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View file @ ba88147b
......@@ -22,6 +22,8 @@ cabal.config
*.nav
*.out
*.snm
*.fdb_latexmk
*.fls
*-nup.pdf
.DS_Store
.iTeXMac
......@@ -30,3 +32,6 @@ cabal.config
html
latex
*.class
# Temporary Excel files
~$*
BlankProjectTemplate/LICENSE deleted 100644 → 0
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LICENSE Information
\ No newline at end of file
BlankProjectTemplate/README.md deleted 100644 → 0
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# Project Name
Developer Name:
This project is a reimplementation of ...
The folders and files for this project are as follows:
Doc - Documentation for the project
Code - Implementation
…
\ No newline at end of file
BlankProjectTemplate/ReferenceMaterial/References.bib deleted 100644 → 0
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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Spencer Smith at 2018-09-18 14:09:50 -0400
%% Saved with string encoding Unicode (UTF-8)
@article{Parnas1972a,
Author = {David L. Parnas},
Date-Added = {2018-09-18 14:09:32 -0400},
Date-Modified = {2018-09-18 14:09:32 -0400},
Journal = {Comm. ACM},
Month = {December},
Number = {2},
Pages = {1053--1058},
Title = {On the Criteria To Be Used in Decomposing Systems into Modules},
Volume = {15},
Year = {1972},
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@inproceedings{Parnas1978,
Address = {Piscataway, NJ, USA},
Author = {David L. Parnas},
Booktitle = {ICSE '78: Proceedings of the 3rd international conference on Software engineering},
Date-Added = {2018-09-18 14:09:32 -0400},
Date-Modified = {2018-09-18 14:09:32 -0400},
Isbn = {none},
Location = {Atlanta, Georgia, United States},
Pages = {264--277},
Publisher = {IEEE Press},
Title = {Designing Software for Ease of Extension and Contraction},
Year = {1978}}
@article{ParnasAndClements1986,
Author = {David L. Parnas and P.C. Clements},
Date-Added = {2018-09-18 14:09:32 -0400},
Date-Modified = {2018-09-18 14:09:32 -0400},
Journal = {IEEE Transactions on Software Engineering},
Number = {2},
Pages = {251--257},
Title = {A Rational Design Process: How and Why to Fake it},
Volume = {12},
Year = {February 1986},
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@inproceedings{ParnasEtAl1984,
Author = {D.L. Parnas and P.C. Clement and D. M. Weiss},
Booktitle = {International Conference on Software Engineering},
Date-Added = {2018-09-18 14:09:32 -0400},
Date-Modified = {2018-09-18 14:09:32 -0400},
Pages = {408-419},
Title = {The modular structure of complex systems},
Year = {1984},
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@book{RobertsonAndRobertson2012,
Author = {James Robertson and Suzanne Robertson},
Date-Added = {2018-09-18 14:09:32 -0400},
Date-Modified = {2018-09-18 14:09:32 -0400},
Edition = {16},
Publisher = {Atlantic Systems Guild Limited},
Title = {Volere Requirements Specification Template},
Year = {2012}}
@article{BenureauAndRougier2017,
Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
Adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170808205B},
Archiveprefix = {arXiv},
Author = {{Benureau}, F. and {Rougier}, N.},
Date-Added = {2018-09-07 00:16:49 -0400},
Date-Modified = {2018-09-07 00:16:49 -0400},
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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@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 = {2018-09-07 00:15:38 -0400},
Date-Modified = {2018-09-07 00:15:38 -0400},
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{JohansonAndHasselbring2018,
Author = {Arne N. Johanson and Wilhelm Hasselbring},
Date-Added = {2018-09-07 00:09:38 -0400},
Date-Modified = {2018-09-07 00:09:38 -0400},
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{Smith2018,
Author = {W. Spencer Smith},
Booktitle = {2018 International Workshop on Software Engineering for Science (held in conjunction with ICSE'18)},
Date-Added = {2018-09-07 00:09:16 -0400},
Date-Modified = {2018-09-07 00:09:16 -0400},
Pages = {1--8},
Title = {Beyond Software Carpentry},
Year = {2018},
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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 = {2018-09-07 00:06:21 -0400},
