineering},
publisher = {Cambridge University Press},
title = {The way of Z: practical programming with formal methods},
year = {1997}}
@book{FreyAndGeorge2000,
author = {Pascal Jean Frey and Paul-Louis George},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {mesh generation},
publisher = {Hermes Science Europe Ltd.},
title = {Mesh Generation Application to Finite Elements},
year = {2000}}
@article{StolleEtAl2004,
author = {Dieter Stolle and Peijun Guo and Gabriel Sedran},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Canadian Geotechnical Journal},
keywords = {random variability, deterministic analysis, soil parameters, constitutive model},
pages = {351--355},
title = {Impact of random soil properties on stress-strain response},
year = {2004}}
@mastersthesis{Chen2003,
author = {Chien-Hsien Chen},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {sofware engineering, mesh generation, commonality analysis, requirements, modular decomposition, module interface specification},
school = {McMaster University, Hamilton, Ontario, Canada},
title = {A software engineering approach to developing mesh generators},
year = {2003}}
@book{Raskin2000,
author = {Jef Raskin},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {human computer interaface},
publisher = {Addison-Wesley},
title = {The Humane Interface New Directions for Designing Interactive Systems},
year = {2000}}
@article{Laughlin2002,
author = {Robert B. Laughlin},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {Computing in Science & Engineering},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Phy_Base_of_Comp.pdf},
month = {May/June},
pages = {27--30},
title = {The Physical Bases of Computability},
year = {2002},
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@inproceedings{Petcu2000,
author = {Dana Petcu},
booktitle = {Proceedings of ALGORITMY 2000, Conference on Scientific Computing},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {software for scientific computations, parallel methods, scientific visualization},
pages = {217-226},
title = {Anatomy of an automatic solution generator for differential equations},
year = {2000}}
@misc{USDeptEnergy2000,
author = {Office of Science, U.S. Department of Energy},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {scientific computing},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ScientificComputing/SciDAC.pdf},
month = mar,
organization = {U.S. Department of Energy},
title = {Scientific Discovery through Advanced Computing},
url = {http://www.osti.gov/scidac/SciDAC.pdf},
year = {2000},
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bdsk-url-1 = {http://www.osti.gov/scidac/SciDAC.pdf}}
@book{Thompson2005,
author = {Erik G. Thompson},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {finite element method, variational calculus, Matlab},
publisher = {John Wiley & Sons, Inc.},
title = {An Introduction to the Finite Element Method Theory, Programming and Applications},
year = {2005}}
@article{PetcuAndNegru1999?,
author = {Dana Petcu and Viorel Negru},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
journal = {?},
keywords = {initial value problems, first order differential equations, mathematical software, difference methods, expert systems},
pages = {1 - 3},
title = {EPODE, a prototype expert system for solving initial value problems of ODEs},
year = {1999?}}
@book{GriesAndSchneider1993,
address = {New York},
author = {David Gries and Fred B. Schneider},
date-added = {2017-09-28 14:24:37 +0000},
date-modified = {2017-09-28 14:24:37 +0000},
keywords = {discrete mathematics},
publisher = {Springer-Verlag Inc.},
title = {A logical approach to discrete math},
year = {1993}}
@article{CukaAndWeiss1997,
annote = {Apparently this article was never published in this form. It looks like it was published as Engineering Domains: Executable Commands as an Example.},
author = {David A. Cuka and David M. Weiss},
date-added = {2017-09-25 13:35:41 +0000},
date-modified = {2017-09-25 13:35:41 +0000},
journal = {Submitted to IEEE Transactions on Software Engineering},
keywords = {software engineering, domain analysis, domain engineering, families, software process, application-oriented languages},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ProgramFamilies/CukaAndWeiss.pdf},
pages = {1 - 12},
title = {Specifying Executable Commands: An example of {FAST} domain engineering},
url = {http://www.research.avayalabs.com/user/weiss/Publications.html},
year = {Submitted 1997},
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bdsk-url-1 = {http://www.research.avayalabs.com/user/weiss/Publications.html}}
@book{WeissAndLai1999,
author = {D. Weiss and C.T.R. Lai},
date-added = {2017-09-25 13:35:34 +0000},
date-modified = {2017-09-25 13:35:34 +0000},
publisher = {Addison-Wesley},
title = {Software Product Line Engineering: A Family-Based Software Development Process},
year = {1999}}
@book{Parnas2001,
author = {D. L. Parnas},
date-added = {2017-09-25 13:35:27 +0000},
date-modified = {2017-09-25 13:35:27 +0000},
editor = {Daniel H.~Hoffman and David M.\ Weiss},
publisher = {Addison-Wesley},
title = {Software Fundamentals: Collected Papers by David L.~ Parnas},
year = {2001}}
@article{ParnasEtAl1983,
author = {David L. Parnas and P.C. Clements and D.M. Weiss},
date-added = {2017-09-25 13:35:22 +0000},
date-modified = {2017-09-25 13:35:22 +0000},
journal = {ITT Proceedings of the Workshop on Reuseability in Programming, Newport, R.I.},
title = {Enhancing Reusability with Information Hiding},
year = {September 1983}}
@article{CukaAndWeiss1998,
address = {Los Alamitos, CA, USA},
author = {D.A. Cuka and D.M. Weiss},
date-added = {2017-09-25 13:35:16 +0000},
date-modified = {2017-09-25 13:35:16 +0000},
doi = {http://doi.ieeecomputersociety.org/10.1109/ICSR.1998.685727},
issn = {1085-9098},
journal = {Software Reuse, International Conference on},
pages = {26--34},
publisher = {IEEE Computer Society},
title = {Engineering Domains: Executable Commands as an Example},
year = {1998},
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bdsk-url-1 = {http://doi.ieeecomputersociety.org/10.1109/ICSR.1998.685727}}
@article{ParnasAndWeiss2001,
author = {David L. Parnas and David M. Weiss},
date-added = {2017-09-25 13:34:39 +0000},
date-modified = {2017-09-25 13:34:39 +0000},
journal = {technical report ALR-2001-023},
title = {Definition and Documentation of Software Architectures},
year = {October 2001},
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@inproceedings{ArdisAndWeiss1997,
author = {Mark Ardis and David M. Weiss},
booktitle = {Proceedings of the Nineteenth International Conference on Software Engineering},
date-added = {2017-09-25 13:34:26 +0000},
date-modified = {2017-09-25 13:34:26 +0000},
keywords = {software engineering, domain analysis, domain engineering, families, software process, application-oriented languages, reuse, requirements engineering},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ProgramFamilies/ArdisAndWeiss_ProgFam.pdf},
pages = {649--650},
publisher = {ACM, Inc.},
title = {Defining families: The commonality analysis},
year = {1997},
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@article{Weiss1998,
author = {David M. Weiss},
date-added = {2017-09-25 13:34:22 +0000},
date-modified = {2017-09-25 13:34:22 +0000},
journal = {Lecture Notes in Computer Science},
keywords = {commonality analysis, program families},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ProgramFamilies/DefiningFamilies.ARES.pdf},
pages = {214--222},
title = {Commonality analysis: A systematic process for defining families},
url = {citeseer.ist.psu.edu/13585.html},
volume = {1429},
year = {1998},
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bdsk-url-1 = {citeseer.ist.psu.edu/13585.html}}
@article{FQS607,
abstract = {This paper outlines my concerns with Qualitative Data Analysis' (QDA) numerous remodelings of Grounded Theory (GT) and the subsequent eroding impact. I cite several examples of the erosion and summarize essential elements of classic GT methodology. It is hoped that the article will clarify my concerns with the continuing enthusiasm but misunderstood embrace of GT by QDA methodologists and serve as a preliminary guide to novice researchers who wish to explore the fundamental principles of GT.
URN: urn:nbn:de:0114-fqs040245},
author = {Barney Glaser and Judith Holton},
date-added = {2017-09-20 20:55:44 +0000},
date-modified = {2017-09-20 20:55:44 +0000},
doi = {10.17169/fqs-5.2.607},
issn = {1438-5627},
journal = {Forum Qualitative Sozialforschung / Forum: Qualitative Social Research},
keywords = {grounded theory; qualitative data analysis; constant comparative method; theoretical sensitivity},
number = {2},
title = {Remodeling Grounded Theory},
url = {http://www.qualitative-research.net/index.php/fqs/article/view/607},
volume = {5},
year = {2004},
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bdsk-url-1 = {http://www.qualitative-research.net/index.php/fqs/article/view/607},
bdsk-url-2 = {http://dx.doi.org/10.17169/fqs-5.2.607}}
@article{Hall:2009:SRT:1525880.1525883,
acmid = {1525883},
address = {New York, NY, USA},
articleno = {10},
author = {Hall, Tracy and Baddoo, Nathan and Beecham, Sarah and Robinson, Hugh and Sharp, Helen},
date-added = {2017-09-20 19:26:39 +0000},
date-modified = {2017-09-20 19:26:39 +0000},
doi = {10.1145/1525880.1525883},
issn = {1049-331X},
issue_date = {May 2009},
journal = {ACM Trans. Softw. Eng. Methodol.},
keywords = {Motivation, software engineering},
month = jun,
number = {3},
numpages = {29},
pages = {10:1--10:29},
publisher = {ACM},
title = {A Systematic Review of Theory Use in Studies Investigating the Motivations of Software Engineers},
url = {http://doi.acm.org/10.1145/1525880.1525883},
volume = {18},
year = {2009},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1525880.1525883},
bdsk-url-2 = {http://dx.doi.org/10.1145/1525880.1525883}}
@inproceedings{adolph2013generating,
author = {Adolph, Steve and Kruchten, Philippe},
booktitle = {Software Engineering (GTSE), 2013 2nd SEMAT Workshop on a General Theory of},
date-added = {2017-09-20 19:24:57 +0000},
date-modified = {2017-09-20 19:24:57 +0000},
organization = {IEEE},
pages = {47--50},
title = {Generating a useful theory of software engineering},
year = {2013},
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@article{BeckertEtAl2018,
adsurl = {https://arxiv.org/abs/1802.02374},
archiveprefix = {arXiv},
author = {Bernhard Beckert and Britta Nestler and Moritz Kiefer and Michael Selzer and Mattias Ulbrich},
date-added = {2017-09-13 01:50:03 +0000},
date-modified = {2018-04-04 11:04:37 +0000},
eprint = {1802.02374},
journal = {ArXiv e-prints},
month = feb,
primaryclass = {cs.SE},
title = {Experience Report: Formal Methods in Material Science},
year = 2018,
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@article{WilsonEtAl2016,
author = {Greg Wilson and Jennifer Bryan and Karen Cranston and Justin Kitzes and Lex Nederbragt and Tracy K. Teal},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/corr/WilsonBCKNT16},
date-added = {2017-09-08 12:18:42 +0000},
date-modified = {2017-09-08 12:18:42 +0000},
journal = {CoRR},
timestamp = {Wed, 07 Jun 2017 14:42:20 +0200},
title = {Good Enough Practices in Scientific Computing},
url = {http://arxiv.org/abs/1609.00037},
volume = {abs/1609.00037},
year = {2016},
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bdsk-url-1 = {http://arxiv.org/abs/1609.00037}}
@article{TaschukAndWilson2017,
abstract = {{[Abstract]
Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer's computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.
[Author summary]
Many researchers have found out the hard way that there's a world of difference between '' works for me on my machine'' and '' works for other people on theirs.'' Many common challenges can be avoided by following a few simple rules; doing so not only improves reproducibility but can accelerate research.
[Excerpt]
[\n] [...]
Best practices in software engineering specifically aim to increase software robustness. However, most bioinformaticians learn what they know about software development on the job or otherwise informally [...]. Existing training programs and initiatives rarely have the time to cover software engineering in depth, especially since the field is so broad and developing so rapidly [...]. In addition, making software robust is not directly rewarded in science, and funding is difficult to come by [...]. Some proposed solutions to this problem include restructuring educational programs, hiring dedicated software engineers [...], partnering with private sector or grassroots organizations [...], or using specific technical tools like containerization or cloud computing [...]. Each of these requires time and, in some cases, institutional change.
[\n] The good news is you don't need to be a professionally trained programmer to write robust software. In fact, some of the best, most reliable pieces of software in many scientific communities are written by researchers [...] who have adopted strong software engineering approaches, have high standards of reproducibility, use good testing practices, and foster strong user bases through constantly evolving, clearly documented, useful, and useable software.
[...]
[\n] So what is '' robust'' software? We implied above that it is software that works for people other than the original author and on machines other than its creator's. More specifically, we mean that:
[::] it can be installed on more than one computer with relative ease,
[::] it works consistently as advertised, and
[::] it can be integrated with other tools.
[\n] Our rules are generic and can be applied to all languages, libraries, packages, documentation styles, and operating systems for both closed-source and open-source software. They are also necessary steps toward making computational research replicable and reproducible: after all, if your tools and libraries cannot be run by others, they cannot be used to verify your results or as a stepping stone for future work [...]
[::] Rule 1: Use version control [...]
[::] Rule 2: Document your code and usage [...]
[::] Rule 3: Make common operations easy to control [...]
[::] Rule 4: Version your releases [...]
[::] Rule 5: Reuse software (within reason) [...]
[::] Rule 6: Rely on build tools and package managers for installation [...]
[::] Rule 7: Do not require root or other special privileges to install or run [...]
[::] Rule 8: Eliminate hard-coded paths [...]
[::] Rule 9: Include a small test set that can be run to ensure the software is actually working [...]
[::] Rule 10: Produce identical results when given identical inputs [...]