Date-Modified = {2018-09-07 00:06:21 -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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@book{OliveiraAndStewart2006,
Address = {New York, NY, USA},
Author = {Suely Oliveira and David E. Stewart},
Date-Added = {2018-09-07 00:01:05 -0400},
Date-Modified = {2018-09-07 00:01:05 -0400},
Isbn = {0521858968},
Publisher = {Cambridge University Press},
Title = {Writing Scientific Software: A Guide to Good Style},
Year = {2006}}
@article{Hatton2007,
Author = {Les Hatton},
Date-Added = {2018-09-06 23:55:06 -0400},
Date-Modified = {2018-09-06 23:55:06 -0400},
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{Miller2006,
Author = {Miller, Greg},
Date-Added = {2018-09-06 23:53:44 -0400},
Date-Modified = {2018-09-06 23:53:44 -0400},
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},
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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 = {2018-05-29 16:52:33 +0000},
Date-Modified = {2018-05-29 16:52:33 +0000},
Month = may,
Note = {2 pp},
Title = {Assurance Cases for Scientific Computing Software (poster)},
Year = {2018},
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@unpublished{SmithEtAl2017,
Author = {W. Spencer Smith and Mojdeh Sayari Nejad and Alan Wassyng},
Date-Added = {2017-11-23 16:40:43 +0000},
Date-Modified = {2017-11-23 16:56:51 +0000},
Month = {November},
Note = {Prepared for ICSE Submission},
Title = {Assurance Cases for Scientific Computing Software},
Year = {2017},
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@article{Kelly2007,
Address = {Los Alamitos, CA, USA},
Author = {Diane F. Kelly},
Date-Added = {2017-11-20 16:06:46 +0000},
Date-Modified = {2017-11-20 16:06:46 +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}}
@inproceedings{Owen1998,
Author = {Steven J. Owen},
Booktitle = {INTERNATIONAL MESHING ROUNDTABLE},
Date-Added = {2017-11-20 16:06:34 +0000},
Date-Modified = {2017-11-20 16:06:34 +0000},
Pages = {239--267},
Title = {A Survey of Unstructured Mesh Generation Technology},
Year = {1998},
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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 = {2017-11-20 16:06:25 +0000},
Date-Modified = {2017-11-20 16:06:25 +0000},
Journal = {Nature},
Pages = {775--777},
Title = {Computational science: ...Error},
Volume = {467},
Year = {2010},
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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 = {2017-11-20 16:06:15 +0000},
Date-Modified = {2017-11-20 16:06:15 +0000},
Pages = {30--36},
Title = {The challenge of testing scientific software},
Year = {2008},
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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 = {2017-11-20 03:50:08 +0000},
Date-Modified = {2017-11-20 03:50:08 +0000},
Month = {November},
Note = {8 pp},
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}}
@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 = {2017-11-20 03:49:27 +0000},
Date-Modified = {2017-11-20 03:49:27 +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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@book{GriesAndSchneider1993,
Address = {New York},
Author = {David Gries and Fred B. Schneider},
Date-Added = {2017-11-06 15:09:37 +0000},
Date-Modified = {2017-11-06 15:09:37 +0000},
Keywords = {discrete mathematics},
Publisher = {Springer-Verlag Inc.},
Title = {A logical approach to discrete math},
Year = {1993}}
@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 = {2017-10-27 03:26:58 +0000},
Date-Modified = {2017-10-27 03:26:58 +0000},
Keywords = {MetaOCaml, Geometry, Generative, Generic},
Month = {January},
Pages = {53--62},
Title = {A Generative Geometric Kernel},
Year = {2011},
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@article{SmithAndYu2009,
Author = {W. Spencer Smith and Wen Yu},
Date-Added = {2017-10-27 03:25:31 +0000},
Date-Modified = {2017-10-27 03:25:31 +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 = {November},
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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Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.advengsoft.2009.05.003}}
@article{ElSheikhEtAl2004,
Author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
Date-Added = {2017-10-23 20:58:24 +0000},
Date-Modified = {2017-10-23 20:58:24 +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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@inproceedings{Parnas1974,
Author = {David L. Parnas},
Booktitle = {IFIP Congress 74},
Date-Added = {2017-10-23 19:36:16 +0000},
Date-Modified = {2017-10-23 19:36:16 +0000},
Pages = {336-339},
Publisher = {North Holland Publishing Company},
Title = {On a 'Buzzword': Hierarchical Structure},
Year = {1974}}
@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 = {2017-10-16 13:46:41 +0000},
Date-Modified = {2017-10-16 13:46:41 +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},
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Bdsk-Url-1 = {http://portal.acm.org/citation.cfm?id=782040#}}
@inproceedings{ShepardAndKelly2001,
Author = {Shepard, Terry and Kelly, Diane},
Booktitle = {Proceedings of the 23rd International Conference on Software Engineering},
Date-Added = {2017-10-16 13:46:41 +0000},
Date-Modified = {2017-10-16 13:46:41 +0000},
Organization = {IEEE Computer Society},
Pages = {718},
Title = {How to do inspections when there is no time},
Year = {2001},
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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 = {2017-10-10 15:14:43 +0000},
Date-Modified = {2017-10-10 15:14:43 +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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@article{Kanewala2015,
Author = {Upulee Kanewala and James M. Bieman and Asa Ben-Hur},
Date-Added = {2017-10-10 15:10:19 +0000},
Date-Modified = {2017-10-10 15:10:19 +0000},
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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@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 = {2017-10-10 15:10:19 +0000},
Date-Modified = {2017-10-10 15:10:19 +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{Hickey2001,
Acmid = {502106},
Address = {New York, NY, USA},
Author = {Hickey, Timothy and Ju, Qun and Van Emden, Maarten H.},
Date-Added = {2017-10-06 03:04:59 +0000},
Date-Modified = {2017-10-06 03:04:59 +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},
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@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 = {2017-10-06 02:42:19 +0000},
Date-Modified = {2017-10-06 02:42:19 +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}}
@inproceedings{BastarricaAndHitschfeld-Kahler2004,
Author = {Bastarrica, M Cecilia and Hitschfeld-Kahler, Nancy},
Booktitle = {International Meshing Roundtable},
Date-Added = {2017-09-14 20:51:36 +0000},
Date-Modified = {2017-09-14 20:51:36 +0000},
Organization = {Citeseer},
Pages = {203--212},
Title = {An Evolvable Meshing Tool Through a Flexible Object-Oriented Design.},
Year = {2004},
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@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 = {2017-09-14 20:51:11 +0000},
Date-Modified = {2017-09-14 20:51:11 +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}}
@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 = {2017-09-14 20:51:11 +0000},
Date-Modified = {2017-09-14 20:51:11 +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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@inproceedings{Bastarrica2002,
Author = {Mar\'{i}a Cecilia Bastarrica},
Booktitle = {Proceedings of the XXVIII Latin American Conference of Informatics, {CLEI'2002}, Montevideo, Uruguay},
Date-Added = {2017-09-14 20:51:11 +0000},
Date-Modified = {2017-09-14 20:51:11 +0000},
Pages = {119},
Title = {Base Architecture in a Software Product Line},
Year = {2002}}
@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 = {2017-09-14 20:51:01 +0000},
Date-Modified = {2017-09-14 20:51:01 +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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@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 = {2017-09-14 20:49:28 +0000},