[\n] [...]}},
author = {Taschuk, Morgan and Wilson, Greg},
citeulike-article-id = {14337051},
citeulike-linkout-0 = {http://mfkp.org/INRMM/article/14337051},
citeulike-linkout-1 = {https://scholar.google.com/scholar?cluster=6425036906123073798},
citeulike-linkout-2 = {http://dx.doi.org/10.1371/journal.pcbi.1005412},
date-added = {2017-09-08 12:18:34 +0000},
date-modified = {2017-09-08 12:18:34 +0000},
day = {13},
doi = {10.1371/journal.pcbi.1005412},
issn = {1553-7358},
journal = {PLOS Computational Biology},
keywords = {bias-disembodied-science-vs-computational-scholarship, check-list, computational-science, free-scientific-knowledge, reproducible-research, software-engineering, software-uncertainty},
month = apr,
number = {4},
pages = {e1005412+},
posted-at = {2017-04-19 10:44:23},
priority = {2},
publisher = {Public Library of Science},
title = {{Ten simple rules for making research software more robust}},
url = {http://mfkp.org/INRMM/article/14337051},
volume = {13},
year = {2017},
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bdsk-url-1 = {http://mfkp.org/INRMM/article/14337051},
bdsk-url-2 = {http://dx.doi.org/10.1371/journal.pcbi.1005412}}
@inproceedings{AdamsAndDuBuisson2012,
address = {New York, NY, USA},
author = {Adams, Michael D. and DuBuisson, Thomas M.},
booktitle = {Proceedings of the 2012 ACM SIGPLAN Haskell symposium},
date-added = {2017-09-06 20:55:15 +0000},
date-modified = {2017-09-06 20:55:15 +0000},
doi = {10.1145/2364506.2364509},
isbn = {978-1-4503-1574-6},
pages = {13--24},
publisher = {ACM},
series = {Haskell '12},
title = {Template Your Boilerplate: Using {T}emplate {H}askell for Efficient Generic Programming},
year = {2012},
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bdsk-url-1 = {http://dx.doi.org/10.1145/2364506.2364509}}
@article{WagnerAndDeissenboeck2017,
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170901304W},
archiveprefix = {arXiv},
author = {{Wagner}, S. and {Deissenboeck}, F.},
date-added = {2017-09-06 20:41:27 +0000},
date-modified = {2017-09-06 20:41:27 +0000},
eprint = {1709.01304},
journal = {ArXiv e-prints},
keywords = {Computer Science - Software Engineering, Computer Science - Programming Languages, D.1.0, D.2.2},
month = sep,
primaryclass = {cs.SE},
title = {{Abstractness, specificity, and complexity in software design}},
year = 2017,
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@techreport{KreymanAndParnas2002,
author = {K. Kreyman and D. L. Parnas},
date-added = {2017-09-05 02:36:58 +0000},
date-modified = {2017-09-05 02:36:58 +0000},
institution = {Software Quality Research Laboratory, McMaster University},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/KreymanAndParnas2002.pdf},
month = jan,
number = {1},
title = {On Documenting the Requirements for Computer Programs Based on Models of Physical Phenomena},
type = {SQRL Report},
year = {2002},
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@article{Storer2017,
abstract = {The use of software is pervasive in all fields of science. Associated software development efforts may be very large, long lived, and complex, requiring the commitment of significant resources. However, several authors have argued that the ``gap'' or ``chasm'' between software engineering and scientific programming is a serious risk to the production of reliable scientific results, as demonstrated in a number of case studies. This article reviews the research that addresses the gap, exploring how both software engineering and research practice may need to evolve to accommodate the use of software in science.},
acmid = {3084225},
address = {New York, NY, USA},
annote = {- makes clear case (with examples) that software brings a variety of benefits to scientific research
- highlights SCS probs with scientific methd, esp repeatability and reproducibilty - examples of retractions
``There is a need to improve the transfer of existing practices and tools from other applications of software engineering to scientific programming. In addition, due to the specialised nature of scientific programming, there is a need for research to specifically develop methods and tools that are tailored to the domain.''},
articleno = {47},
author = {Storer, Tim},
date-added = {2017-08-30 13:36:37 +0000},
date-modified = {2018-09-06 11:42:30 -0400},
doi = {10.1145/3084225},
issn = {0360-0300},
issue_date = {August 2017},
journal = {ACM Comput. Surv.},
keywords = {Software engineering, scientific programming},
month = aug,
number = {4},
numpages = {32},
pages = {47:1--47:32},
publisher = {ACM},
title = {Bridging the Chasm: A Survey of Software Engineering Practice in Scientific Programming},
url = {http://doi.acm.org/10.1145/3084225},
volume = {50},
year = {2017},
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bdsk-url-1 = {http://doi.acm.org/10.1145/3084225},
bdsk-url-2 = {http://dx.doi.org/10.1145/3084225}}
@inbook{MarkerEtAl2013,
abstract = {To implement dense linear algebra algorithms for distributed-memory computers, an expert applies knowledge of the domain, the target architecture, and how to parallelize common operations. This is often a rote process that becomes tedious for a large collection of algorithms. We have developed a way to encode this expert knowledge such that it can be applied by a system to generate mechanically the same (and sometimes better) highly-optimized code that an expert creates by hand. This paper illustrates how we have encoded a subset of this knowledge and how our system applies it and searches a space of generated implementations automatically.},
address = {Berlin, Heidelberg},
author = {Marker, Bryan and Poulson, Jack and Batory, Don and van de Geijn, Robert},
booktitle = {High Performance Computing for Computational Science - VECPAR 2012: 10th International Conference, Kope, Japan, July 17-20, 2012, Revised Selected Papers},
date-added = {2017-07-19 18:39:00 +0000},
date-modified = {2017-07-19 18:39:00 +0000},
doi = {10.1007/978-3-642-38718-0_34},
editor = {Dayd{\'e}, Michel and Marques, Osni and Nakajima, Kengo},
isbn = {978-3-642-38718-0},
pages = {362--378},
publisher = {Springer Berlin Heidelberg},
title = {Designing Linear Algebra Algorithms by Transformation: Mechanizing the Expert Developer},
url = {https://doi.org/10.1007/978-3-642-38718-0_34},
year = {2013},
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bdsk-url-1 = {https://doi.org/10.1007/978-3-642-38718-0_34},
bdsk-url-2 = {http://dx.doi.org/10.1007/978-3-642-38718-0_34}}
@article{CamererEtAl2016,
abstract = {The reproducibility of scientific findings has been called into question. To contribute data about reproducibility in economics, we replicate 18 studies published in the American Economic Review and the Quarterly Journal of Economics in 2011-2014. All replications follow predefined analysis plans publicly posted prior to the replications, and have a statistical power of at least 90\% to detect the original effect size at the 5\% significance level. We find a significant effect in the same direction as the original study for 11 replications (61\%); on average the replicated effect size is 66\% of the original. The reproducibility rate varies between 67\% and 78\% for four additional reproducibility indicators, including a prediction market measure of peer beliefs.},
author = {Camerer, Colin F. and Dreber, Anna and Forsell, Eskil and Ho, Teck-Hua and Huber, J{\"u}rgen and Johannesson, Magnus and Kirchler, Michael and Almenberg, Johan and Altmejd, Adam and Chan, Taizan and Heikensten, Emma and Holzmeister, Felix and Imai, Taisuke and Isaksson, Siri and Nave, Gideon and Pfeiffer, Thomas and Razen, Michael and Wu, Hang},
date-added = {2017-07-19 13:35:26 +0000},
date-modified = {2017-07-19 13:35:26 +0000},
doi = {10.1126/science.aaf0918},
eprint = {http://science.sciencemag.org/content/early/2016/03/02/science.aaf0918.full.pdf},
issn = {0036-8075},
journal = {Science},
publisher = {American Association for the Advancement of Science},
title = {Evaluating replicability of laboratory experiments in economics},
url = {http://science.sciencemag.org/content/early/2016/03/02/science.aaf0918},
year = {2016},
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bdsk-url-1 = {http://science.sciencemag.org/content/early/2016/03/02/science.aaf0918},
bdsk-url-2 = {http://dx.doi.org/10.1126/science.aaf0918}}
@article{NeumannEtAl2017,
author = {Gerardo Cerda Neumann and Hector Antillanca Espina and Victor Parada Daza},
date-added = {2017-07-18 18:12:42 +0000},
date-modified = {2017-07-18 18:12:42 +0000},
journal = {Journal of Software},
month = jul,
number = {2},
pages = {114--124},
title = {Development of scientific software and practices for software development: A systematic literature review.},
volume = {12},
year = {2017},
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@article{KuksenokEtAl2017,
abstract = {Computing affects how scientific knowledge is constructed, verified, and validated. Rapid changes in hardware capability, and software flexibility, are coupled with a volatile tool and skill set, particularly in the interdisciplinary scientific contexts of oceanography. Existing research considers the role of scientists as both users and producers of code. We focus on how an intentional, individually-initiated but socially-situated, process of uptake influences code written by scientists. We present an 18-month interview and observation study of four oceanography teams, with a focus on ethnographic shadowing of individuals undertaking code work. Through qualitative analysis, we developed a framework of deliberate individual change, which builds upon prior work on programming practices in science through the lens of sociotechnical infrastructures. We use qualitative vignettes to illustrate how our theoretical framework helps to understand changing programming practices. Our findings suggest that scientists use and produce software in a way that deliberately mitigates the potential pitfalls of their programming practice. In particular, the object and method of visualization is subject to restraint intended to prevent accidental misuse.},
author = {Kuksenok, Kateryna and Aragon, Cecilia and Fogarty, James and Lee, Charlotte P. and Neff, Gina},
date-added = {2017-07-18 17:56:57 +0000},
date-modified = {2017-07-18 17:56:57 +0000},
day = {24},
doi = {10.1007/s10606-017-9285-x},
issn = {1573-7551},
journal = {Computer Supported Cooperative Work (CSCW)},
month = may,
title = {Deliberate Individual Change Framework for Understanding Programming Practices in four Oceanography Groups},
url = {http://dx.doi.org/10.1007/s10606-017-9285-x},
year = {2017},
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bdsk-url-1 = {http://dx.doi.org/10.1007/s10606-017-9285-x}}
@article{WilsonAndLumsdaine2006,
abstract = {For the past years, my colleagues and I have developed a one-semester course that teaches scientists and engineers the "common core" of modern software development. Our experience shows that an investment of 150 hours-25 of lectures and the rest of practical work-can improve productivity by roughly 20 percent. That's one day a week, one less semester in a master's degree, or one less year for a typical PhD. The course is called software carpentry, rather than software engineering, to emphasize the fact that it focuses on small-scale and immediately practical issues. All of the material is freely available under an open-source license at www.swc.scipy.org and can be used both for self-study and in the classroom. This article describes what the course contains, and why},
author = {Greg Wilson and Andrew Lumsdaine},
date-added = {2017-06-13 17:22:20 +0000},
date-modified = {2017-06-13 17:22:20 +0000},
doi = {10.1109/MCSE.2006.122},
issn = {1521-9615},
journal = {Computing in Science Engineering},
keywords = {computer science education;software engineering;software carpentry;software development course;software engineering;Computer science;Debugging;Ethics;Java;Open source software;Physics;Portable computers;Programming profession;Teamwork;World Wide Web;computation in undergraduate education;continuing education;physics education;software engineering},
month = nov,
number = {6},
pages = {66-69},
title = {Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive},
volume = {8},
year = {2006},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2006.122}}
@article{CarverEtAl2017,
abstract = {Despite the increasing demand for utilizing high-performance computing (HPC) for CSE applications, software development for HPC historically attracted little attention from the software engineering (SE) community. Paradoxically, the HPC CSE community has increasingly been adopting SE techniques and tools. Indeed, the development of CSE software for HPC differs significantly from the development of more traditional business information systems, from which many SE best practices and tools have been drawn. The workshop summarized in this column, the fourth in the series to be collocated with the Supercomputing conference series, examined two main topics: testing and tradeoffs. Through presentations of work in this area and structured group discussions, the participants highlighted some of the key issues, as well as indicated the direction the community needs to go. In particular, there is a need for more high-quality research in this area that we can use as an evidence base to help developers of CSE applications change practice and benefit from advances in software engineering.},
author = {J. C. Carver and N. C. Hong and S. Ciraci},
date-added = {2017-05-25 17:20:07 +0000},
date-modified = {2017-05-25 17:20:07 +0000},
doi = {10.1109/MCSE.2017.28},
issn = {1521-9615},
journal = {Computing in Science Engineering},
keywords = {Best practices;Computational modeling;Graphics processing units;Scientific computing;Software engineering;HPC;computational engineering;computational science;scientific computing;software engineering;workshop},
month = mar,
number = {2},
pages = {91-95},
title = {The 4th International Workshop on Software Engineering for HPC in Computational Science and Engineering},
volume = {19},
year = {2017},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2017.28}}
@article{KatzEtAl2017,
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170502607K},
annote = {``Supporting technical sustainability in (scientific) software is very near to supporting properties like longevity and resilience, i.e., the ability of a software system or application to fulfill its intent [10],''},
archiveprefix = {arXiv},
author = {{Katz}, D.~S. and {Niemeyer}, K.~E. and {Gesing}, S. and {Hwang}, L. and {Bangerth}, W. and {Hettrick}, S. and {Idaszak}, R. and {Salac}, J. and {Chue Hong}, N. and {N{\'u}{\~n}ez Corrales}, S. and {Allen}, A. and {Geiger}, R.~S. and {Miller}, J. and {Chen}, E. and {Dubey}, A. and {Lago}, P.},
date-added = {2017-05-10 14:10:33 +0000},
date-modified = {2019-10-01 10:11:06 -0400},
eprint = {1705.02607},
journal = {ArXiv e-prints},
keywords = {Computer Science - Software Engineering},
month = may,
primaryclass = {cs.SE},
title = {{Report on the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)}},
year = 2017,
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@article{GrebhahnEtAl2017,
author = {Grebhahn, Alexander and Engwer, Christian and Bolten, Matthias and Apel, Sven},
date-added = {2017-04-17 19:36:11 +0000},
date-modified = {2017-04-17 19:36:11 +0000},
doi = {10.1002/cpe.4119},
issn = {1532-0634},
journal = {Concurrency and Computation: Practice and Experience},
keywords = {variability models, porous media, stencil},
note = {e4119 cpe.4119},
pages = {e4119--n/a},
title = {Variability of stencil computations for porous media},
url = {http://dx.doi.org/10.1002/cpe.4119},
year = {2017},
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bdsk-url-1 = {http://dx.doi.org/10.1002/cpe.4119}}
@article{DonohoEtAl2009,
author = {D. L. Donoho and A. Maleki and I. U. Rahman and M. Shahram and V. Stodden},
date-added = {2016-10-15 19:03:17 +0000},
date-modified = {2016-10-15 19:03:17 +0000},
doi = {10.1109/MCSE.2009.15},
issn = {1521-9615},
journal = {Computing in Science Engineering},
keywords = {electronic publishing;harmonic analysis;mathematics computing;software packages;computational harmonic analysis;reproducible research;scientific publication;software publishing;Computational modeling;Computer errors;Data mining;Harmonic analysis;Image recognition;Information management;Laboratories;Large-scale systems;Logic testing;Scientific computing;computational science;reproducible research;scientific computing;scientific publication},
month = jan,
number = {1},
pages = {8-18},
title = {Reproducible Research in Computational Harmonic Analysis},
volume = {11},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.15}}
@article{HattonAndRoberts1994,
address = {Piscataway, NJ, USA},
author = {Les Hatton and Andy Roberts},
date-added = {2016-10-15 18:54:41 +0000},
date-modified = {2016-10-15 18:54:41 +0000},
doi = {http://dx.doi.org/10.1109/32.328993},
issn = {0098-5589},
journal = {IEEE Trans. Softw. Eng.},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/HattonAndRoberts1994.pdf},
number = {10},
pages = {785--797},
publisher = {IEEE Press},
title = {How Accurate is Scientific Software?},
volume = {20},
year = {1994},
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bdsk-url-1 = {http://dx.doi.org/10.1109/32.328993}}
@article{Hatton2007,
author = {Les Hatton},
date-added = {2016-10-15 18:54:36 +0000},
date-modified = {2016-10-15 18:54:36 +0000},
journal = {Computer},
keywords = {computers and society, computing profession, software quality},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Hatton2007.pdf},
month = aug,
number = {8},
title = {The chimera of software quality},
volume = {40},
year = {2007},
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@article{IoannidisEtAl2009,
author = {Ioannidis, John PA and Allison, David B and Ball, Catherine A and Coulibaly, Issa and Cui, Xiangqin and Culhane, Aed{\'\i}n C and Falchi, Mario and Furlanello, Cesare and Game, Laurence and Jurman, Giuseppe and others},
date-added = {2016-10-15 14:21:41 +0000},
date-modified = {2016-10-15 14:21:41 +0000},
journal = {Nature genetics},
number = {2},
pages = {149--155},
publisher = {Nature Publishing Group},
title = {Repeatability of published microarray gene expression analyses},
volume = {41},
year = {2009},
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@article{QueirozAndSpitz2016,
author = {Francisco Queiroz and Rejane Spitz},
date-added = {2016-10-14 15:41:22 +0000},
date-modified = {2016-10-14 15:41:22 +0000},
journal = {The International Journal of Design Management and Professional Practice},
number = {3},
pages = {17--45},
title = {The Lens of the Lab: Design Challenges in Scientific Software},
volume = {10},
year = {2016},
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@inbook{BaileyEtAl2016,
address = {New York},
author = {David H. Bailey and Jonathan M. Borwein and Victoria Stodden},
chapter = {Facilitating reproducibility in scientific computing: principles and practice},
date-added = {2016-10-14 15:25:01 +0000},
date-modified = {2016-10-14 15:29:44 +0000},
editor = {Harald Atmanspacher and Sabine Maasen},
pages = {205--232},
publisher = {John Wiley and Sons},
title = {Reproducibility: Principles, Problems, Practices},
year = {2016},
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bdsk-url-1 = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.432.8990&rep=rep1&type=pdf}}
@article{GentlemanAndTempleLang2007,
abstract = { It is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, and so on with the documents that describe and rely on them. This integration allows readers to both verify and adapt the claims in the documents. Authors can easily reproduce the results in the future, and they can present the document's contents in a different medium, for example, with interactive controls. This article describes a software framework for both authoring and distributing these integrated, dynamic documents that contain text, code, data, and any auxiliary content needed to recreate the computations. The documents are dynamic in that the contents---including figures, tables, and so on---can be recalculated each time a view of the document is generated. Our model treats a dynamic document as a master or ``source'' document from which one can generate different views in the form of traditional, derived documents for different audiences.We introduce the concept of a compendium as a container for one or more dynamic documents and the different elements needed when processing them, such as code and data. The compendium serves as a means for distributing, managing, and updating the collection.The step from disseminating analyses via a compendium to reproducible research is a small one. By reproducible research, we mean research papers with accompanying software tools that allow the reader to directly reproduce the results and employ the computational methods that are presented in the research paper. Some of the issues involved in paradigms for the production, distribution, and use of such reproducible research are discussed.},