Date-Modified = {2017-09-14 20:49:28 +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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@techreport{CaretteEtAl2007_TR,
Annote = {Acknowledgment: NSERC},
Author = {Jacques Carette and W. Spencer Smith and John McCutchan and Christopher Anand and Alexandre Korobkine},
Date-Added = {2017-09-14 20:48:49 +0000},
Date-Modified = {2017-09-14 20:48:49 +0000},
Institution = {Software Quality Research Laboratory, McMaster University},
Month = {December},
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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@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 = {2017-09-14 20:48:35 +0000},
Date-Modified = {2017-09-14 20:48:35 +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{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 = {2017-09-14 20:47:28 +0000},
Date-Modified = {2017-09-14 20:47:28 +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 = {October},
Pages = {39--47},
Title = {Program Families in Scientific Computing},
Year = {2007},
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@mastersthesis{Cao2006,
Author = {Fang Cao},
Date-Added = {2017-09-14 20:47:14 +0000},
Date-Modified = {2017-09-14 20:47:14 +0000},
Month = {April},
School = {McMaster University},
Title = {A Program Family Approach to Developing Mesh Generators},
Year = {2006}}
@article{BastarricaAndHitschfeld2006,
Author = {Mar\'{i}a Cecilia Bastarrica and Nancy Hischfeld-Kahler},
Date-Added = {2017-09-14 20:47:06 +0000},
Date-Modified = {2017-09-14 20:47:06 +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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@mastersthesis{Chen2003,
Author = {Chien-Hsien Chen},
Date-Added = {2017-09-14 20:46:56 +0000},
Date-Modified = {2017-09-14 20:46:56 +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{Saaty1980,
Address = {New York, New York},
Author = {T. L. Saaty},
Date-Added = {2017-09-14 20:46:45 +0000},
Date-Modified = {2017-09-14 20:46:45 +0000},
Publisher = {McGraw-Hill Publishing Company},
Title = {The Analytic Hierarchy Process: Planning, Priority Setting, Resource Allocation},
Year = {1980}}
@book{WeissAndLai1999,
Author = {D. Weiss and C.T.R. Lai},
Date-Added = {2017-09-14 20:46:33 +0000},
Date-Modified = {2017-09-14 20:46:33 +0000},
Publisher = {Addison-Wesley},
Title = {Software Product Line Engineering: A Family-Based Software Development Process},
Year = {1999}}
@article{CukaAndWeiss1998,
Address = {Los Alamitos, CA, USA},
Author = {D.A. Cuka and D.M. Weiss},
Date-Added = {2017-09-14 20:46:24 +0000},
Date-Modified = {2017-09-14 20:46:24 +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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@article{Weiss1998,
Author = {David M. Weiss},
Date-Added = {2017-09-14 20:46:19 +0000},
Date-Modified = {2017-09-14 20:46:19 +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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@article{Weiss1997,
Author = {David M. Weiss},
Date-Added = {2017-09-14 20:46:14 +0000},
Date-Modified = {2017-09-14 20:46:14 +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{ArdisAndWeiss1997,
Author = {Mark Ardis and David M. Weiss},
Booktitle = {Proceedings of the Nineteenth International Conference on Software Engineering},
Date-Added = {2017-09-14 20:45:55 +0000},
Date-Modified = {2017-09-14 20:45:55 +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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@mastersthesis{McCutchan2007,
Address = {Hamilton, ON, Canada},
Author = {John McCutchan},
Date-Added = {2017-09-14 20:45:41 +0000},
Date-Modified = {2017-09-14 20:45:41 +0000},
Local-Url = {file://localhost/Users/smiths/Work/Research/GradStudents/JohnMcCutchan/thesis/thesis/build/Thesis.pdf},
Month = {September},
School = {McMaster University},
Title = {A generative approach to a virtual material testing laboratory},
Year = {2007},
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@techreport{SmithAndChen2004b,
Author = {W. Spencer Smith and Chien-Hsien Chen},
Date-Added = {2017-09-14 20:45:24 +0000},
Date-Modified = {2017-09-14 20:45:24 +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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@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 = {2017-09-14 20:45:16 +0000},
Date-Modified = {2017-09-14 20:45:16 +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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@misc{Blitz2010,
Author = {Blitz},
Date-Added = {2017-09-14 20:45:01 +0000},
Date-Modified = {2017-09-14 20:45:01 +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/}}
@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 = {2017-09-14 20:44:29 +0000},
Date-Modified = {2017-09-14 20:44:29 +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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@article{WhaleyEtAl2001,
Author = {R. C. Whaley and A. Petitet and J. J. Dongarra},
Date-Added = {2017-09-14 20:43:34 +0000},
Date-Modified = {2017-09-14 20:43:34 +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{Carette2006,
Author = {Jacques Carette},
Date-Added = {2017-09-14 20:43:20 +0000},
Date-Modified = {2017-09-14 20:43:20 +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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@incollection{Dijkstra1972,
Acmid = {1243381},
Address = {London, UK, UK},
Author = {Dijkstra, Edsger W.},
Booktitle = {Structure Programming},
Date-Added = {2017-09-14 20:42:43 +0000},
Date-Modified = {2017-09-14 20:42:43 +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}}
@article{Parnas1979,
Author = {David L. Parnas},
Date-Added = {2017-09-14 20:42:25 +0000},
Date-Modified = {2017-09-14 20:42:25 +0000},
Journal = {IEEE Transactions on Software Engineering},
Month = {March},
Pages = {128-138},
Title = {Designing Software for Ease of Extension and Contraction},
Year = {1979}}
@article{Parnas1976,
Author = {David Parnas},
Date-Added = {2017-09-14 20:42:18 +0000},
Date-Modified = {2017-09-14 20:42:18 +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}}
@book{PohlEtAl2005,
Author = {K. Pohl and G. B\"{o}ckle and F. van der Linden},
Date-Added = {2017-09-14 20:42:09 +0000},
Date-Modified = {2017-09-14 20:42:09 +0000},
Publisher = {Springer-Verlag},
Title = {Software Product Line Engineering: Foundations, Principles, and Techniques},
Year = {2005}}
@book{ClementsAndNorthrop2001,
Address = {Boston, MA, USA},
Author = {Paul Clements and Linda M. Northrop},
Date-Added = {2017-09-14 20:42:02 +0000},
Date-Modified = {2017-09-14 20:42:02 +0000},
Publisher = {Addison-Wesley Longman Publishing Co., Inc.},
Title = {Software product lines: practices and patterns},
Year = {2002}}
@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 = {2017-09-14 19:18:08 +0000},
Date-Modified = {2017-09-14 19:18:08 +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}}
@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 = {2017-09-14 19:18:04 +0000},
Date-Modified = {2017-09-14 19:18:04 +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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Bdsk-Url-1 = {http://www.ifi.unizh.ch/req/events/RE06/}}
@techreport{SmithMcCutchanAndCarette2017,
Author = {W. Spencer Smith and John McCutchan and Jacques Carette},
Date-Added = {2017-09-14 19:17:57 +0000},
Date-Modified = {2017-09-14 19:17:57 +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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@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 = {2017-09-13 21:03:06 +0000},
Date-Modified = {2017-09-13 21:03:06 +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 = {April},
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{Parnas2010,
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 = {2017-09-08 04:00:01 +0000},
Date-Modified = {2017-09-08 04:00:01 +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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@book{Roache1998,
Address = {Albuquerque, New Mexico},
Author = {Patrick J. Roache},
Date-Added = {2017-09-08 03:59:45 +0000},
Date-Modified = {2017-09-08 03:59:45 +0000},
Publisher = {Hermosa Publishers},
Title = {Verification and Validation in Computational Science and Engineering},
Year = {1998}}
@article{SegalAndMorris2008,
Annote = {Some extra information on the citation.