author = {Robert Gentleman and Duncan Temple Lang},
date-added = {2016-10-14 15:18:48 +0000},
date-modified = {2016-10-14 15:18:48 +0000},
doi = {10.1198/106186007X178663},
eprint = {http://dx.doi.org/10.1198/106186007X178663},
journal = {Journal of Computational and Graphical Statistics},
number = {1},
pages = {1-23},
title = {Statistical Analyses and Reproducible Research},
url = {http://dx.doi.org/10.1198/106186007X178663},
volume = {16},
year = {2007},
bdsk-file-1 = {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},
bdsk-url-1 = {http://dx.doi.org/10.1198/106186007X178663}}
@mastersthesis{Tang2008,
address = {Hamilton, ON},
author = {Jin Tang},
date-added = {2016-10-04 14:11:23 +0000},
date-modified = {2016-10-04 14:11:23 +0000},
local-url = {file://localhost/Users/smiths/Work/Research/GradStudents/JinTang/Thesis_FinalVersionAsPrinted.pdf},
school = {McMaster University},
title = {Developing Scientific Computing Software: Current Processes and Future Directions},
year = {2008},
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@article{Parnas1972MIS,
author = {D. L. Parnas},
date-added = {2016-10-04 12:53:24 +0000},
date-modified = {2016-10-04 12:53:24 +0000},
journal = {CACM},
key = {Parnas},
number = {5},
pages = {330--336},
title = {A Technique for the Specification of Software Modules with Examples},
volume = {15},
year = {1972},
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@inproceedings{BrittonEtAl1981,
author = {Britton, Kathryn Heninger and Parker, R Alan and Parnas, David L},
booktitle = {Proceedings of the 5th international conference on Software engineering},
date-added = {2016-10-04 12:46:10 +0000},
date-modified = {2016-10-04 12:46:10 +0000},
organization = {IEEE Press},
pages = {195--204},
title = {A procedure for designing abstract interfaces for device interface modules},
year = {1981},
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@article{PflugerEtAl2016,
author = {Dirk Pfl{\"{u}}ger and Miriam Mehl and Julian Valentin and Florian Lindner and Stefan Wagner and Daniel Graziotin and Yang Wang},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/corr/PflugerMVLWGW16},
date-added = {2016-10-01 19:25:09 +0000},
date-modified = {2016-10-01 19:25:09 +0000},
journal = {CoRR},
timestamp = {Sun, 04 Sep 2016 09:50:53 +0200},
title = {The {SE/MP} Trade-off in Simulation Software Engineering: Examples and a Preliminary Systematic Literature Review},
url = {http://arxiv.org/abs/1608.04336},
volume = {abs/1608.04336},
year = {2016},
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bdsk-url-1 = {http://arxiv.org/abs/1608.04336}}
@article{Parnas1985,
acmid = {214961},
address = {New York, NY, USA},
author = {Parnas, David Lorge},
date-added = {2016-09-28 17:54:30 +0000},
date-modified = {2016-09-28 17:54:30 +0000},
doi = {10.1145/214956.214961},
issn = {0001-0782},
issue_date = {Dec. 1985},
journal = {Commun. ACM},
month = dec,
number = {12},
numpages = {10},
pages = {1326--1335},
publisher = {ACM},
title = {Software Aspects of Strategic Defense Systems},
url = {http://doi.acm.org/10.1145/214956.214961},
volume = {28},
year = {1985},
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@inproceedings{SmithJegatheesanAndKelly2016,
author = {W. Spencer Smith and Thulasi Jegatheesan and Diane F. Kelly},
booktitle = {Proceedings of the Fourth International Workshop on Software Engineering for High Performance Computing in Computational Science and Engineering (SE-HPCCE)},
date-added = {2016-09-19 19:43:47 +0000},
date-modified = {2022-10-27 14:13:15 -0400},
month = nov,
note = {8 pp},
organization = {In conjunction with SC16: The International Conference for High Performance Computing, Networking, Storage and Analysis},
title = {Advantages, Disadvantages and Misunderstandings About Document Driven Design for Scientific Software},
year = {2016},
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bdsk-url-1 = {http://se4science.org/workshops/sehpccse16/cfp.htm}}
@inbook{Wassyng2016,
author = {Wassyng, Alan and Joannou, Paul and Lawford, Mark and Maibaum, Thomas S. E. and Singh, N. K.},
date-added = {2016-09-09 13:24:03 +0000},
date-modified = {2016-09-09 13:24:13 +0000},
publisher = {CRC},
title = {New Standards for Trustworthy Cyber-Physical Systems},
year = {2016},
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@book{HaveraaenEtAl1999,
author = {Haveraaen, M. and Friis, H.A. and Johansen, T.A. and Universitetet i Bergen. Department of Informatics},
date-added = {2016-08-22 14:08:11 +0000},
date-modified = {2016-08-22 14:08:11 +0000},
publisher = {Department of Informatics, University of Bergen},
series = {Reports in informatics},
title = {Formal Software Engineering for Computational Modeling},
url = {https://books.google.ca/books?id=pzI0HQAACAAJ},
year = {1999},
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@incollection{PawlikEtAl2012,
address = {D{\"u}sseldorf},
author = {Pawlik, Aleksandra and Segal, Judith and Sharp, Helen and Petre, Marian},
booktitle = {Science and the {I}nternet},
date-added = {2016-08-22 13:48:42 +0000},
date-modified = {2016-08-22 13:48:42 +0000},
editor = {Tokar, A. and Beurskens, M. and Keuneke, S. and Mahrt, M. and Peters, I. and Puschmann, C. and van Treeck, T. and Weller, K.},
isbn = {978-3-943460-16-2},
pages = {263--273},
publisher = {D{\"u}sseldorf University Press},
title = {Developing Scientific Software: The Role of the Internet},
year = {2012},
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@article{ParnasEtAl1991,
author = {Parnas, D. L. and Asmis, G. J. K. and Madey, J.},
citeulike-article-id = {699933},
date-added = {2016-08-22 13:36:04 +0000},
date-modified = {2016-08-22 13:36:04 +0000},
journal = {Nuclear Safety},
keywords = {formal, industry, nuclear, safety, scr, software},
month = jun,
number = {2},
pages = {189--198},
posted-at = {2006-06-18 19:46:27},
priority = {0},
title = {{Assessment of Safety-Critical Software in Nuclear Power Plants}},
volume = {32},
year = {1991},
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@inproceedings{SzymczakEtAl2016,
address = {Austin, Texas, United States},
author = {Daniel Szymczak and W. Spencer Smith and Jacques Carette},
booktitle = {Proceedings of SE4Science'16 in conjunction with the International Conference on Software Engineering (ICSE)},
date-added = {2016-07-28 19:16:32 +0000},
date-modified = {2021-11-18 17:33:50 -0500},
month = may,
note = {4 pp.},
title = {Position Paper: A Knowledge-Based Approach to Scientific Software Development},
year = {2016},
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@article{KitchenhamAndPfleeger1996,
acmid = {625544},
address = {Los Alamitos, CA, USA},
author = {Kitchenham, Barbara and Pfleeger, Shari Lawrence},
date-added = {2016-07-28 02:53:12 +0000},
date-modified = {2016-07-28 02:53:12 +0000},
doi = {10.1109/52.476281},
issn = {0740-7459},
issue_date = {January 1996},
journal = {IEEE Softw.},
month = jan,
number = {1},
numpages = {10},
pages = {12--21},
publisher = {IEEE Computer Society Press},
title = {Software Quality: The Elusive Target},
url = {http://dx.doi.org/10.1109/52.476281},
volume = {13},
year = {1996},
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@article{KellyEtAl2014,
author = {Kelly, Diane and Wassyng, Alan and Orton, Colin G.},
date-added = {2016-07-26 03:50:27 +0000},
date-modified = {2016-07-26 03:50:27 +0000},
doi = {http://dx.doi.org/10.1118/1.4883877},
eid = 090601,
journal = {Medical Physics},
number = {9},
title = {The most suitable person to establish quality assurance guidelines for the generation and use of noncommercial clinical software is a medical physicist},
url = {http://scitation.aip.org/content/aapm/journal/medphys/41/9/10.1118/1.4883877},
volume = {41},
year = {2014},
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@phdthesis{Eid2010,
author = {Ahmad Hosney Awad Eid},
date-added = {2016-07-19 15:58:04 +0000},
date-modified = {2016-07-19 15:58:04 +0000},
school = {Port-Said},
title = {Optimized Automatic Code Generation for Geometric Algebra Based Algorithms with Ray Tracing Application},
year = {2010},
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bdsk-url-1 = {http://128.84.21.199/abs/1607.04767}}
@article{SmithEtAl2016,
author = {W. Spencer Smith and Adam Lazzarato and Jacques Carette},
date-added = {2016-07-05 03:21:18 +0000},
date-modified = {2016-07-05 03:21:18 +0000},
journal = {Advances in Engineering Software},
month = oct,
pages = {53--71},
title = {State of Practice for Mesh Generation Software},
volume = {100},
year = {2016},
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bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S0965997816301296}}
@inproceedings{KanewalaAndBieman2013,
author = {U. Kanewala and J. M. Bieman},
booktitle = {Software Engineering for Computational Science and Engineering (SE-CSE), 2013 5th International Workshop on},
date-added = {2016-06-29 20:18:56 +0000},
date-modified = {2016-06-29 20:18:56 +0000},
doi = {10.1109/SECSE.2013.6615099},
keywords = {learning (artificial intelligence);program diagnostics;program testing;domain knowledge;fault finding ability;machine learning;metamorphic testing;run-time assertions;scientific programs;software testing;static analysis;structural analysis;test oracles;Automation;Decision trees;Predictive models;Software;Software testing;Training;Assertion checking;Machine learning;Metamorphic relation;Metamorphic testing;Mutation analysis;Scientific software testing;Test oracles},
month = may,
pages = {48-57},
title = {Techniques for testing scientific programs without an oracle},
year = {2013},
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bdsk-url-1 = {http://dx.doi.org/10.1109/SECSE.2013.6615099}}
@article{FarhoodiEtAl2013,
abstract = {Scientific and engineering research is heavily dependent on effective development and use of software artifacts. Many of these artifacts are produced by the scientists themselves, rather than by trained software engineers. To address the challenges in this area, a research community often referred to as "Development of Scientific Software" has emerged in the last few decades. As this research area has matured, there has been a sharp increase in the number of papers and results made available, and it has thus become important to summarize and provide an overview about those studies. Through a systematic mapping and bibliometrics study, we have reviewed 130 papers in this area. We present the results of our study in this paper. Also we have made the mapping data available on an online repository which is planned to be updated on a regular basis. The results of our study seem to suggest that many software engineering techniques and activities are being used in the development of scientif},
author = {FARHOODI, ROSHANAK and GAROUSI, VAHID and PFAHL, DIETMAR and SILLITO, JONATHAN},
date-added = {2016-06-28 17:59:06 +0000},
date-modified = {2016-06-28 17:59:06 +0000},
issn = {02181940},
journal = {International Journal of Software Engineering & Knowledge Engineering},
keywords = {COMPUTER software, ENGINEERING, RESEARCH, SOFTWARE engineers, COMPUTER systems, BIBLIOMETRICS, SCIENTISTS, bibliometrics study, Development of scientific software, paper repository, systematic mapping},
number = {4},
pages = {463 - 506},
title = {DEVELOPMENT OF SCIENTIFIC SOFTWARE: A SYSTEMATIC MAPPING, A BIBLIOMETRICS STUDY, AND A PAPER REPOSITORY.},
url = {http://libaccess.mcmaster.ca.libaccess.lib.mcmaster.ca/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=bth&AN=89396166&site=ehost-live&scope=site},
volume = {23},
year = {2013},
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bdsk-url-1 = {http://libaccess.mcmaster.ca.libaccess.lib.mcmaster.ca/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=bth&AN=89396166&site=ehost-live&scope=site}}
@inproceedings{ShepardAndKelly2001,
author = {Shepard, Terry and Kelly, Diane},
booktitle = {Proceedings of the 23rd International Conference on Software Engineering},
date-added = {2016-06-24 16:11:32 +0000},
date-modified = {2016-06-24 16:11:32 +0000},
organization = {IEEE Computer Society},
pages = {718},
title = {How to do inspections when there is no time},
year = {2001},
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@article{KellyAndShepard2004,
author = {Kelly, Diane and Shepard, Terry},
date-added = {2016-06-24 16:11:23 +0000},
date-modified = {2016-06-24 16:11:23 +0000},
journal = {Software Testing, Verification and Reliability},
number = {4},
pages = {243--256},
publisher = {Wiley Online Library},
title = {Eight maxims for software inspectors},
volume = {14},
year = {2004},
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@inproceedings{KellyAndShepard2000,
author = {Diane Kelly and Terry Shepard},
booktitle = {CASCON '00: Proceedings of the 2000 conference of the Centre for Advanced Studies on Collaborative research},
date-added = {2016-06-24 16:04:56 +0000},
date-modified = {2016-06-24 16:04:56 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/KellyAndShepard2000.pdf},
location = {Mississauga, Ontario, Canada},
pages = {6},
publisher = {IBM Press},
title = {Task-directed software inspection technique: an experiment and case study},
url = {http://portal.acm.org/citation.cfm?id=782040#},
year = {2000},
bdsk-file-1 = {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},
bdsk-url-1 = {http://portal.acm.org/citation.cfm?id=782040#}}
@article{Easterbrook2014,
abstract = {{Open source software is often seen as a path to reproducibility in computational science. In practice there are many obstacles, even when the code is freely available, but open source policies should at least lead to better quality code.}},
author = {Easterbrook, Steve M.},
citeulike-article-id = {13413203},
citeulike-linkout-0 = {http://dx.doi.org/10.1038/ngeo2283},
citeulike-linkout-1 = {http://dx.doi.org/10.1038/ngeo2283},
date-added = {2016-06-14 20:10:35 +0000},
date-modified = {2016-06-14 20:10:43 +0000},
day = {30},
doi = {10.1038/ngeo2283},
issn = {1752-0894},
journal = {Nature Geoscience},
keywords = {communication, computing, social},
month = oct,
number = {11},
pages = {779--781},
posted-at = {2014-10-31 19:32:30},
priority = {2},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
title = {{Open code for open science?}},
url = {http://dx.doi.org/10.1038/ngeo2283},
volume = {7},
year = {2014},
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bdsk-url-1 = {http://dx.doi.org/10.1038/ngeo2283}}
@inproceedings{LundgrenAndKanewala2016,
acmid = {2897678},
address = {New York, NY, USA},
author = {Lundgren, Anders and Kanewala, Upulee},
booktitle = {Proceedings of the International Workshop on Software Engineering for Science},
date-added = {2016-06-14 19:33:39 +0000},
date-modified = {2016-06-14 19:33:39 +0000},
doi = {10.1145/2897676.2897678},
isbn = {978-1-4503-4167-7},
location = {Austin, Texas},
numpages = {7},
pages = {16--22},
publisher = {ACM},
series = {SE4Science '16},
title = {Experiences of Testing Bioinformatics Programs for Detecting Subtle Faults},
url = {http://doi.acm.org/10.1145/2897676.2897678},
year = {2016},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2897676.2897678},
bdsk-url-2 = {http://dx.doi.org/10.1145/2897676.2897678}}
@inproceedings{MoserAndPichler2016,
acmid = {2897679},
address = {New York, NY, USA},
author = {Moser, Michael and Pichler, Josef},
booktitle = {Proceedings of the International Workshop on Software Engineering for Science},
date-added = {2016-06-14 19:31:42 +0000},
date-modified = {2016-06-14 19:31:42 +0000},
doi = {10.1145/2897676.2897679},
isbn = {978-1-4503-4167-7},
keywords = {documentation generator, reverse engineering, scientific software, software engineering tools},
location = {Austin, Texas},
numpages = {4},
pages = {12--15},
publisher = {ACM},
series = {SE4Science '16},
title = {Documentation Generation from Annotated Source Code of Scientific Software: Position Paper},
url = {http://doi.acm.org/10.1145/2897676.2897679},
year = {2016},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2897676.2897679},
bdsk-url-2 = {http://dx.doi.org/10.1145/2897676.2897679}}
@inproceedings{FangohrEtAl2016,
acmid = {2897677},
address = {New York, NY, USA},
author = {Fangohr, Hans and Albert, Maximilian and Franchin, Matteo},
booktitle = {Proceedings of the International Workshop on Software Engineering for Science},
date-added = {2016-06-14 19:18:39 +0000},
date-modified = {2016-06-14 19:18:39 +0000},
doi = {10.1145/2897676.2897677},
isbn = {978-1-4503-4167-7},
keywords = {computational science software engineering, finite elements, nmag, python},
location = {Austin, Texas},
numpages = {7},
pages = {1--7},
publisher = {ACM},
series = {SE4Science '16},
title = {Nmag Micromagnetic Simulation Tool: Software Engineering Lessons Learned},
url = {http://doi.acm.org/10.1145/2897676.2897677},
year = {2016},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2897676.2897677},
bdsk-url-2 = {http://dx.doi.org/10.1145/2897676.2897677}}
@inproceedings{IonescuAndJansson2013,
author = {Cezar Ionescu and Patrik Jansson},
booktitle = {{Revised Selected Papers of the 24th International Symposium on Implementation and Application of Functional Languages}},
date-added = {2016-06-14 17:37:53 +0000},
date-modified = {2016-06-14 17:37:53 +0000},
doi = {10.1007/978-3-642-41582-1_9},
pages = {140--156},
publisher = {{Springer International Publishing}},
series = {{Lecture Notes in Computer Science}},
title = {{Dependently-Typed Programming in Scientific Computing --- Examples from Economic Modelling}},
volume = 8241,
year = 2012,
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bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-642-41582-1_9}}
@inproceedings{Nguyen-HoanEtAl2010,
acmid = {1852802},
address = {New York, NY, USA},
annote = {3.5 Documentation
Figure 13 shows the number of respondents who indi- cated they produce certain types of documentation. The most common type of documentation produced by respon- dents was comments in the code, selected by 51 out of 60 respondents. At the other end of the scale, requirements documentation is the least commonly produced type of doc- umentation with only 18 respondents indicating that they commonly produce such artifacts.
The comparative lack of documentation for requirements and design matches the experiences described by Sanders and Kelly [12]. In their study which involved interviewing 16 scientists, `none of [the] interviewees created an up-front formal requirements specification', and `Only one intervie- wee ... demonstrated his design documentation'.
In our survey, 42 out of 60 respondents indicated they commonly produced user manuals and/or guides. However, as seen in Section 3.4, only 25 respondents indicated they often or always produced software for larger groups of up to 100 people and/or an international community of users. Therefore, at least 17 respondents are producing user manu- als and/or guides for themselves or users in their local area. This is at odds with Sanders and Kelly [12], who noted that none of their interviewees `produced user documentation un- less their software was intended for use outside their research group'.
Only three respondents in our survey mentioned docu- mentation being required or compulsory by users or cus- tomers. However, each type of documentation was com- monly produced by around 20 to 40 of the 60 respondents. This contrasts to Segal [15] who identified that professional end user developers (non-software domain specialists who produce software for specific purposes) `did not voluntar- ily produce documentation, apart from the occasional user guide'.
The survey respondents were also asked why documenta- tion is or is not commonly produced for scientific software applications which they have worked on. From the 50 re- sponses to this open-ended question, a range of reasons both for an against the production of documentation were identi- fied using the coding data collection and analysis technique [13].
The most common reasons for and against the production of documentation and their popularity are shown in Figure 14. Note that these these reasons are not mutually exclusive and are not complete. Many respondents provided both rea- sons for and against the production of documentation. Some reasons were only provided by a single respondent and are not included above.},
articleno = {12},
author = {Nguyen-Hoan, Luke and Flint, Shayne and Sankaranarayana, Ramesh},
booktitle = {Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement},
date-added = {2016-06-03 19:39:48 +0000},
date-modified = {2022-02-07 14:55:09 -0500},
doi = {10.1145/1852786.1852802},
isbn = {978-1-4503-0039-1},
keywords = {scientific software, scientists, software engineering, survey},
location = {Bolzano-Bozen, Italy},
numpages = {10},
pages = {12:1--12:10},
publisher = {ACM},
series = {ESEM '10},
title = {A Survey of Scientific Software Development},
url = {http://doi.acm.org/10.1145/1852786.1852802},
year = {2010},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1852786.1852802},
bdsk-url-2 = {http://dx.doi.org/10.1145/1852786.1852802}}
@article{KlocknerEtAl2016,
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
adsurl = {http://adsabs.harvard.edu/abs/2016arXiv160408501K},
archiveprefix = {arXiv},
author = {{Kl{\"o}ckner}, A. and {Wilcox}, L.~C. and {Warburton}, T.},
date-added = {2016-05-31 18:35:43 +0000},
date-modified = {2016-05-31 18:35:55 +0000},
eprint = {1604.08501},
journal = {ArXiv e-prints},
keywords = {Computer Science - Programming Languages, Computer Science - Performance, Mathematics - Numerical Analysis, D.3.4, D.1.3, G.4},
month = apr,
primaryclass = {cs.PL},
title = {{Array Program Transformation with Loo.py by Example: High-Order Finite Elements}},
year = 2016,
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@article{SmithAndKoothoor2016,
abstract = {This paper presents a documentation and development method to facilitate the certification of scientific computing software used in the safety analysis of nuclear facilities. To study the problems faced during quality assurance and certification activities, a case study was performed on legacy software used for thermal analysis of a fuelpin in a nuclear reactor. Although no errors were uncovered in the code, 27 issues of incompleteness and inconsistency were found with the documentation. This work proposes that software documentation follow a rational process, which includes a software requirements specification following a template that is reusable, maintainable, and understandable. To develop the design and implementation, this paper suggests literate programming as an alternative to traditional structured programming. Literate programming allows for documenting of numerical algorithms and code together in what is termed the literate programmer's manual. This manual is developed with explicit traceability to the software requirements specification. The traceability between the theory, numerical algorithms, and implementation facilitates achieving completeness and consistency, as well as simplifies the process of verification and the associated certification.},
author = {W. Spencer Smith and Nirmitha Koothoor},
date-added = {2016-04-18 22:54:19 +0000},
date-modified = {2016-04-18 22:54:19 +0000},
doi = {http://dx.doi.org/10.1016/j.net.2015.11.008},
issn = {1738-5733},
journal = {Nuclear Engineering and Technology},
keywords = {Software Quality},
month = apr,
number = {2},
pages = {404-418},
title = {A Document-Driven Method for Certifying Scientific Computing Software for Use in Nuclear Safety Analysis},
url = {http://www.sciencedirect.com/science/article/pii/S1738573315002582},
volume = {48},
year = {2016},
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bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S1738573315002582},
bdsk-url-2 = {http://dx.doi.org/10.1016/j.net.2015.11.008}}
@inproceedings{ParnasEtAl1984,
author = {D.L. Parnas and P.C. Clement and D. M. Weiss},
booktitle = {International Conference on Software Engineering},
date-added = {2016-04-05 18:58:49 +0000},
date-modified = {2016-04-05 18:58:49 +0000},
pages = {408-419},
title = {The modular structure of complex systems},
year = {1984},
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@article{BeckhausEtAl2009,
author = {Arne Beckhause and Dirk Neumann and Lars Karg},
date-added = {2016-04-01 20:24:49 +0000},
date-modified = {2016-04-01 20:24:49 +0000},
journal = {Issues in Information Systems},
number = {2},
pages = {316--323},
publisher = {IACIS},
title = {The Impact of Communcation Structure on Issue Tracking Efficiency at a Large Business Software Vendor},
volume = {X},
year = {2009},
bdsk-file-1 = {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}}
@article{HuttonEtAl2014,
author = {Eric W. H. Hutton and Mark D. Piper and Irina Overeem and Albert J. Kettner and James P. M. Syvitski},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/corr/HuttonPOKS14},
date-added = {2016-03-30 17:18:02 +0000},
date-modified = {2016-03-30 17:18:02 +0000},
journal = {CoRR},
timestamp = {Fri, 01 Aug 2014 13:50:01 +0200},
title = {Building Sustainable Software - The {CSDMS} Approach},
url = {http://arxiv.org/abs/1407.4106},
volume = {abs/1407.4106},
year = {2014},
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bdsk-url-1 = {http://arxiv.org/abs/1407.4106}}
@book{LoggEtAl2012,
date-added = {2016-03-30 15:38:28 +0000},
date-modified = {2016-03-30 15:38:28 +0000},
doi = {10.1007/978-3-642-23099-8},
editor = {A. Logg and K.-A. Mardal and G. N. Wells},
publisher = {Springer},
series = {Lecture Notes in Computational Science and Engineering},
title = {Automated Solution of Differential Equations by the Finite Element Method},
url = {http://dx.doi.org/10.1007/978-3-642-23099-8},
volume = {84},
year = {2012},
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bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-642-23099-8}}
@article{GewaltigAndCannon2012,
author = {Marc-Oliver Gewaltig and Robert Cannon},
date-added = {2016-03-22 18:57:06 +0000},
date-modified = {2016-03-22 18:57:06 +0000},
journal = {Cornell University Library},
month = may,
pages = {20 pp},
title = {Quality and sustainability of software tools in neuroscience},
year = {2012},
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@incollection{DavisonEtAl2014,
address = {Boca Raton, Florida.},
author = {Davison, Andrew P. and Mattioni, M. and Samarkanov, D. and Tele{\'n}czuk, B.},
book_link = {http://www.amazon.com/Implementing-Reproducible-Research-Chapman-Series/dp/1466561599},
booktitle = {Implementing Reproducible Research},
date-added = {2016-03-18 18:45:29 +0000},
date-modified = {2016-03-18 18:45:29 +0000},
editor = {V. Stodden and F. Leisch and R.D. Peng},
full_text = {https://osf.io/w6fp4/osffiles/Andrew_Davison_chapter.pdf/version/1/download/},
month = mar,
pages = {57--79},
publisher = {Chapman \& Hall/CRC},
title = {Sumatra: A Toolkit for Reproducible Research},
year = {2014},
bdsk-file-1 = {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}}
@book{Malvern1969,
address = {Englewood Cliffs, New Jersey},
author = {L. E. Malvern},
date-added = {2016-01-21 14:18:04 +0000},
date-modified = {2016-01-21 14:18:04 +0000},
publisher = {Prentice Hall},
title = {Introduction to the Mechanics of Continuous Medium},
year = {1969},
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@unpublished{Mileta2016,
author = {Ernest Mileta},
date-added = {2016-01-20 19:22:46 +0000},
date-modified = {2016-01-20 19:22:46 +0000},
month = jan,
note = {Presentation for Annual Review of NSERC CRD: A Literate Process for the Certification of Scientific and Engineering Software},
title = {Management System Requirements in new edition 15/16 Standard},
year = {2016},
bdsk-file-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAZLi4vLi4vcHViL01pbGV0YTIwMTYucHB0eE8RAUYAAAAAAUYAAgAADE1hY2ludG9zaCBIRAAAAAAAAAAAAAAAAAAAAAAAAABCRAAB/////w9NaWxldGEyMDE2LnBwdHgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAD/////AAAAAAAAAAAAAAAAAAIAAgAACiBjdQAAAAAAAAAAAAAAAAADcHViAAACACgvOlVzZXJzOnNtaXRoczpSZXBvczpwdWI6TWlsZXRhMjAxNi5wcHR4AA4AIAAPAE0AaQBsAGUAdABhADIAMAAxADYALgBwAHAAdAB4AA8AGgAMAE0AYQBjAGkAbgB0AG8AcwBoACAASABEABIAJlVzZXJzL3NtaXRocy9SZXBvcy9wdWIvTWlsZXRhMjAxNi5wcHR4ABMAAS8AABUAAgAN//8AAAAIAA0AGgAkAEAAAAAAAAACAQAAAAAAAAAFAAAAAAAAAAAAAAAAAAABig==}}
@unpublished{Mileta2015,
author = {Ernest Mileta},
date-added = {2016-01-20 19:19:31 +0000},
date-modified = {2016-01-20 19:25:02 +0000},
month = jan,
note = {Presentation for Annual Review of NSERC CRD: A Literate Process for the Certification of Scientific and Engineering Software},
title = {Management System Requirements \& Analytical Software},
year = {2015},
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@inproceedings{Parnas2010,
annote = {- never mix reference documents with introductions
- only relevant information should be included},
author = {David Lorge Parnas},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/conf/birthday/Parnas10},
booktitle = {The Future of Software Engineering},
date-added = {2016-01-05 20:55:38 +0000},
date-modified = {2018-02-05 04:28:32 +0000},
doi = {10.1007/978-3-642-15187-3_8},
pages = {125--148},
timestamp = {Tue, 30 Aug 2011 14:09:42 +0200},
title = {Precise Documentation: The Key to Better Software},
url = {http://dx.doi.org/10.1007/978-3-642-15187-3_8},
year = {2010},
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@inproceedings{CourtoisAndParnas1993,
added-at = {2012-05-14T00:00:00.000+0200},
author = {Courtois, Pierre-Jacques and Parnas, David Lorge},
biburl = {http://www.bibsonomy.org/bibtex/24471498d6d01bc7b1c974e1ba3decfc7/dblp},
booktitle = {ICSE},
crossref = {conf/icse/1993},
date-added = {2016-01-05 20:48:37 +0000},
date-modified = {2016-01-05 20:48:37 +0000},
editor = {Basili, Victor R. and DeMillo, Richard A. and Katayama, Takuya},
ee = {http://portal.acm.org/citation.cfm?id=257572.257650},
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isbn = {0-89791-588-7},
keywords = {dblp},
pages = {315-323},
publisher = {IEEE Computer Society / ACM Press},
timestamp = {2012-05-15T11:50:47.000+0200},
title = {Documentation for Safety Critical Software.},
url = {http://dblp.uni-trier.de/db/conf/icse/icse93.html#CourtoisP93},
year = 1993,
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@article{ParnasEtAl1994,
acmid = {203107},
address = {Piscataway, NJ, USA},
author = {Parnas, David Lorge and Madey, Jan and Iglewski, Michal},
date-added = {2016-01-03 21:33:54 +0000},
date-modified = {2016-01-03 21:33:54 +0000},
doi = {10.1109/32.368133},
issn = {0098-5589},
issue_date = {December 1994},
journal = {IEEE Trans. Softw. Eng.},
keywords = {displays, formal specification, functional approach, index, lexicon, precise documentation, program correctness, program documentation, program fragments, program verification, reference document, software engineering, software inspection, software maintenance, specification, structured programming, system documentation, tabular form, well-structured programs},
month = dec,
number = {12},
numpages = {29},
pages = {948--976},
publisher = {IEEE Press},
title = {Precise Documentation of Well-Structured Programs},
url = {http://dx.doi.org/10.1109/32.368133},
volume = {20},
year = {1994},
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@inproceedings{HannayEtAl2009,
acmid = {1556928},
address = {Washington, DC, USA},
author = {Hannay, Jo Erskine and MacLeod, Carolyn and Singer, Janice and Langtangen, Hans Petter and Pfahl, Dietmar and Wilson, Greg},
booktitle = {Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering},
date-added = {2016-01-01 14:01:19 +0000},
date-modified = {2016-01-01 14:01:19 +0000},
doi = {10.1109/SECSE.2009.5069155},
isbn = {978-1-4244-3737-5},
numpages = {8},
pages = {1--8},
publisher = {IEEE Computer Society},
series = {SECSE '09},
title = {How Do Scientists Develop and Use Scientific Software?},
url = {http://dx.doi.org/10.1109/SECSE.2009.5069155},
year = {2009},
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@article{AckroydEtAl2008,
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month = {July/August},
number = {4},
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title = {Scientific Software Development at a Research Facility},
volume = {25},
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@article{SegalAndMorris2008,
annote = {Some extra information on the citation.
@article{Segal2008IEEE,
Address = {Los Alamitos, CA, USA},
Author = {Segal, Judith and Morris, Chris},
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Date-Modified = {2011-01-28 14:00:35 -0500},
Doi = {http://dx.doi.org/10.1109/MS.2008.85},
Issn = {0740-7459},
Journal = {IEEE Softw.},
Number = {4},
Pages = {18--20},
Publisher = {IEEE Computer Society Press},
Title = {Developing Scientific Software},
Url = {http://cs.ua.edu/\~{}SECSE08/Papers/Segal.pdf},
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journal = {IEEE Software},
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@article{Easterbrook2009,
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doi = {http://dx.doi.org/10.1109/MCSE.2009.193},
issn = {0740-7475},
journal = {IEEE Des. Test},
number = {6},
pages = {65--74},
publisher = {IEEE Computer Society Press},
title = {Engineering the Software for Understanding Climate Change},
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@article{Kanewala2015,
author = {Upulee Kanewala and James M. Bieman and Asa Ben-Hur},
date-added = {2015-12-21 19:51:57 +0000},
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journal = {Software Testing Verification and Reliability},
title = {Predicting Metamorphic Relations for Testing Scientific Software: A Machine Learning Approach Using Graph Kernels},
volume = {preprint},
year = {2015},
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@article{Kelly2015,
author = {Diane Kelly},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/jss/Kelly15},
date-added = {2015-12-21 19:44:54 +0000},
date-modified = {2015-12-21 19:44:54 +0000},
doi = {10.1016/j.jss.2015.07.027},
journal = {Journal of Systems and Software},
pages = {50--61},
timestamp = {Thu, 26 Nov 2015 09:26:40 +0100},
title = {Scientific software development viewed as knowledge acquisition: Towards understanding the development of risk-averse scientific software},
url = {http://dx.doi.org/10.1016/j.jss.2015.07.027},
volume = {109},
year = {2015},
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@book{Zobel2004,
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isbn = {1852338024},
publisher = {SpringerVerlag},
title = {Writing for Computer Science},
year = {2004},
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@article{HofnerEtAl2011,
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author = {Peter H\"{o}fner and Ridha Khedri and Bernhard M\"{o}ller},
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date-added = {2015-10-13 19:06:49 +0000},
date-modified = {2015-10-13 19:06:49 +0000},
ee = {http://dx.doi.org/10.1007/s10270-009-0127-2},
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journal = {Software and System Modeling},
keywords = {dblp},
number = {2},
pages = {161--182},
timestamp = {2011-05-31T11:33:08.000+0200},
title = {An algebra of product families},
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year = {2011},
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@book{Leveson2011,
author = {Leveson, N.},
date-added = {2015-10-10 12:54:38 +0000},
date-modified = {2015-10-10 12:55:44 +0000},
isbn = {9780262016629},
lccn = {2011014046},
publisher = {MIT Press},
series = {Engineering systems},
title = {Engineering a Safer World: Systems Thinking Applied to Safety},
url = {https://books.google.ca/books?id=0gZ\_7n5p8MQC},
year = {2011},
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bdsk-url-1 = {https://books.google.ca/books?id=0gZ%5C_7n5p8MQC}}
@techreport{Rushby2015,
address = {Menlo Park, CA},
author = {John Rushby},
date-added = {2015-09-18 13:41:01 +0000},
date-modified = {2015-09-18 13:41:01 +0000},
institution = {Computer Science Laboratory, SRI International},
month = jul,
note = {Available at \url{http://www.csl.sri.com/users/rushby/papers/sri-csl-15-1-assurance-cases.pdf}},
number = {SRI-CSL-15-01},
title = {The Interpretation and Evaluation of Assurance Cases},
year = 2015,
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@book{HoffmanAndStrooper1995,
address = {New York, NY, USA},
author = {Daniel M. Hoffman and Paul A. Strooper},
date-added = {2015-06-04 04:39:02 +0000},
date-modified = {2016-07-03 13:49:29 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SoftwareEngineering/software-design-automated-testing.pdf},
publisher = {International Thomson Computer Press},
title = {Software Design, Automated Testing, and Maintenance: A Practical Approach},
url = {http:// citeseer.ist.psu.edu/428727.html},
year = {1995},
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bdsk-url-1 = {http://%20citeseer.ist.psu.edu/428727.html}}
@techreport{SmithEtAl2015-Seism-TR,
author = {W. Spencer Smith and Zheng Zeng and Jacques Carette},
date-added = {2015-05-27 20:39:18 +0000},
date-modified = {2016-07-03 16:04:32 +0000},
institution = {McMaster University},
month = may,
note = {51 pp},
number = {CAS-15-06-SS},
title = {State of Practice for Seismology Software},
type = {Technical Report},
year = {2015},
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@mastersthesis{Koothoor2013,
author = {Nirmitha Koothoor},
date-added = {2015-05-27 17:12:43 +0000},
date-modified = {2015-05-27 17:12:43 +0000},
school = {McMaster University, Hamilton, Ontario, Canada},
title = {A Document Driven Approach to Certifying Scientific Computing Software},
year = {2013},
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@inproceedings{CaretteEtAl2011,
abstract = {We present the design and implementation of a generative geometric kernel. The kernel generator is generic, type-safe, parametrized by many design-level choices and extensible. The resulting code has minimal traces of the design abstractions. We achieve genericity through a layered design deriving concepts from affine geometry, linear algebra and abstract algebra. We achieve parametrization and type-safety by using OCaml's module system, including higher order modules. The cost of abstraction is removed by using MetaOCaml's support for code generation coupled with some annotations atop the code type.},
author = {Jacques Carette and Mustafa ElSheikh and W. Spencer Smith},
booktitle = {ACM SIGPLAN 2011 Workshop on Partial Evaluation and Program Manipulation (PEPM'11)},
date-added = {2015-05-21 18:46:39 +0000},
date-modified = {2016-07-03 16:03:31 +0000},
keywords = {MetaOCaml, Geometry, Generative, Generic},
month = jan,
pages = {53--62},
title = {A Generative Geometric Kernel},
year = {2011},
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@inproceedings{KellyAndSanders2008a,
author = {Diane Kelly and Rebecca Sanders},
booktitle = {Proceedings of the Conference for the Association for Software Testing},
date-added = {2015-05-05 17:56:21 +0000},