@article{Segal2008IEEE,
Address = {Los Alamitos, CA, USA},
Author = {Segal, Judith and Morris, Chris},
Date-Added = {2011-01-28 14:00:17 -0500},
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},
Volume = {25},
Year = {2008},
Bdsk-Url-1 = {http://cs.ua.edu/%5C~%7B%7DSECSE08/Papers/Segal.pdf},
Bdsk-Url-2 = {http://dx.doi.org/10.1109/MS.2008.85}}},
Author = {Judith Segal and Chris Morris},
Date-Added = {2017-09-08 03:59:33 +0000},
Date-Modified = {2017-09-08 03:59:33 +0000},
Journal = {IEEE Software},
Local-Url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/SegalAndMorris2008.pdf},
Month = {July/August},
Number = {4},
Pages = {18--20},
Title = {Developing Scientific Software},
Volume = {25},
Year = {2008},
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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 = {2017-09-08 03:59:12 +0000},
Date-Modified = {2017-09-08 03:59:12 +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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@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 = {2017-09-08 03:59:00 +0000},
Date-Modified = {2017-09-08 03:59:00 +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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@article{EasterbrookAndJohns2009,
Address = {Los Alamitos, CA, USA},
Author = {Easterbrook, Steve M. and Johns, Timothy C.},
Date-Added = {2017-09-08 03:58:34 +0000},
Date-Modified = {2017-09-08 03:58:34 +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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@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 = {2017-09-08 03:58:12 +0000},
Date-Modified = {2017-09-08 03:58:12 +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{AckroydEtAl2008,
Author = {Karen S. Ackroyd and Steve H. Kinder and Geoff R. Mant and Mike C. Miller and Christine A. Ramsdale and Paul C. Stephenson},
Date-Added = {2017-09-08 03:57:39 +0000},
Date-Modified = {2017-09-08 03:57:39 +0000},
Journal = {IEEE Software},
Local-Url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/AckroydEtAl2008.pdf},
Month = {July/August},
Number = {4},
Pages = {44--51},
Title = {Scientific Software Development at a Research Facility},
Volume = {25},
Year = {2008},
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@book{VanVliet2000,
Address = {New York, NY, USA},
Author = {Hans van Vliet},
Date-Added = {2017-09-08 03:57:00 +0000},
Date-Modified = {2017-09-08 03:57:00 +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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@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 = {2017-09-07 18:14:58 +0000},
Date-Modified = {2017-09-07 18:14:58 +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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@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 = {2017-09-07 18:14:51 +0000},
Date-Modified = {2017-09-07 18:14:51 +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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@book{HoffmanAndStrooper1995,
Address = {New York, NY, USA},
Author = {Daniel M. Hoffman and Paul A. Strooper},
Date-Added = {2017-09-07 18:01:05 +0000},
Date-Modified = {2017-09-07 18:01:05 +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}}
@article{SmithEtAl2007,
Author = {W. Spencer Smith and Lei Lai and Ridha Khedri},
Date-Added = {2017-09-05 03:00:52 +0000},
Date-Modified = {2017-09-05 03:00:52 +0000},
Journal = {Reliable Computing, Special Issue on Reliable Engineering Computation},
Local-Url = {/Users/smiths/Work/Research/Papers/ReliableComputing/SmithLaiAndKhedri2007fulltext.pdf},
Month = {February},
Number = {1},
Pages = {83--107},
Title = {Requirements Analysis for Engineering Computation: A Systematic Approach for Improving Software Reliability},
Volume = {13},
Year = {2007},