date-modified = {2015-05-05 17:56:21 +0000},
pages = {30--36},
title = {The challenge of testing scientific software},
year = {2008},
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bdsk-url-1 = {https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.464.7432&rep=rep1&type=pdf}}
@inproceedings{HookAndKelly2009,
acmid = {1556936},
address = {Washington, DC, USA},
author = {Hook, Daniel and Kelly, Diane},
booktitle = {Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering},
date-added = {2015-05-05 15:11:28 +0000},
date-modified = {2015-05-05 15:11:28 +0000},
doi = {10.1109/SECSE.2009.5069163},
isbn = {978-1-4244-3737-5},
numpages = {6},
pages = {59--64},
publisher = {IEEE Computer Society},
series = {SECSE '09},
title = {Testing for Trustworthiness in Scientific Software},
url = {http://dx.doi.org/10.1109/SECSE.2009.5069163},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/SECSE.2009.5069163}}
@article{Carver2006,
author = {Jeffrey Carver and Lorin Hochstein and Richard Kendall and Taiga Nakamura and Marvin Zelkowitz and Victor Basili and Douglass Post},
date-added = {2015-05-05 14:53:49 +0000},
date-modified = {2015-05-05 14:53:49 +0000},
journal = {CTWatch Quarterly},
month = nov,
number = {4A},
pages = {33-38},
title = {{Observations about Software Development for High End Computing}},
url = {http://www.ctwatch.org/quarterly/archives/november-2006-a},
volume = {2},
year = {2006},
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bdsk-url-1 = {http://www.ctwatch.org/quarterly/archives/november-2006-a}}
@article{MatthewsEtAl2008,
acmid = {1477139},
address = {Piscataway, NJ, USA},
author = {Matthews, David and Wilson, Greg and Easterbrook, Steve},
date-added = {2015-05-05 14:41:18 +0000},
date-modified = {2015-05-05 14:41:18 +0000},
doi = {10.1109/MCSE.2008.144},
issn = {1521-9615},
issue_date = {November 2008},
journal = {Computing in Science and Engg.},
keywords = {climate modeling, climate modeling, configuration management, software development tools, configuration management, software development tools},
month = nov,
number = {6},
numpages = {9},
pages = {56--64},
publisher = {IEEE Educational Activities Department},
title = {Configuration Management for Large-Scale Scientific Computing at the UK Met Office},
url = {http://dx.doi.org/10.1109/MCSE.2008.144},
volume = {10},
year = {2008},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2008.144}}
@article{Dubois2005,
author = {P. F. Dubois},
date-added = {2015-05-05 14:41:10 +0000},
date-modified = {2016-07-03 13:45:01 +0000},
doi = {10.1109/MCSE.2005.54},
journal = {Computing in Science \& Engineering},
month = {May-June},
number = {3},
pages = {80-85},
title = {Maintaining Correctness in Scientific Programs},
volume = {7},
year = {2005},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2005.54}}
@inproceedings{RemmelEtAll2013,
acmid = {2663379},
address = {Piscataway, NJ, USA},
author = {Remmel, Hanna and Paech, Barbara and Engwer, Christian and Bastian, Peter},
booktitle = {Proceedings of the 5th International Workshop on Software Engineering for Computational Science and Engineering},
date-added = {2015-04-30 13:57:07 +0000},
date-modified = {2015-05-05 15:26:09 +0000},
isbn = {978-1-4673-6261-0},
keywords = {quality assurance process, scientific software development, software product line engineering, test strategy},
location = {San Francisco, California},
numpages = {10},
pages = {58--67},
publisher = {IEEE Press},
series = {SE-CSE '13},
title = {Design and Rationale of a Quality Assurance Process for a Scientific Framework},
url = {http://dl.acm.org/citation.cfm?id=2663370.2663379},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2663370.2663379}}
@inproceedings{RemmelEtAl2011,
acmid = {1985785},
address = {New York, NY, USA},
author = {Remmel, Hanna and Paech, Barbara and Engwer, Christian and Bastian, Peter},
booktitle = {Proceedings of the 4th International Workshop on Software Engineering for Computational Science and Engineering},
date-added = {2015-04-30 13:57:04 +0000},
date-modified = {2015-05-05 15:26:00 +0000},
doi = {10.1145/1985782.1985785},
isbn = {978-1-4503-0598-3},
keywords = {framework, scientific software, software product line engineering, testing, variability modeling},
location = {Waikiki, Honolulu, HI, USA},
numpages = {9},
pages = {10--18},
publisher = {ACM},
series = {SECSE '11},
title = {Supporting the Testing of Scientific Frameworks with Software Product Line Engineering: A Proposed Approach},
url = {http://doi.acm.org/10.1145/1985782.1985785},
year = {2011},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1985782.1985785},
bdsk-url-2 = {http://dx.doi.org/10.1145/1985782.1985785}}
@article{LarmanAndBasili2003,
author = {Larman, Craig and Basili, Victor R},
date-added = {2015-04-16 18:14:14 +0000},
date-modified = {2015-04-16 18:14:14 +0000},
journal = {Computer},
number = {6},
pages = {47--56},
publisher = {IEEE Computer Society},
title = {Iterative and incremental development: A brief history},
volume = {36},
year = {2003},
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@phdthesis{Yu2011,
address = {Hamilton, ON, Canada},
author = {Wen Yu},
date-added = {2015-03-27 15:01:41 +0000},
date-modified = {2015-03-27 15:01:41 +0000},
school = {McMaster University},
title = {{FASCS}: A Family Approach for Developing Scientific Computing Software},
year = {2011},
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@article{RosselEtAl2014,
author = {Pedro O. Rossel and Mar{\'{\i}}a Cecilia Bastarrica and Nancy Hitschfeld{-}Kahler and Violeta D{\'{\i}}az and Mario Medina},
bibsource = {dblp computer science bibliography, http://dblp.org},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/aes/RosselBHDM14},
date-added = {2015-03-20 20:44:36 +0000},
date-modified = {2015-03-20 20:44:36 +0000},
doi = {10.1016/j.advengsoft.2014.01.011},
journal = {Advances in Engineering Software},
pages = {77--89},
timestamp = {Thu, 02 Oct 2014 16:18:42 +0200},
title = {Domain modeling as a basis for building a meshing tool software product line},
url = {http://dx.doi.org/10.1016/j.advengsoft.2014.01.011},
volume = {70},
year = {2014},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.advengsoft.2014.01.011}}
@inproceedings{BastarricaEtAl2006,
author = {M. Cecilia Bastarrica and Nancy Hitschfeld-Kahler and Pedro O. Rossel},
biburl = {http://www.bibsonomy.org/bibtex/2e9f4f53cc36e64502f528f99ae02239c/dblp},
booktitle = {ICSR},
date = {2006-08-21},
date-added = {2015-03-20 20:44:32 +0000},
date-modified = {2015-03-20 20:44:32 +0000},
description = {dblp},
editor = {Maurizio Morisio},
ee = {http://dx.doi.org/10.1007/11763864_33},
isbn = {3-540-34606-6},
keywords = {dblp},
pages = {403-406},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
title = {Product Line Architecture for a Family of Meshing Tools.},
url = {http://dblp.uni-trier.de/db/conf/icsr/icsr2006.html#BastarricaHR06},
volume = {4039},
year = {2006},
bdsk-url-1 = {http://dblp.uni-trier.de/db/conf/icsr/icsr2006.html#BastarricaHR06}}
@article{BastarricaAndHitschfeld2006,
author = {Mar\'{i}a Cecilia Bastarrica and Nancy Hischfeld-Kahler},
date-added = {2015-03-20 20:44:28 +0000},
date-modified = {2015-03-20 20:44:28 +0000},
journal = {Advances in Engineering Software},
keywords = {meshing tools, object-oriented design, software product line},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/BastarricaAndHitschfeld2005.pdf},
number = {1},
pages = {1--10},
title = {Designing a product family of meshing tools},
volume = {37},
year = {2006},
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@inproceedings{BastarricaAndHitschfeld2004,
address = {Williamsburg, Virginia},
author = {Mar\'{i}a Cecilia Bastarrica and Nancy Hischfeld-Kahler},
booktitle = {Proceedings of the 13th International Meshing Roundtable},
date-added = {2015-03-20 20:44:22 +0000},
date-modified = {2015-03-20 20:44:22 +0000},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/MeshGeneration/Bastarrica2004.pdf},
pages = {203--212},
publisher = {Sandia National Laboratories},
title = {An Evolvable Meshing Tool Through a Flexible Object-Oriented Design, September 2004},
year = {2004},
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@article{WilsonEtAl2014,
added-at = {2014-03-03T18:16:10.000+0100},
author = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Chue Hong, Neil P. and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul},
biburl = {http://www.bibsonomy.org/bibtex/2e9c3845ce2e86e3f7114c49315c27225/quantentunnel},
description = {PLOS Biology: Best Practices for Scientific Computing},
doi = {10.1371/journal.pbio.1001745},
file = {Wilson2014.pdf:Artikel/Wilson2014.pdf:PDF},
groups = {public},
interhash = {fd2c034991e7c6c9ca88116ce0a09eab},
intrahash = {e9c3845ce2e86e3f7114c49315c27225},
journal = {PLoS Biol},
keywords = {coding programming scientific-practice},
month = jan,
number = 1,
pages = {e1001745},
publisher = {Public Library of Science},
timestamp = {2014-03-14T11:31:44.000+0100},
title = {Best Practices for Scientific Computing},
url = {http://dx.doi.org/10.1371%2Fjournal.pbio.1001745},
username = {quantentunnel},
volume = 12,
year = 2014,
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bdsk-url-1 = {http://dx.doi.org/10.1371%2Fjournal.pbio.1001745},
bdsk-url-2 = {http://dx.doi.org/10.1371/journal.pbio.1001745}}
@article{WilsonEtAl2013,
author = {Greg Wilson and D.A. Aruliah and C. Titus Brown and Neil P. Chue Hong and Matt Davis and Richard T. Guy and Steven H.D. Haddock and Kathryn D. Huff and Ian M. Mitchell and Mark D. Plumblet and Ben Waugh and Ethan P. White and Paul Wilson},
bibsource = {DBLP, http://dblp.uni-trier.de},
date-added = {2015-03-19 19:44:59 +0000},
date-modified = {2015-03-19 19:44:59 +0000},
ee = {http://arxiv.org/abs/1210.0530},
journal = {CoRR},
title = {Best Practices for Scientific Computing},
volume = {abs/1210.0530},
year = {2013},
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@article{Wilson2006,
author = {Gregory V.~Wilson},
date-added = {2015-03-19 19:44:49 +0000},
date-modified = {2015-03-19 19:44:49 +0000},
journal = {American Scientist},
number = {1},
title = {Where's the Real Bottleneck in Scientific Computing? {S}cientists would do well to pick some tools widely used in the software industry},
url = {http://www.americanscientist.org/issues/pub/wheres-the-real-bottleneck-in-scientific-computing},
volume = {94},
year = {2006},
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bdsk-url-1 = {http://www.americanscientist.org/issues/pub/wheres-the-real-bottleneck-in-scientific-computing}}
@article{Parnas1972a,
author = {David L. Parnas},
date-added = {2015-03-19 19:29:44 +0000},
date-modified = {2016-07-03 13:57:54 +0000},
journal = {Comm. ACM},
month = dec,
number = {2},
pages = {1053--1058},
title = {On the Criteria To Be Used in Decomposing Systems into Modules},
volume = {15},
year = {1972},
bdsk-file-1 = {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}}
@inproceedings{Moore1996,
abstract = {The assurance argument that a trusted system satisfies
its information security requirements mast be
convincing, because the argument supports the
accreditation decision to allow the computer to process
classified information in an operational environment.
Assurance is achieved through understanding, but some
evidence that supports the assurance argument can be
difficult to understand. The paper describes a novel
application of a technique, called literate programming
(D.E. Knuth, 1984), that significantly improves the
readability of the assurance argument while maintaining
its consistency with formal specifications that are
input to specification and verification systems. We
describe an application of this technique to a simple
example and discuss the lessons learned from this
effort},
acknowledgement = ack-nhfb,
affiliation = {Naval Res. Lab., Washington, DC, USA},
author = {A. P. Moore and C. N. {Payne, Jr.}},
bibdate = {Thu Feb 13 07:02:10 MST 1997},
bibsource = {http://www.math.utah.edu/pub/tex/bib/litprog.bib},
booktitle = {Proceedings of 11th Annual Conference on Computer Assurance. COMPASS '96},
date-added = {2015-03-19 19:29:18 +0000},
date-modified = {2015-03-19 19:29:18 +0000},
doi = {http://dx.doi.org/10.1109/CMPASS.1996.507887},
pages = {187--198},
title = {Increasing assurance with literate programming techniques},
year = {1996},
bdsk-url-1 = {http://dx.doi.org/10.1109/CMPASS.1996.507887}}
@article{Knuth1984,
abstract = {The author and his associates have been experimenting for the past several years with a programming language and documentation system called WEB. This paper presents WEB by example, and discusses why the new system appears to be an improvement over previous ones.},
author = {Knuth, D. E.},
date-added = {2015-03-19 19:28:55 +0000},
date-modified = {2015-03-19 19:28:55 +0000},
doi = {10.1093/comjnl/27.2.97},
eprint = {http://comjnl.oxfordjournals.org/content/27/2/97.full.pdf+html},
journal = {The Computer Journal},
number = {2},
pages = {97-111},
title = {Literate Programming},
url = {http://comjnl.oxfordjournals.org/content/27/2/97.abstract},
volume = {27},
year = {1984},
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bdsk-url-1 = {http://comjnl.oxfordjournals.org/content/27/2/97.abstract},
bdsk-url-2 = {http://dx.doi.org/10.1093/comjnl/27.2.97}}
@article{Davison2012,
abstract = {Reproducibility is part of the definition of the scientific method. In computational science, reproducibility has practical benefits in allowing code reuse and hence enabling more rapid progress and the ability to develop more complex models and analysis methods. However, it is widely recognized that published research in diverse scientific domains that rely on numerical computation is too infrequently reproducible, with some commentators speaking of a ``credibility crisis'' [4, 11]. In this article, I examine the reasons why reproducibility is di�cult to achieve, argue that for computational research to become consistently and reliably reproducible requires that reproducibility become easy to achieve, as part of day-to-day research and not just for that subset of research that is published, and suggest a combination of best practices and automated tools that can make reproducible research easier.},
annote = {- focuses on the definition of reproducibility that means being able to run the same code in the future and get the same results
- requires recording exact details of what code was run
``automatically capturing the details of the code and environment, may be approached in two ways: (i) taking a digital copy of the entire environment using a system virtual machine/hardware virtualization approach; (ii) capturing and storing metadata about the code and environment that allows it to be recreated later.''
- the author presents a tool (Sumatra) for partially accomplishing (ii)
``The metadata that needs to be captured to ensure replication of a computational result (or at least to assist in tracking down the reason in the event replication cannot be achieved) includes at least the following: (i) the hardware platform on which a computation was performed, insofar as the details of the platform can a↵ect the numerical outcome of the computation: for a distributed or otherwise parallelized computation, the number of nodes and how the computation was divided between them; for each node, the processor architecture, word size, byte order; (ii) the operating system: identity, version; (iii) for compiled code, the source code (or a stable URL where the specific version of the code may be obtained), the source code of any libraries used, the compilation procedure including details of compiler options, compilation order, etc.; (iv) for code run on a process virtual machine/run-time system such as the Java Virtual Machine, the precise version of the VM and ideally its source code and details of how it was compiled, (iv) for interpreted code, the code itself, the source code of any libraries/dependencies, the interpreter identity, version, how it was compiled, how any compiled dependencies (e.g. C extensions for Python) were built; (v) the identity of input data (including parameter/configuration files), which may include a stable URL where the file may be obtained or database accessed.''},
author = {A. P. Davison},
date-added = {2015-03-19 19:27:24 +0000},
date-modified = {2022-02-25 17:50:10 -0500},
journal = {Computing in Science \& Engineering},
month = {July-Aug},
number = {4},
pages = {48--56},
title = {Automated Capture of Experiment Context for Easier Reproducibility in Computational Research},
volume = {14},
year = {2012},
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@book{GhezziEtAl2003,
address = {Upper Saddle River, NJ, USA},
annote = {Some summary notes
Chapter 8, Productivity
- one of the basic requirments of management in any engineering discipline is to measure the productivity of the people and processes involved in production
- need a metric for measuring software productivity
- an ideal productivity metric measures not lines of code, but the amount of value or functionaly produced per unit time - problem is we have no good way of quantifying the concept of functionality - motivated development of function points metric
- according to the function point method, five items (number of inputs, number of outputs, number of inquiries, number of files and number of interfaces) determine the complexity of an application. The function point is the weighted sum of these five items. The weights have been derived empirically.
- function point only counts user facing inputs, intefaces, etc.
- function point was derived empircally and has been used extensively for business applications and information systems
- {function point is not necessarily suited to research software - different from business applications and the input and output can be relatively simple, with the complexity happening in the calculation step}
- productivity is also measured with size of code, need to make the definition unambiguous - should we count comments? should we count programming language ``statements'' or simply the number of lines? How many times should we count the lines in a file that is ``included'' several times? Should we count declarations, or just executable statements?
- DSI - Delivered Source Instructions
- NSS - Noncommented Source Statements
- KLOC - thousand of lines of code
- easy to measure
- problematic because a program that is twice is big is not necessarily twice as good in any sense
- reuse is not rewarded, productivity is better if you write it yourself
- clever abstraction that reduces code size is generally good, but would be seen as negative productivity
- using DSI means producing internal tools is a worthless activity
- how should cancelled projects be counted?
- fixing code decay looks like negative productivity
- an advantage of function points is that they can be measured without the code - they can even be used after the design to esimate the cost of a project (see COCOMO)
- Factors affecting productivity
- changing to a new programming language?
- new development process?
- hiring an efficiency expert?