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@incollection{Smith2016,
Author = {W. Spencer Smith},
Booktitle = {Software Engineering for Science},
Chapter = {Section {I} -- Examples of the Application of Traditional Software Engineering Practices to Science},
Date-Added = {2017-09-05 02:57:01 +0000},
Date-Modified = {2017-09-05 03:02:48 +0000},
Editor = {Jeffrey C. Carver and Neil Chue Hong and George Thiruvathukal},
Pages = {33--63},
Publisher = {Taylor \& Francis},
Title = {A Rational Document Driven Design Process for Scientific Computing Software},
Year = {2016},
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@techreport{KreymanAndParnas2002,
Author = {K. Kreyman and D. L. Parnas},
Date-Added = {2017-09-05 02:36:31 +0000},
Date-Modified = {2017-09-05 02:36:31 +0000},
Institution = {Software Quality Research Laboratory, McMaster University},
Local-Url = {/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/KreymanAndParnas2002.pdf},
Month = {January},
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{Wilson2006,
Author = {Gregory V.~Wilson},
Date-Added = {2017-09-05 02:26:32 +0000},
Date-Modified = {2017-09-05 02:26:32 +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{Dubois2002,
Author = {Paul F. Dubois},
Date-Added = {2017-09-05 02:25:03 +0000},
Date-Modified = {2017-09-05 02:25:03 +0000},
Journal = {Computing in Science and Engineering},
Local-Url = {file://localhost/Users/smiths/LongTermArchives/Work/Research/References/SciCompAndSoftEng/Dubois2002.pdf},
Month = {September},
Number = {5},
Pages = {84--90},
Title = {Designing Scientific Components},
Volume = {4},
Year = {2002},
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@article{Segal2005,
Author = {Segal, Judith},
Citeulike-Article-Id = {342252},
Date-Added = {2017-09-05 02:24:54 +0000},
Date-Modified = {2017-09-05 02:24:54 +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 = {October},
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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@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 = {2017-09-05 02:24:42 +0000},
Date-Modified = {2017-09-05 02:24:42 +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}}
@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 = {2017-09-05 02:24:33 +0000},
Date-Modified = {2017-09-05 02:24:33 +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}}
@inproceedings{Segal2007_Dagsthul,
Author = {Judith Segal},
Booktitle = {Dagstuhl Seminar Proceedings 07081, End-User Software Engineering},
Date-Added = {2017-09-05 02:24:30 +0000},
Date-Modified = {2017-09-05 02:24:30 +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}}
@book{GhezziEtAl2003,
Address = {Upper Saddle River, NJ, USA},
Author = {Carlo Ghezzi and Mehdi Jazayeri and Dino Mandrioli},
Date-Added = {2017-09-05 02:24:05 +0000},
Date-Modified = {2017-09-05 02:24:05 +0000},
Edition = {2nd},
Keywords = {software engineering},
Publisher = {Prentice Hall},
Title = {Fundamentals of Software Engineering},
Year = {2003}}
@article{JanickiAndKhedri2001,
Author = {R. Janicki and R. Khedri},
Date-Added = {2017-09-05 02:24:00 +0000},
Date-Modified = {2017-09-05 02:24:00 +0000},
Journal = {Science of Computer Programming},
Number = {2-3},
Pages = {189-213},
Title = {On a formal semantics of tabular expression},
Volume = {39},
Year = {2001}}
@article{DesharnaisEtAl2004,
Author = {Jules Desharnais and Ridha Khedri and Ali Mili},
Date-Added = {2017-09-05 02:23:52 +0000},
Date-Modified = {2017-09-05 02:23:52 +0000},
Journal = {Formal Methods in System Design},
Note = {To appear},
Pages = {40},
Title = {Representation, Validation and Integration of Scenarios Using Tabular Expressions},
Year = {2004}}
@inbook{RobertsonAndRobertson1999Vol,
Address = {New York, NY, USA},
Author = {Suzanne Robertson and James Robertson},