- one study that used lines of code as a metric found that the sinple most important factor affecting productivity was the capability of the personnel. Half as import, but second on the list, was the complexity of the product, followed by required reliability and timing constrints. Least important were scheduling constraints and previous experience with the languages on the project
- problems caused by an overly aggressive schedule
},
author = {Carlo Ghezzi and Mehdi Jazayeri and Dino Mandrioli},
date-added = {2015-03-19 19:27:08 +0000},
date-modified = {2020-06-24 16:35:41 -0400},
edition = {2nd},
keywords = {software engineering},
publisher = {Prentice Hall},
title = {Fundamentals of Software Engineering},
year = {2003}}
@book{Roache1998,
address = {Albuquerque, New Mexico},
author = {Patrick J. Roache},
date-added = {2015-03-19 19:26:55 +0000},
date-modified = {2015-03-19 19:26:55 +0000},
publisher = {Hermosa Publishers},
title = {Verification and Validation in Computational Science and Engineering},
year = {1998}}
@article{MaibaumAndWassyng2008,
author = {Thomas Maibaum and Alan Wassyng},
date-added = {2015-03-19 19:26:38 +0000},
date-modified = {2015-03-19 19:26:38 +0000},
journal = {IEEE Computer},
number = {2},
pages = {91--93},
title = {A Product-Focused Approach to Software Certification},
volume = {41},
year = {2008},
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@article{Dubois2002,
author = {Paul F. Dubois},
date-added = {2015-03-19 19:25:17 +0000},
date-modified = {2015-03-19 19:25:17 +0000},
journal = {Computing in Science and Engineering},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Dubois2002.pdf},
month = sep,
number = {5},
pages = {84--90},
title = {Designing Scientific Components},
volume = {4},
year = {2002},
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@article{SandersAndKelly2008,
annote = {``None of our interviewees created an up-front formal requirements specification. If regulations in their field mandated a requirements document, they wrote it when the software was almost complete. Customers of the scientific software might provide a vision statement, but nothing more. In all cases, customers ceded decisions about the software to the scientists, giving them broad sway in deciding what to include in the software.''},
author = {Rebecca Sanders and Diane Kelly},
date-added = {2015-03-19 19:24:48 +0000},
date-modified = {2022-02-07 14:58:25 -0500},
journal = {IEEE Software},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/SandersAndKelly2008.pdf},
month = {July/August},
pages = {21--28},
title = {Dealing with Risk in Scientific Software Development},
volume = {4},
year = {2008},
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@article{KellyEtAl2011,
author = {Diane F. Kelly and W. Spencer Smith and Nicholas Meng},
date-added = {2015-03-19 19:24:44 +0000},
date-modified = {2015-03-19 19:24:44 +0000},
journal = {Computing in Science \& Engineering},
month = oct,
number = {5},
pages = {7--11},
title = {Software Engineering for Scientists},
volume = {13},
year = {2011},
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@inproceedings{KellyEtAl2007,
address = {St.\ John, New Brunswick},
author = {Diane F. Kelly and N. Cote and T. Shepard},
booktitle = {Proceedings of the Canadian Nuclear Society Conference},
date-added = {2015-03-19 19:24:40 +0000},
date-modified = {2015-03-19 19:24:40 +0000},
title = {Software engineers and nuclear engineers: teaming up to do testing},
year = {2007}}
@inproceedings{KellyAndSanders2008,
address = {Leipzig, Germany},
author = {Diane F. Kelly and Rebecca Sanders},
booktitle = {Proceedings of the First International Workshop on Software Engineering for Computational Science and Engineering (SECSE 2008)},
date-added = {2015-03-19 19:24:31 +0000},
date-modified = {2015-03-19 19:24:31 +0000},
organization = {In conjunction with the 30th International Conference on Software Engineering (ICSE)},
title = {Assessing the Quality of Scientific Software},
url = {http://www.cse.msstate.edu/~SECSE08/schedule.htm},
year = {2008},
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bdsk-url-1 = {http://www.cse.msstate.edu/~SECSE08/schedule.htm}}
@inproceedings{Kelly2013,
acmid = {2555555},
address = {Riverton, NJ, USA},
author = {Kelly, Diane},
booktitle = {Proceedings of the 2013 Conference of the Center for Advanced Studies on Collaborative Research},
date-added = {2015-03-19 19:24:26 +0000},
date-modified = {2015-03-19 19:24:26 +0000},
location = {Ontario, Canada},
numpages = {12},
pages = {299--310},
publisher = {IBM Corp.},
series = {CASCON '13},
title = {Industrial Scientific Software: A Set of Interviews on Software Development},
url = {http://dl.acm.org/citation.cfm?id=2555523.2555555},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2555523.2555555}}
@inproceedings{Segal2008,
address = {Leipzig, Germany},
author = {Judith Segal},
booktitle = {Proceedings of the First International Workshop on Software Engineering for Computational Science and Engineering (SECSE 2008)},
date-added = {2015-03-19 19:24:05 +0000},
date-modified = {2015-03-19 19:24:05 +0000},
organization = {In conjunction with the 30th International Conference on Software Engineering (ICSE)},
pages = {1--6},
title = {Models of Scientific Software Development},
url = {http://www.cse.msstate.edu/~SECSE08/schedule.htm},
year = {2008},
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bdsk-url-1 = {http://secse08.cs.ua.edu/schedule.htm},
bdsk-url-2 = {http://www.cse.msstate.edu/~SECSE08/schedule.htm}}
@inproceedings{Segal2007_Dagsthul,
author = {Judith Segal},
booktitle = {Dagstuhl Seminar Proceedings 07081, End-User Software Engineering},
date-added = {2015-03-19 19:23:57 +0000},
date-modified = {2015-03-19 19:23:57 +0000},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Segal2007_Dagstuhl.pdf},
title = {End-User Software Engineering and Professional End-User Developers},
url = {http://drops.dagstuhl.de/opus/volltexte/2007/1095},
year = {2007},
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bdsk-url-1 = {http://drops.dagstuhl.de/opus/volltexte/2007/1095}}
@inproceedings{Segal2007,
address = {Washington, DC, USA},
author = {Judith Segal},
booktitle = {VLHCC '07: Proceedings of the IEEE Symposium on Visual Languages and Human-Centric Computing},
date-added = {2015-03-19 19:23:54 +0000},
date-modified = {2015-03-19 19:23:54 +0000},
doi = {http://dx.doi.org/10.1109/VLHCC.2007.50},
isbn = {0-7695-2987-9},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Segal2007.pdf},
pages = {111--118},
publisher = {IEEE Computer Society},
title = {Some Problems of Professional End User Developers},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1109/VLHCC.2007.50}}
@article{Segal2005,
author = {Segal, Judith},
citeulike-article-id = {342252},
date-added = {2015-03-19 19:23:49 +0000},
date-modified = {2015-03-19 19:23:49 +0000},
doi = {10.1007/s10664-005-3865-y},
issn = {1382-3256},
journal = {Empirical Software Engineering},
keywords = {components, enginner, experiment, research, science},
local-url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Segal2005.pdf},
month = oct,
number = {4},
pages = {517--536},
posted-at = {2006-08-11 01:21:33},
priority = {4},
publisher = {Kluwer Academic Publishers},
title = {When Software Engineers Met Research Scientists: A Case Study},
url = {http://dx.doi.org/10.1007/s10664-005-3865-y},
volume = {10},
year = {2005},
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@inbook{Segal2001,
address = {Berlin/Heidelberg},
author = {Judith Segal},
chapter = {Organisational Learning and Software Process Improvement: A Case Study},
date-added = {2015-03-19 19:23:40 +0000},
date-modified = {2015-03-19 19:23:40 +0000},
editor = {K-D Althoff and R. L. Feldmann and W. Muller},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Segal2001.pdf},
pages = {68--82},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
title = {Advances in Learning Software Organizations},
url = {http://www.springerlink.com/content/84wh8fymrrdkjt05/},
volume = {2176},
year = {2001},
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@article{Weiss1997,
author = {David M. Weiss},
date-added = {2015-03-19 19:22:59 +0000},
date-modified = {2015-03-19 19:22:59 +0000},
journal = {Submitted to IEEE Transactions on Software Engineering},
keywords = {software engineering, domain analysis, domain engineering, families, software process, application-oriented languages},
local-url = {/Users/smiths/LongTermArchives/Work/Research/References/ProgramFamilies/DefiningFamilies.pdf},
title = {Defining families: The commonality analysis},
url = {http://www.research.avayalabs.com/user/weiss/Publications.html},
year = {1997},
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@inproceedings{YuAndSmith2009,
address = {Vancouver, Canada},
author = {Wen Yu and W. Spencer Smith},
booktitle = {Proceedings of the Second International Workshop on Software Engineering for Computational Science and Engineering (SECSE 2009)},
date-added = {2015-03-19 19:21:49 +0000},
date-modified = {2018-05-19 18:03:48 +0000},
doi = {10.1109/SECSE.2009.5069161},
keywords = {finite element analysis;software maintenance;software reusability;FEA software reusability;finite element analysis;program family approach;software maintainability;Asset management;Computational modeling;Design engineering;Documentation;Finite element methods;Knowledge engineering;Partial differential equations;Software maintenance;Software reusability;Usability},
local-url = {file://localhost/Users/smiths/Work/Research/GradStudents/WenYuPhD/PhD/Papers/SECSE/SECSE.pdf},
month = jun,
organization = {In conjunction with the 31st International Conference on Software Engineering (ICSE)},
pages = {43--50},
title = {Reusability of {FEM} Software: A Program Family Approach},
year = {2009},
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@inproceedings{SmithMcCutchanAndCao2007,
address = {Montr\'{e}al, Qu\'{e}bec},
author = {W. Spencer Smith and John McCutchan and Fang Cao},
booktitle = {7$^{th}$ OOPSLA Workshop on Domain Specific Modelling ({DSM}'07)},
date-added = {2015-03-19 19:20:32 +0000},
date-modified = {2015-03-19 19:20:32 +0000},
editor = {Jonathan Sprinkle and Jeff Gray and Matti Rossi and Juha-Pekka Tolvanen},
local-url = {/Users/smiths/Work/Research/Papers/OOPSLA_Workshop2007/ProgFamiliesInSciComp_CameraReady.pdf},
month = oct,
pages = {39--47},
title = {Program Families in Scientific Computing},
year = {2007},
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@inproceedings{SmithEtAl2008,
address = {Leipzig, Germany},
author = {W. Spencer Smith and John McCutchan and Jacques Carette},
booktitle = {Proceedings of the First International Workshop on Software Engineering for Computational Science and Engineering (SECSE 2008)},
date-added = {2015-03-19 19:17:40 +0000},
date-modified = {2015-03-19 19:17:40 +0000},
month = may,
note = {8 pp},
organization = {In conjunction with the 30th International Conference on Software Engineering (ICSE)},
title = {Commonality Analysis of Families of Physical Models for use in Scientific Computing},
url = {http://www.cse.msstate.edu/~SECSE08/schedule.htm},
year = {2008},
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bdsk-url-1 = {http://www.cse.msstate.edu/~SECSE08/schedule.htm}}
@techreport{SmithAndChen2004b,
author = {W. Spencer Smith and Chien-Hsien Chen},
date-added = {2015-03-19 19:16:21 +0000},
date-modified = {2015-03-19 19:16:21 +0000},
institution = {McMaster University, Department of Computing and Software},
local-url = {file://localhost/Users/smiths/Work/Research/WorkingDocs/MeshGenSyst/CommAnalysisMeshGen/CAS%2004-10-SS.pdf},
note = {45 pp},
number = {CAS-04-10-SS},
title = {Commonality analysis for mesh generating systems},
type = {Technical Report},
year = {2004},
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@techreport{CSA1999,
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author = {CSA},
date-added = {2014-11-17 16:33:26 +0000},
date-modified = {2014-11-17 16:33:26 +0000},
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number = {N286.7-99},
title = {Quality assurance of analytical, scientific, and design computer programs for nuclear power plants},
year = {1999},
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@techreport{CSA2009,
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author = {CSA},
date-added = {2014-11-17 16:33:26 +0000},
date-modified = {2014-11-17 16:33:26 +0000},
institution = {Canadian Standards Association},
number = {N286.7.1-09},
title = {Guideline for the application of {N286.7-99}, Quality assurance of analytical, scientific, and design computer programs for nuclear power plants},
year = {2009},
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@inproceedings{SmithEtAl2013,
author = {W. Spencer Smith and Nirmitha Koothoor and Nedialko Nedialkov},
booktitle = {Proceedings of the First International Workshop on Software Engineering for High Performance Computing in Computational Science and Engineering (SE-HPCCE)},
date-added = {2014-10-03 23:55:31 +0000},
date-modified = {2022-10-27 14:12:23 -0400},
month = nov,
organization = {In conjuction with SC13: International Conference for High Performance Computing, Networking, Storage and Analysis},
pages = {[8 p.]},
title = {Document Driven Certification of Computational Science and Engineering Software},
year = {2013},
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@inproceedings{SmithAndLai2005,
address = {Paris, France},
author = {W. Spencer Smith and Lei Lai},
booktitle = {Proceedings of the First International Workshop on Situational Requirements Engineering Processes -- Methods, Techniques and Tools to Support Situation-Specific Requirements Engineering Processes, SREP'05},
date-added = {2014-10-03 23:54:42 +0000},
date-modified = {2014-10-03 23:54:42 +0000},
editor = {J. Ralyt\'{e} and P. \.{A}gerfalk and N. Kraiem},
local-url = {file://localhost/Users/smiths/Work/Research/Papers/SREP05/SREP05_ReformatAndRevise/SmithAndLai_2005.pdf},
organization = {In conjunction with 13th IEEE International Requirements Engineering Conference},
pages = {107--121},
title = {A New Requirements Template for Scientific Computing},
year = {2005},
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@inproceedings{SmithAndChen2004,
address = {Banff, Alberta},
author = {W. Spencer Smith and Chien-Hsien Chen},
booktitle = {Proceedings of the Sixteenth International Conference on Software Engineering and Knowledge Engineering (SEKE 2004)},
date-added = {2014-10-03 23:54:24 +0000},
date-modified = {2014-10-03 23:54:24 +0000},
editor = {F. Maurer and G. Ruhe},
local-url = {/Users/smiths/Work/Research/Papers/CommReqAnal_MeshGen_SEKE04/AsSubmitted_SmithAndChen.pdf},
pages = {384--387},
title = {Commonality and Requirements Analysis for Mesh Generating Software},
year = {2004},
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@inproceedings{Smith2006,
address = {Minneapolis / St.\ Paul, Minnesota},
author = {W. Spencer Smith},
booktitle = {Proceedings of the 14th IEEE International Requirements Engineering Conference, RE 2006},
date-added = {2014-10-03 23:53:30 +0000},
date-modified = {2014-10-03 23:53:30 +0000},
local-url = {/Users/smiths/Work/Research/Papers/RE_2006/Smith2006_VersionAsPublished.pdf},
pages = {209--218},
title = {Systematic Development of Requirements Documentation for General Purpose Scientific Computing Software},
url = {http://www.ifi.unizh.ch/req/events/RE06/},
year = {2006},
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@article{SmithEtAl2014,
author = {W. Spencer Smith and Nirmitha Koothoor and Ned Nedialkov},
date-added = {2014-10-03 23:52:21 +0000},
date-modified = {2016-07-03 16:03:19 +0000},
journal = {IEEE Transactions on Software Engineering},
title = {A Document Driven Method for Facilitating Certification of Scientific Computing Software},
year = {Submitted 2014},
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@article{SmithEtAl2007,
author = {W. Spencer Smith and Lei Lai and Ridha Khedri},
date-added = {2014-10-03 23:49:56 +0000},
date-modified = {2018-05-19 17:58:44 +0000},
doi = {10.1007/s11155-006-9020-7},
issn = {1573-1340},
journal = {Reliable Computing, Special Issue on Reliable Engineering Computation},
local-url = {/Users/smiths/Work/Research/Papers/ReliableComputing/SmithLaiAndKhedri2007fulltext.pdf},
month = feb,
number = {1},
pages = {83--107},
title = {Requirements Analysis for Engineering Computation: A Systematic Approach for Improving Software Reliability},
url = {https://doi.org/10.1007/s11155-006-9020-7},
volume = {13},
year = {2007},
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@article{SmithAndYu2009,
author = {W. Spencer Smith and Wen Yu},
date-added = {2014-10-03 23:49:13 +0000},
date-modified = {2014-10-03 23:49:13 +0000},
doi = {http://dx.doi.org/10.1016/j.advengsoft.2009.05.003},
journal = {Advances in Engineering Software},
local-url = {/Users/smiths/Work/Research/Papers/SmithAndYu2008_AdvEngSoft/SmithAndYu2008_ResubmissionToAdvEngSoft.pdf},
month = nov,
number = {11},
pages = {1155--1167},
title = {A Document Driven Methodology for Improving the Quality of a Parallel Mesh Generation Toolbox},
volume = {40},
year = {2009},
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author = {Lucas N. Joppa and Greg McInerny and Richard Harper and Lara Salido and Kenji Takeda and Kenton O'Hara and David Gavaghan and Stephen Emmott},
journal = {Science},
number = {6134},
pages = {814--815},
title = {Troubling trends in scientific software use},
volume = {340},
year = {2013}}
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author = {Marian Petre and Greg Wilson},
date-modified = {2017-09-29 19:30:39 +0000},
title = {Code review for and by scientists: preliminary findings},
url = {https://arxiv.org/abs/1407.5648},
year = {2014},
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bdsk-url-1 = {https://arxiv.org/abs/1407.5648}}
@article{Roache1997,
author = {Patrick J. Roache},
journal = {Annual review of fluid Mechanics},
number = {1},
pages = {123--160},
title = {Quantification of uncertainty in computational fluid dynamics},
volume = {29},
year = {1997}}
@inproceedings{Roy2009,
author = {Christoper J. Roy},
booktitle = {Proceedings of the 19th AIAA Computational Fluid Dynamics Conference},
pages = {1473--1485},
title = {Practical software engineering strategies for scientific computing},
year = {2009}}
@article{SandveEtAl2013,
author = {Geir Kjetil Sandve and Anton Nekrutenko and James Taylor and Eivind Hovig},
journal = {PLOS Computational Biology},
number = {10},
title = {Ten Simple Rules for Reproducible Computational Research},
volume = {9},
year = {October 2013},
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@article{PNAS2016,
author = {Anders Eklund and Thomas E. Nichols and Hans Knutsson},
journal = {PNAS},
number = {28},
pages = {7900--7905},
title = {Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates},
url = {http://www.pnas.org/content/113/28/7900.full.pdf},
volume = {113},
year = {July 2016},
bdsk-url-1 = {http://www.pnas.org/content/113/28/7900.full.pdf}}
@article{Kulkarni:2012:GPF:2089116.2089121,
acmid = {2089121},
address = {New York, NY, USA},
articleno = {11},
author = {Kulkarni, Devdatta and Ahmed, Tanvir and Tripathi, Anand},
doi = {10.1145/2089116.2089121},
issn = {1049-331X},
issue_date = {March 2012},
journal = {ACM Trans. Softw. Eng. Methodol.},
keywords = {Context-aware computing, generative middleware, pervasive computing},
month = mar,
number = {2},
numpages = {35},
pages = {11:1--11:35},
publisher = {ACM},
title = {A Generative Programming Framework for Context-Aware CSCW Applications},
url = {http://doi.acm.org/10.1145/2089116.2089121},
volume = {21},
year = {2012},
bdsk-url-1 = {http://doi.acm.org/10.1145/2089116.2089121},
bdsk-url-2 = {http://dx.doi.org/10.1145/2089116.2089121}}
@inproceedings{AhaltEtAl2013,
author = {Stan Ahalt and Larry Band and Barbara Minsker and Margaret Palmer and Michael Tiemann and Ray Idaszak and Chris Lenhardt and Mary Whitton},
booktitle = {2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)},
doi = {10.1109/SECSE.2013.6615098},
keywords = {environmental science computing;public domain software;software prototyping;water resources;Agile;OCEP model;WSSI;open source engagement process;open source software development;public-private water science software institute;Acceleration;Communities;Educational institutions;Open source software;Technological innovation;Water resources;Agile software development;Open Source software;Scientific Software Innovation Institute;water science},
month = may,
pages = {40--47},
title = {Water science software institute: An open source engagement process},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2013.6615098}}
@article{AllanEtAl2006,
author = {Benjamin A. Allan and Robert Armstrong and David E. Bernholdt and Felipe Bertrand and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende and Theresa L. Windus and Shujia Zhou},
journal = {Int. J. High Perform. Comput. Appl.},
month = {Summer},
number = {2},
pages = {163--202},
title = {A component architecture for high performance scientific computing},
volume = {20},
year = {2006}}
@article{EmamAndKoru2008,
abstract = {Despite various industry reports about the failure rates of software projects, there's still uncertainty about the actual figures. Researchers performed a global Web survey of IT departments in 2005 and 2007. The results suggest that the software crisis is perhaps exaggerated and that most software projects deliver. However, the overall project failure rate, including cancelled and completed but poorly performing projects, remains arguably high for an applied discipline.},
added-at = {2008-09-28T00:03:51.000+0200},
author = {Emam, Khaled El and Koru, A. G{\"u}ne{\c s}},
biburl = {https://www.bibsonomy.org/bibtex/2dd7d71bb02462f23b6acb0a159c4bd52/neilernst},
doi = {10.1109/MS.2008.107},
interhash = {0707fb418e94c670485d825036b14cb1},
intrahash = {dd7d71bb02462f23b6acb0a159c4bd52},
issn = {0740-7459},
journal = {IEEE Software},
keywords = {empirical software},
month = {September/October},
number = 5,
pages = {84-90},
timestamp = {2008-09-28T00:03:51.000+0200},
title = {A Replicated Survey of IT Software Project Failures},
volume = 25,
year = 2008,
bdsk-url-1 = {https://doi.org/10.1109/MS.2008.107}}
@article{FayadEtAl2000,
acmid = {330555},
address = {New York, NY, USA},
author = {Fayad, Mohamed E. and Laitinen, Mauri and Ward, Robert P.},
doi = {10.1145/330534.330555},
issn = {0001-0782},
issue_date = {March 2000},
journal = {Commun. ACM},
month = mar,
number = {3},
numpages = {4},
pages = {115--118},
publisher = {ACM},
title = {Thinking Objectively: Software Engineering in the Small},
url = {http://doi.acm.org/10.1145/330534.330555},
volume = {43},
year = {2000},
bdsk-url-1 = {http://doi.acm.org/10.1145/330534.330555},
bdsk-url-2 = {https://doi.org/10.1145/330534.330555}}
@book{Fowler1999,
address = {Boston, MA, USA},
author = {Fowler, Martin},
isbn = {0-201-48567-2},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
title = {Refactoring: Improving the Design of Existing Code},
year = {1999}}
@book{GardnerAndManduchi2007,
author = {Gardner, Henry J. and Manduchi, Gabriele},
catalogue-url = {https://nla.gov.au/nla.cat-vn4360147},
isbn = {9783540680888 3540680888},
language = {English},
life-dates = {2007 -},
pages = {xx, 382 p. :},
publisher = {Springer Berlin ; New York},
subjects = {Java (Computer program language); Graphical user interfaces (Computer systems); Software engineering.; Science -- Data processing.; Software refactoring.; Science -- Software.},
title = {Design Patterns for e-Science},
type = {Book},
year = {2007}}
@inproceedings{GavishAndDonoho2011,
author = {Matan Gavish and David L. Donoho},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/journals/procedia/GavishD11},
booktitle = {Proceedings of the International Conference on Computational Science, {ICCS} 2011, Nanyang Technological University, Singapore, 1-3 June, 2011},
crossref = {DBLP:conf/iccS/2011},
doi = {10.1016/j.procs.2011.04.067},
pages = {637--647},
timestamp = {Mon, 21 Aug 2017 16:43:25 +0200},
title = {A Universal Identifier for Computational Results},
url = {https://doi.org/10.1016/j.procs.2011.04.067},
year = {2011},
bdsk-url-1 = {https://doi.org/10.1016/j.procs.2011.04.067}}
@article{Gent2013,
archiveprefix = {arXiv},
arxivid = {arXiv:1304.3674v1},
author = {Gent, Ip Ian P},
eprint = {arXiv:1304.3674v1},
file = {http://bib.unthinkingdepths.fr/seb/pdf/Gent_2013_The recomputation manifesto.pdf},
journal = {arXiv preprint arXiv:1304.3674},
keywords = {computer science,manifeste,replication,tools},
mendeley-tags = {computer science,manifeste,replication,tools},
number = apr,
pages = {1--6},
title = {The Recomputation Manifesto},
url = {http://arxiv.org/abs/1304.3674},
year = {2013},
bdsk-url-1 = {http://arxiv.org/abs/1304.3674}}
@inproceedings{GobleAndDeRoure2007,
acmid = {1273361},
address = {New York, NY, USA},
author = {Goble, Carole Anne and De Roure, David Charles},
booktitle = {Proceedings of the 2Nd Workshop on Workflows in Support of Large-scale Science},
doi = {10.1145/1273360.1273361},
isbn = {978-1-59593-715-5},
keywords = {Taverna, bioinformatics, e-Science, myExperiment, myGrid, scientist, social networking, workflow},
location = {Monterey, California, USA},
numpages = {2},
pages = {1--2},
publisher = {ACM},
series = {WORKS '07},
title = {myExperiment: Social Networking for Workflow-using e-Scientists},
url = {http://doi.acm.org/10.1145/1273360.1273361},
year = {2007},
bdsk-url-1 = {http://doi.acm.org/10.1145/1273360.1273361},
bdsk-url-2 = {https://doi.org/10.1145/1273360.1273361}}
@article{Goldberg1991,
acmid = {103163},
address = {New York, NY, USA},
author = {Goldberg, David},
doi = {10.1145/103162.103163},
issn = {0360-0300},
issue_date = {March 1991},
journal = {ACM Comput. Surv.},
keywords = {NaN, denormalized number, exception, floating-point, floating-point standard, gradual underflow, guard digit, overflow, relative error, rounding error, rounding mode, ulp, underflow},
month = mar,
number = {1},
numpages = {44},
pages = {5--48},
publisher = {ACM},
title = {What Every Computer Scientist Should Know About Floating-point Arithmetic},
url = {http://doi.acm.org/10.1145/103162.103163},
volume = {23},
year = {1991},
bdsk-url-1 = {http://doi.acm.org/10.1145/103162.103163},
bdsk-url-2 = {https://doi.org/10.1145/103162.103163}}
@inbook{Hatton1997,
abstract = {This paper covers two very large experiments carried out concurrently between 1990 and 1994, together known as the T-experiments. Experiment Ti had the objective of measuring the consistency of several million lines of scientific software written in C and Fortran 77 by static deep-flow analysis across many different industries and application areas, and experiment T2 had the objective of measuring the level of dynamic disagreement between independent implementations of the same algorithms acting on the same input data with the same parameters in just one of these industrial application areas.},
address = {Boston, MA},
author = {Hatton, L.},
booktitle = {Quality of Numerical Software: Assessment and enhancement},
doi = {10.1007/978-1-5041-2940-4_2},
editor = {Boisvert, Ronald F.},
isbn = {978-1-5041-2940-4},
pages = {12--31},
publisher = {Springer US},
title = {The T-experiments: errors in scientific software},
url = {https://doi.org/10.1007/978-1-5041-2940-4_2},
year = {1997},
bdsk-url-1 = {https://doi.org/10.1007/978-1-5041-2940-4_2}}
@article{HerndonEtAl2014,
author = {Herndon, Thomas and Ash, Michael and Pollin, Robert},
doi = {10.1093/cje/bet075},
eprint = {/oup/backfile/content_public/journal/cje/38/2/10.1093/cje/bet075/2/bet075.pdf},
journal = {Cambridge Journal of Economics},
number = {2},
pages = {257-279},
title = {Does high public debt consistently stifle economic growth? A critique of Reinhart and Rogoff},
url = {http://dx.doi.org/10.1093/cje/bet075},
volume = {38},
year = {2014},
bdsk-url-1 = {http://dx.doi.org/10.1093/cje/bet075}}
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acmid = {1089021},
address = {New York, NY, USA},
author = {Heroux, Michael A. and Bartlett, Roscoe A. and Howle, Vicki E. and Hoekstra, Robert J. and Hu, Jonathan J. and Kolda, Tamara G. and Lehoucq, Richard B. and Long, Kevin R. and Pawlowski, Roger P. and Phipps, Eric T. and Salinger, Andrew G. and Thornquist, Heidi K. and Tuminaro, Ray S. and Willenbring, James M. and Williams, Alan and Stanley, Kendall S.},
doi = {10.1145/1089014.1089021},
issn = {0098-3500},
issue_date = {September 2005},
journal = {ACM Trans. Math. Softw.},
keywords = {Software Quality Engineering, Software framework, interfaces},
month = sep,
number = {3},
numpages = {27},
pages = {397--423},
publisher = {ACM},
title = {An Overview of the Trilinos Project},
url = {http://doi.acm.org/10.1145/1089014.1089021},
volume = {31},
year = {2005},
bdsk-url-1 = {http://doi.acm.org/10.1145/1089014.1089021},
bdsk-url-2 = {https://doi.org/10.1145/1089014.1089021}}
@inproceedings{FalessiAndShull2013,
author = {Davide Falessi and Forrest Shull},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/conf/icse/FalessiS13},
booktitle = {Proceedings of the 5th International Workshop on Software Engineering for Computational Science and Engineering, {SE-CSE} 2013, San Francisco, California, USA, May 18, 2013},
crossref = {DBLP:conf/icse/2013secse},
doi = {10.1109/SECSE.2013.6615104},
pages = {88--91},
timestamp = {Tue, 23 May 2017 01:11:51 +0200},
title = {Towards flexible automated support to improve the quality of computational science and engineering software},
url = {https://doi.org/10.1109/SECSE.2013.6615104},
year = {2013},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2013.6615104}}
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author = {L. Hochstein and V. R. Basili},
doi = {10.1109/MC.2008.101},
issn = {0018-9162},
journal = {Computer},
keywords = {software engineering; computing methodologies; scientific code development; simulation},
month = feb,
pages = {50-58},
title = {The ASC-Alliance Projects: A Case Study of Large-Scale Parallel Scientific Code Development},
url = {doi.ieeecomputersociety.org/10.1109/MC.2008.101},
volume = {41},
year = {2008},
bdsk-url-1 = {doi.ieeecomputersociety.org/10.1109/MC.2008.101},
bdsk-url-2 = {https://doi.org/10.1109/MC.2008.101}}
@book{GreatBritianScienceAndTechnologyCommittee2010Vol1,
author = {Great Britain: Parliament: House of Commons: Science and Technology Committee},
isbn = {9780215553362},
publisher = {Stationery Office},
series = {Eighth Report of Session 2009-10 - Volume I: Report, Together With Formal Minutes},
title = {The Disclosure of Climate Data from the Climatic Research Unit at the University of East Anglia},
url = {https://books.google.ca/books?id=p0yX7ibQGZAC},
year = {2010},
bdsk-url-1 = {https://books.google.ca/books?id=p0yX7ibQGZAC}}
@article{SendallAndKozaczynski2003,
author = {Shane Sendall and Wojtek Kozaczynski},
doi = {10.1109/MS.2003.1231150},
issn = {0740-7459},
journal = {IEEE Software},
keywords = {object-oriented programming;software reusability;specification languages;common application fragments;development productivity;human-friendly abstractions;language characteristics;model-driven approach;quality;templates;Automation;Computer languages;Context modeling;Heart;Java;Metamodeling;Productivity;Programming;Unified modeling language;XML},
month = {Sept},
number = {5},
pages = {42-45},
title = {Model transformation: the heart and soul of model-driven software development},
volume = {20},
year = {2003},
bdsk-url-1 = {https://doi.org/10.1109/MS.2003.1231150}}
@book{GreatBritianScienceAndTechnologyCommittee2010Vol2,
author = {Great Britain Parliament House of Commons Science and Technology Committee},
isbn = {9780215553409},
number = {v. 2},
publisher = {Stationery Office},
series = {HC (Series) (Great Britain. Parliament},
title = {The Disclosure of Climate Data from the Climatic Research Unit at the University of East Anglia: Eighth Report of Session 2009-10, Vol. 2: Oral and Written Evidence},
url = {https://books.google.ca/books?id=woxi6XI4u14C},
year = {2010},
bdsk-url-1 = {https://books.google.ca/books?id=woxi6XI4u14C}}
@article{Howden1982,
acmid = {356880},
address = {New York, NY, USA},
author = {Howden, William E.},
doi = {10.1145/356876.356880},
issn = {0360-0300},
issue_date = {June 1982},
journal = {ACM Comput. Surv.},
month = jun,
number = {2},
numpages = {35},
pages = {193--227},
publisher = {ACM},
title = {Validation of Scientific Programs},
url = {http://doi.acm.org/10.1145/356876.356880},
volume = {14},
year = {1982},
bdsk-url-1 = {http://doi.acm.org/10.1145/356876.356880},
bdsk-url-2 = {https://doi.org/10.1145/356876.356880}}
@inproceedings{Kane2003,
acmid = {942811},
address = {Washington, DC, USA},
author = {Kane, David},
booktitle = {Proceedings of the Conference on Agile Development},
isbn = {0-7695-2013-8},
pages = {132--},
publisher = {IEEE Computer Society},
series = {ADC '03},
title = {Introducing Agile Development into Bioinformatics: An Experience Report},
url = {http://dl.acm.org/citation.cfm?id=942789.942811},
year = {2003},
bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=942789.942811}}
@article{GrayEtAl2011,
author = {Robert Gray and Diane Kelly and Yizhen Shao},
doi = {https://doi.org/10.1016/j.jocs.2010.12.002},
issn = {1877-7503},
journal = {Journal of Computational Science},
keywords = {Software testing, Tolerance problem, Random testing, Computational software},
number = {1},
pages = {47 - 56},
title = {Examining random and designed tests to detect code mistakes in scientific software},
url = {http://www.sciencedirect.com/science/article/pii/S187775031000075X},
volume = {2},
year = {2011},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S187775031000075X},
bdsk-url-2 = {https://doi.org/10.1016/j.jocs.2010.12.002}}
@article{HookEtAl2011,
acmid = {1978417},
address = {Los Alamitos, CA, USA},
author = {Hook, Daniel and Kelly, Diane and Thorsteinson, Stefan},
doi = {10.1109/MS.2010.88},
issn = {0740-7459},
issue_date = {May 2011},
journal = {IEEE Softw.},
keywords = {scientific software, software testing, multidisciplinary team},
month = may,
number = {3},
numpages = {7},
pages = {84--90},
publisher = {IEEE Computer Society Press},
title = {Scientific Software Testing: Analysis with Four Dimensions},
url = {https://doi.org/10.1109/MS.2010.88},
volume = {28},
year = {2011},
bdsk-url-1 = {https://doi.org/10.1109/MS.2010.88}}
@article{KellyEtAl2009,
acmid = {2220165},
address = {Piscataway, NJ, USA},
author = {Kelly, D. and Hook, D. and Sanders, R.},
doi = {10.1109/MCSE.2009.139},
issn = {1521-9615},
issue_date = {September 2009},
journal = {Computing in Science and Engg.},
keywords = {scientific software},
month = sep,
number = {5},
numpages = {6},
pages = {48--53},
publisher = {IEEE Educational Activities Department},
title = {Five Recommended Practices for Computational Scientists Who Write Software},
url = {http://dx.doi.org/10.1109/MCSE.2009.139},
volume = {11},
year = {2009},
bdsk-file-1 = {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},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.139}}
@article{ShepardandKelly2004,
acmid = {1035110},
address = {New York, NY, USA},
author = {Shepard, Terry and Kelly, Diane},
doi = {10.1016/j.jss.2003.10.027},
issn = {0164-1212},
issue_date = {October 2004},
journal = {J. Syst. Softw.},
keywords = {TDI, safety related software, software process, structured software inspection technique, task directed inspection},
month = oct,
number = {2},
numpages = {8},
pages = {361--368},
publisher = {Elsevier Science Inc.},
title = {Task-directed Software Inspection},
url = {http://dx.doi.org/10.1016/j.jss.2003.10.027},
volume = {73},
year = {2004},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.jss.2003.10.027}}
@article{KendallEtAl2008,
acmid = {1383174},
address = {Los Alamitos, CA, USA},
author = {Kendall, Richard and Carver, Jeffrey C. and Fisher, David and Henderson, Dale and Mark, Andrew and Post, Douglass and Rhoades Jr., Clifford E. and Squires, Susan},
doi = {10.1109/MS.2008.86},
issn = {0740-7459},
issue_date = {July 2008},
journal = {IEEE Softw.},
keywords = {management, physical sciences and engineering, software engineering, software engineering process: life cycle, software engineering, management, software engineering process: life cycle, physical sciences and engineering},
month = jul,
number = {4},
numpages = {7},
pages = {59--65},
publisher = {IEEE Computer Society Press},
title = {Development of a Weather Forecasting Code: A Case Study},
url = {http://dx.doi.org/10.1109/MS.2008.86},
volume = {25},
year = {2008},
bdsk-file-1 = {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},
bdsk-url-1 = {http://dx.doi.org/10.1109/MS.2008.86}}
@article{KendallEtAl2016,
acmid = {2878900},
address = {Piscataway, NJ, USA},
author = {Kendall, Richard P. and Post, Douglass E. and Atwood, Chris A. and Newmeyer, Kevin P. and Votta, Lawrence G. and Gibson, Paula A. and Borovitcky, Deborah L. and Miller, Loren K. and Meakin, Robert L. and Hurwitz, Miles M. and Dey, Saikat and D'Angelo, John N. and Vogelsong, Richard L. and Goldfarb, Oscar A. and Allwerdt, Sunita B.},
doi = {10.1109/MCSE.2015.135},
issn = {1521-9615},
issue_date = {January 2016},
journal = {Computing in Science and Engg.},
month = jan,
number = {1},
numpages = {12},
pages = {40--51},
publisher = {IEEE Educational Activities Department},
title = {A Risk-Based, Practice-Centered Approach to Project Management for HPCMP CREATE},
url = {http://dx.doi.org/10.1109/MCSE.2015.135},
volume = {18},
year = {2016},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2015.135}}
@inproceedings{Kerievsky2004,
abstract = {This tutorial, which has been steadily maturing at conferences since 2000, examined how to combine the art of refactoring with the practice of designing with patterns. Attendees learned how to do pattern-based refactoring by combining low-level refactorings. They also learned which code smells indicate the need for pattern-based refactorings, which patterns are commonly refactored to, towards or away from, and how automated tools help us refactor. The tutorial concluded with an overview of the 27 refactorings from the book, Refactoring to Patterns.},
address = {Berlin, Heidelberg},
author = {Kerievsky, Joshua},
booktitle = {Extreme Programming and Agile Methods - XP/Agile Universe 2004},
editor = {Zannier, Carmen and Erdogmus, Hakan and Lindstrom, Lowell},
isbn = {978-3-540-27777-4},
pages = {232--232},
publisher = {Springer Berlin Heidelberg},
title = {Refactoring to Patterns},
year = {2004}}
@article{KillcoyneAndBoyle2009,
acmid = {2220177},
address = {Piscataway, NJ, USA},
author = {Killcoyne, Sarah and Boyle, John},
doi = {10.1109/MCSE.2009.198},
issn = {1521-9615},
issue_date = {November 2009},
journal = {Computing in Science and Engg.},
keywords = {Software development process, agile, life sciences research, rapid application development, software design},
month = nov,
number = {6},
numpages = {10},
pages = {20--29},
publisher = {IEEE Educational Activities Department},
title = {Managing Chaos: Lessons Learned Developing Software in the Life Sciences},
url = {http://dx.doi.org/10.1109/MCSE.2009.198},
volume = {11},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.198}}
@article{KrogstieEtAl2006,
author = {John Krogstie and Arthur Jahr and Dag I.K. Sj{\o}berg},
doi = {https://doi.org/10.1016/j.infsof.2005.12.008},
issn = {0950-5849},
journal = {Information and Software Technology},
keywords = {Application evolution, Application portfolio upkeep, Survey investigation},
number = {11},
pages = {993 - 1005},
title = {A longitudinal study of development and maintenance in Norway: Report from the 2003 investigation},
url = {http://www.sciencedirect.com/science/article/pii/S0950584905001941},
volume = {48},
year = {2006},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S0950584905001941},
bdsk-url-2 = {https://doi.org/10.1016/j.infsof.2005.12.008}}
@article{MitchellEtAl2012,
acmid = {2360933},
address = {Piscataway, NJ, USA},
author = {Mitchell, Ian and LeVeque, Randall and Stodden, Victoria},
doi = {10.1109/MCSE.2012.38},
issn = {1521-9615},
issue_date = {July 2012},
journal = {Computing in Science and Engg.},
keywords = {Hidden Markov models,Research and development,Scientific computing,Computational complexity,Reproducibility of results,computational science and engineering,Hidden Markov models,Research and development,Scientific computing,Computational complexity,Reproducibility of results,scientific computing,reproducible research,data and code disclosure,reproducibility},
month = jul,
number = {4},
numpages = {5},
pages = {13--17},
publisher = {IEEE Educational Activities Department},
title = {Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture},
url = {http://dx.doi.org/10.1109/MCSE.2012.38},
volume = {14},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2012.38}}
@article{McCulloughEtAl2006,
abstract = {We examine the online archive of the Journal of Money, Credit, and Banking, in which an author is required to deposit the data and code that replicate the results of his paper. We find that most authors do not fulfill this requirement. Of more than 150 empirical articles, fewer than 15 could be replicated. Despite all this, there is no doubt that a data/code archive is more conducive to replicable research than the alternatives. We make recommendations to improve the functioning of the archive.},
author = {McCullough, B and McGeary, Kerry Anne and Harrison, Teresa},
journal = {Journal of Money, Credit and Banking},
number = {4},
pages = {1093-1107},
title = {Lessons from the JMCB Archive},
url = {https://EconPapers.repec.org/RePEc:mcb:jmoncb:v:38:y:2006:i:4:p:1093-1107},
volume = {38},
year = {2006},
bdsk-url-1 = {https://EconPapers.repec.org/RePEc:mcb:jmoncb:v:38:y:2006:i:4:p:1093-1107}}
@inproceedings{Mesh2015,
author = {Mesh, E. S.},
booktitle = {2015 IEEE/ACM 37th IEEE International Conference on Software Engineering},
issn = {0270-5257},
keywords = {natural sciences computing, project management, risk management, software development management, software process improvement, spi decision, scispif, scientific software process improvement framework, risk mitigation, scientific se process improvement, scientific software community, scientific software complexity, scientific software development project, software development process, software engineering experts, best practices, conferences, encoding, interviews, scientific computing, software, software engineering, process improvement, scientific software},
pages = {923-926},
title = {Supporting Scientific SE Process Improvement},
volume = {2},
year = {2015}}
@article{NaylorAndFinger1967,
abstract = {The problem of validating computer simulation models of industrial systems has received only limited attention in the management science literature. The purpose of this paper is to consider the problem of validating computer models in the light of contemporary thought in the fields of philosophy of science, economic theory, and statistics. In order to achieve this goal we have attempted to gather together and present some of the ideas of scientific philosophers, economists, statisticians, and practitioners in the field of simulation which are relevant to the problem of verifying simulation models. We have paid particular attention to the writings of economists who have been concerned with testing the validity of economic models. Among the questions which we shall consider are included: What does it mean to verify a computer model of an industrial system? Are there any differences between the verification of computer models and the verification of other types of models? If so, what are some of these differences? Also considered are a number of measures and techniques for testing the ``goodness of fit'' of time series generated by computer models to observed historical series. },
author = {Thomas H. Naylor and J. M. Finger},
doi = {10.1287/mnsc.14.2.B92},
eprint = {https://doi.org/10.1287/mnsc.14.2.B92},
journal = {Management Science},
number = {2},
pages = {B-92-B-101},
title = {Verification of Computer Simulation Models},
url = {https://doi.org/10.1287/mnsc.14.2.B92},
volume = {14},
year = {1967},
bdsk-url-1 = {https://doi.org/10.1287/mnsc.14.2.B92}}
@article{NortonEtAl2007,
acmid = {1377000},
address = {Amsterdam, The Netherlands, The Netherlands},
author = {Norton, Charles D. and Decyk, Viktor K. and Szymanski, Boleslaw K. and Gardner, Henry},
doi = {10.1155/2007/146752},
issn = {1058-9244},
issue_date = {January 2007},
journal = {Sci. Program.},
month = jan,
number = {1},
numpages = {18},
pages = {27--44},
publisher = {IOS Press},
title = {The Transition and Adoption to Modern Programming Concepts for Scientific Computing in Fortran},
url = {http://dx.doi.org/10.1155/2007/146752},
volume = {15},
year = {2007},
bdsk-url-1 = {http://dx.doi.org/10.1155/2007/146752}}
@article{OinnEtAl2006,
abstract = {Abstract Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co‐ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The myGrid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science. Copyright {\copyright} 2005 John Wiley \& Sons, Ltd.},
author = {Tom Oinn and Mark Greenwood and Matthew Addis and M. Nedim Alpdemir and Justin Ferris and Kevin Glover and Carole Goble and Antoon Goderis and Duncan Hull and Darren Marvin and Peter Li and Phillip Lord and Matthew R. Pocock and Martin Senger and Robert Stevens and Anil Wipat and Chris Wroe},
doi = {10.1002/cpe.993},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpe.993},
journal = {Concurrency and Computation: Practice and Experience},
keywords = {scientific workflow, Semantic Grid environment, life sciences, Web services},
month = dec,
number = {10},
pages = {1067-1100},
title = {Taverna: lessons in creating a workflow environment for the life sciences},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpe.993},
volume = {18},
year = {2006},
bdsk-url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpe.993},
bdsk-url-2 = {https://doi.org/10.1002/cpe.993}}
@techreport{Pernice2013,
author = {Pernice, Michael},
institution = {The Consortium for Advanced Simulation of Light Water Reactors},
month = mar,
title = {Survey of Software Quality Assurance and Code Verification Practices in CASL},
type = {Technical Report},
year = {2013}}
@inproceedings{OverbeyEtAl2009,
author = {Jeffrey L. Overbey and Stas Negara and Ralph E. Johnson},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/conf/icse/OverbeyNJ09},
booktitle = {{ICSE} Workshop on Software Engineering for Computational Science and Engineering, {SE-CSE} 2009, Vancouver, BC, Canada, May 23, 2009},
crossref = {DBLP:conf/icse/2009secse},
doi = {10.1109/SECSE.2009.5069159},
pages = {28--34},
timestamp = {Tue, 23 May 2017 01:11:36 +0200},
title = {Refactoring and the evolution of Fortran},
url = {https://doi.org/10.1109/SECSE.2009.5069159},
year = {2009},
bdsk-url-1 = {https://doi.org/10.1109/SECSE.2009.5069159}}
@book{OberkampfEtAl2007,
author = {Oberkampf, W.L. and Pilch, M. and Trucano, T.G.},
publisher = {Sandia National Laboratories},
series = {Sand (Sandia National Laboratories)},
title = {Predictive Capability Maturity Model for Computational Modeling and Simulation},
url = {https://books.google.ca/books?id=Amz8cQAACAAJ},
year = {2007},
bdsk-url-1 = {https://books.google.ca/books?id=Amz8cQAACAAJ}}
@article{NowakowskiEtAl2011,
author = {Piotr Nowakowski and Eryk Ciepiela and Daniel Har{\k e}{\.z}lak and Joanna Kocot and Marek Kasztelnik and Tomasz Barty{\'n}ski and Jan Meizner and Grzegorz Dyk and Maciej Malawski},
doi = {https://doi.org/10.1016/j.procs.2011.04.064},
issn = {1877-0509},
journal = {Procedia Computer Science},
keywords = {Executable paper, High performance computing, e-Science, Scientific publishing},
note = {Proceedings of the International Conference on Computational Science, ICCS 2011},
pages = {608 - 617},
title = {The Collage Authoring Environment},
url = {http://www.sciencedirect.com/science/article/pii/S1877050911001220},
volume = {4},
year = {2011},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S1877050911001220},
bdsk-url-2 = {https://doi.org/10.1016/j.procs.2011.04.064}}
@inproceedings{NielsenEtAl2011,
author = {Nielsen, Thomas A. and Matheson, Tom and Nilsson, Henrik},
booktitle = {Trends in Functional Programming Volume 10 ({TFP 2009}, Revised Selected Papers)},
editor = {Horv{\'a}th, Zolt{\'a}n and Zs{\'o}k, Vikt{\'o}ria and Koopman, Pieter},
isbn = {978-18-41-50405-6},
month = sep,
pages = {161--176},
publisher = {Intellect},
title = {{B}raincurry: A domain-specific language for integrative neuroscience},
year = {2011}}
@inproceedings{NevesEtAl2013,
acmid = {2663385},
address = {Piscataway, NJ, USA},
author = {Neves, Vitor C. and Braganholo, Vanessa and Murta, Leonardo},
booktitle = {Proceedings of the 5th International Workshop on Software Engineering for Computational Science and Engineering},
isbn = {978-1-4673-6261-0},
keywords = {configuration management, implicit data flows, provenance, scientific experiment, scientific workflow},
location = {San Francisco, California},
numpages = {4},
pages = {92--95},
publisher = {IEEE Press},
series = {SE-CSE '13},
title = {Implicit Provenance Gathering Through Configuration Management},
url = {http://dl.acm.org/citation.cfm?id=2663370.2663385},
year = {2013},
bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2663370.2663385}}
@techreport{NaurAndRandell1969,
author = {Naur, P. and Randell, B.},
institution = {NATO Science Committee},
publisher = {NATO},
title = {Software Engineering - Report on a Conference Sponsored by the Nato Science Committee},
url = {https://books.google.ca/books?id=48EpswEACAAJ},
year = {1969},
bdsk-url-1 = {https://books.google.ca/books?id=48EpswEACAAJ}}
@article{NaguibAndLi2010,
author = {Hoda Naguib and Yang Li},
doi = {https://doi.org/10.1016/j.procs.2010.04.167},
issn = {1877-0509},
journal = {Procedia Computer Science},
keywords = {software engineering, atlas, seissol, bug report, release planning, reverse engineering, scientific computing, high performance computing},
note = {ICCS 2010},
number = {1},
pages = {1505 - 1509},
title = {(Position Paper) Applying Software Engineering Methods and Tools to CSE Research Projects},
url = {http://www.sciencedirect.com/science/article/pii/S1877050910001687},
volume = {1},
year = {2010},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S1877050910001687},
bdsk-url-2 = {https://doi.org/10.1016/j.procs.2010.04.167}}
@techreport{Morris2008,
author = {Morris, Chris},
institution = {Science and Technology Facilities Council},
month = jan,
title = {Some lessons learned reviewing scientific code},
year = {2008}}
@inproceedings{MattmannEtAl2006,
acmid = {1134400},
address = {New York, NY, USA},
author = {Mattmann, Chris A. and Crichton, Daniel J. and Medvidovic, Nenad and Hughes, Steve},
booktitle = {Proceedings of the 28th International Conference on Software Engineering},
doi = {10.1145/1134285.1134400},
isbn = {1-59593-375-1},
keywords = {OODT, data management, software architecture},
location = {Shanghai, China},
numpages = {10},
pages = {721--730},
publisher = {ACM},
series = {ICSE '06},
title = {A Software Architecture-based Framework for Highly Distributed and Data Intensive Scientific Applications},
url = {http://doi.acm.org/10.1145/1134285.1134400},
year = {2006},
bdsk-url-1 = {http://doi.acm.org/10.1145/1134285.1134400},
bdsk-url-2 = {https://doi.org/10.1145/1134285.1134400}}
@article{Markus2008,
author = {Markus, Adriaan},
booktitle = {ACM SIGPLAN Fortran Forum},
month = nov,
pages = {2-15},
title = {Design patterns and Fortran 2003},
volume = {27},
year = {2008}}
@book{MacKenzie2001,
address = {Cambridge, MA, USA},
author = {MacKenzie, Donald},
isbn = {0-262-13393-8},
publisher = {MIT Press},
title = {Mechanizing Proof: Computing, Risk, and Trust},
year = {2001}}
@inproceedings{Li2011,
acmid = {1985789},
address = {New York, NY, USA},
author = {Li, Yang},
booktitle = {Proceedings of the 4th International Workshop on Software Engineering for Computational Science and Engineering},
doi = {10.1145/1985782.1985789},
isbn = {978-1-4503-0598-3},
keywords = {domain specific, maintenance, reengineering, requirements modeling, scientific computing},
location = {Waikiki, Honolulu, HI, USA},
numpages = {5},
pages = {41--45},
publisher = {ACM},
series = {SECSE '11},
title = {Reengineering a Scientific Software and Lessons Learned},
url = {http://doi.acm.org/10.1145/1985782.1985789},
year = {2011},
bdsk-url-1 = {http://doi.acm.org/10.1145/1985782.1985789},
bdsk-url-2 = {https://doi.org/10.1145/1985782.1985789}}
@techreport{Lampoudi2012,
author = {Lampoudi, Sotiria},
institution = {University of California Santa Barbara},
month = may,
title = {The Path to Virtual Machine Images as First Class Provenance},
type = {Technical Report},
year = {2018}}
@techreport{KreymanEtAl999,
author = {Konstantin Kreyman, David Lorge Parnas, and Sanzheng Qiao},
institution = {McMaster University},
title = {Inspection Procedures for Critical Programs that Model Physical Phenomena},
type = {Technical Report},
year = {1999}}
@mastersthesis{Hook2009,
achool = {Queen's University},
address = {Kingston, Ontario, Canada},
author = {Daniel Alan Hook},
title = {Using Code Mutation to Study Code Faults in Scientific Software},
year = {2009}}
@article{Hoffman1999,
author = {Douglas Hoffman},
journal = {Software Testing & Quality Engineering},
month = {May-April},
pages = {29--32},
title = {Heuristic test oracles},
year = {1999}}
@inproceedings{HigginsEtAl2009,
author = {Higgins, C and Koutroumpas, Michael and Sinnott, Richard O and Watt, John and Doherty, Thomas and Hume, Ally C and Turner, Andrew GD and Rawnsley, David},
booktitle = {Proc. 5th Int. Conf. on e-Social Science, Maternushaus, Cologne},
pages = {24--26},
title = {Spatial data e-infrastructure},
year = {2009}}
@book{HeyEtAl2009,
added-at = {2010-02-16T09:54:37.000+0100},
address = {Redmond, Washington},
astract = {Increasingly, scientific breakthroughs will be powered by advanced computing capabilities that help researchers manipulate and explore massive datasets. The speed at which any given scientific discipline advances will depend on how well its researchers collaborate with one another, and with technologists, in areas of eScience such as databases, workflow management, visualization, and cloud computing technologies. In The Fourth Paradigm: Data-Intensive Scientific Discovery, the collection of essays expands on the vision of pioneering computer scientist Jim Gray for a new, fourth paradigm of discovery based on data-intensive science and offers insights into how it can be fully realized.},
biburl = {https://www.bibsonomy.org/bibtex/28b203c0313656b6ced70c14c86a4c42a/acka47},
editor = {Hey, Tony and Tansley, Stewart and Tolle, Kristin},
interhash = {296450016ca8a5f8ab16ae4d92d1fc15},
intrahash = {8b203c0313656b6ced70c14c86a4c42a},
keywords = {research scholarly_communication science},
publisher = {Microsoft Research},
timestamp = {2010-02-16T09:54:54.000+0100},
title = {The Fourth Paradigm: Data-Intensive Scientific Discovery},
url = {http://research.microsoft.com/en-us/collaboration/fourthparadigm/},
year = 2009,
bdsk-url-1 = {http://research.microsoft.com/en-us/collaboration/fourthparadigm/}}
@inproceedings{HendersonAndPerry2013,
author = {J. Henderson and D. E. Perry},
booktitle = {2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)},
doi = {10.1109/SECSE.2013.6615106},
keywords = {case study;domain-expert-developed software;domain specific software;fault study},
month = may,
pages = {96-99},
title = {Exploring issues in software systems used and developed by domain experts},
url = {doi.ieeecomputersociety.org/10.1109/SECSE.2013.6615106},
volume = {00},
year = {2013},
bdsk-url-1 = {doi.ieeecomputersociety.org/10.1109/SECSE.2013.6615106},
bdsk-url-2 = {https://doi.org/10.1109/SECSE.2013.6615106}}
@techreport{GentEtAl1997,
author = {Ian P. Gent, Stuart A. Grant, Ewan MacIntyre, Patrick Prosser, Paul Shaw, Barbara M. Smith, and Toby Walsh},
institution = {University of Leeds},
month = may,
title = {How Not To Do It},
type = {Technical Report},
year = {1997}}
@book{Glass1998,
author = {Glass, R.L.},
isbn = {9780136734437},
lccn = {97029566},
publisher = {Prentice Hall PTR},
title = {Software Runaways: Lessons Learned from Massive Software Project Failures},
url = {https://books.google.ca/books?id=w6ZQAAAAMAAJ},
year = {1998},
bdsk-url-1 = {https://books.google.ca/books?id=w6ZQAAAAMAAJ}}
@article{Hoffman1998,
author = {Douglas Hoffman},
journal = {In Quality Week},
title = {Analysis of a Taxonomy of Test Oracles},
year = {1998}}
@article{Allan2003,
author = {George Allan},
journal = {Electronic Journal of Business Research Methods},
pages = {1--10},
title = {A critique of using grounded theory as a research method},
volume = {2},
year = {2003}}
@book{Whitman2003,
author = {Whitman, M.},
isbn = {9781591401452},
lccn = {20038880},
publisher = {Idea Group Pub.},
series = {ITPro collection},
title = {The Handbook of Information Systems Research},
url = {https://books.google.ca/books?id=jXlL38SQ-TQC},
year = {2003},
bdsk-url-1 = {https://books.google.ca/books?id=jXlL38SQ-TQC}}
@book{GlaserAndStrauss1967,
added-at = {2010-01-29T10:11:35.000+0100},
address = {New York, NY},
author = {Glaser, Barney G. and Strauss, Anselm L.},
biburl = {https://www.bibsonomy.org/bibtex/2e5908e55e1123b12d7419347c6292742/wiljami74},
interhash = {1a6c1e4d038265d26035b66bbdf6f891},
intrahash = {e5908e55e1123b12d7419347c6292742},
keywords = {grounded_theory},
publisher = {Aldine de Gruyter},
timestamp = {2010-01-29T10:11:35.000+0100},
title = {The Discovery of Grounded Theory: Strategies for Qualitative Research},
year = 1967}
@inproceedings{DevanbuEtAl1990,
author = {Premkumar Devanbu and Ronald J. Brachman and Peter G. Selfridge and Bruce W. Ballard},
booktitle = {Proceedings of the 12th International Conference on Software Engineering},
title = {LaSSIE: A Knowledge-based Software Information System},
year = {1990}}
@inproceedings{Lowry1989,
author = {Lowry, Michael R},
booktitle = {Handbook of Artificial Intelligence, volume IV},
organization = {Citeseer},
title = {Knowledge-based software engineering},
year = {1989}}
@article{Kunze2002,
author = {Kunze, John},
journal = {Journal of Digital Information},
number = {2},
title = {A Metadata Kernel for Electronic Permanence},
volume = {2},
year = {2002}}