Chapter = {Volere Requirements Specification Template},
Date-Added = {2017-09-05 02:23:44 +0000},
Date-Modified = {2017-09-05 02:23:44 +0000},
Pages = {353--391},
Publisher = {ACM Press/Addison-Wesley Publishing Co},
Title = {Mastering the Requirements Process},
Year = {1999}}
@book{IEEE2000_ThayerAndDorfman,
Author = {{The Institute of Electrical and Electronics Engineers, Inc.}},
Date-Added = {2017-09-05 02:23:00 +0000},
Date-Modified = {2017-09-05 02:23:00 +0000},
Edition = {2nd},
Editor = {Richard H. Thayer and Merlin Dorfman},
Publisher = {{IEEE} Computer Society Press},
Title = {Software Requirements Engineering},
Year = {2000}}
@book{IEEE2000,
Date-Added = {2017-09-05 02:22:55 +0000},
Date-Modified = {2017-09-05 02:22:55 +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}}
@article{IEEE1998,
Author = {IEEE},
Date-Added = {2017-09-05 02:22:45 +0000},
Date-Modified = {2017-09-05 02:22:45 +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},
Bdsk-File-1 = {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},
Bdsk-Url-1 = {http://dx.doi.org/10.1109/IEEESTD.1998.88286}}
@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 = {2017-09-05 02:21:52 +0000},
Date-Modified = {2017-09-05 02:21:52 +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},
Bdsk-File-1 = {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}}
@inproceedings{SmithEtAl2004,
Address = {Savannah, Georgia},
Author = {W. Spencer Smith and Lei Lai and Ridha Khedri},
Booktitle = {Proceedings of the NSF Workshop on Reliable Engineering Computing},
Date-Added = {2017-09-05 02:21:40 +0000},
Date-Modified = {2017-09-05 02:21:40 +0000},
Editor = {R. Muhanna and R. Mullen},
Pages = {29--51},
Title = {Requirements Analysis for Engineering Computation},
Year = {2004}}
@mastersthesis{Lai2004,
Author = {Lei Lai},
Date-Added = {2017-09-05 02:21:22 +0000},
Date-Modified = {2017-09-05 02:21:22 +0000},
School = {McMaster University, Hamilton, Ontario, Canada},
Title = {Requirements Documentation for Engineering Mechanics Software: Guidelines, Template and a Case Study},
Year = {2004}}
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%% Comments
\usepackage{color}
\newif\ifcomments\commentstrue
\ifcomments
\newcommand{\authornote}[3]{\textcolor{#1}{[#3 ---#2]}}
\newcommand{\todo}[1]{\textcolor{red}{[TODO: #1]}}
\else
\newcommand{\authornote}[3]{}
\newcommand{\todo}[1]{}
\fi
\newcommand{\wss}[1]{\authornote{blue}{SS}{#1}}
\newcommand{\an}[1]{\authornote{magenta}{Author}{#1}}
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\documentclass[12pt, titlepage]{article}
\usepackage{fullpage}
\usepackage[round]{natbib}
\usepackage{multirow}
\usepackage{booktabs}
\usepackage{tabularx}
\usepackage{graphicx}
\usepackage{float}
\usepackage{hyperref}
\hypersetup{
colorlinks,
citecolor=black,
filecolor=black,
linkcolor=red,
urlcolor=blue
}
\input{../../Comments}
\newcounter{acnum}
\newcommand{\actheacnum}{AC\theacnum}
\newcommand{\acref}[1]{AC\ref{#1}}
\newcounter{ucnum}
\newcommand{\uctheucnum}{UC\theucnum}
\newcommand{\uref}[1]{UC\ref{#1}}
\newcounter{mnum}
\newcommand{\mthemnum}{M\themnum}
\newcommand{\mref}[1]{M\ref{#1}}
\begin{document}
\title{Module Guide: Project Title}
\author{Author Name}
\date{\today}
\maketitle
\pagenumbering{roman}
\section{Revision History}
\begin{tabularx}{\textwidth}{p{3cm}p{2cm}X}
\toprule {\bf Date} & {\bf Version} & {\bf Notes}\\
\midrule
Date 1 & 1.0 & Notes\\
Date 2 & 1.1 & Notes\\
\bottomrule
\end{tabularx}
\newpage
\tableofcontents
\listoftables
\listoffigures
\newpage
\pagenumbering{arabic}
\section{Introduction}
Decomposing a system into modules is a commonly accepted approach to developing
software. A module is a work assignment for a programmer or programming
team~\citep{ParnasEtAl1984}. We advocate a decomposition
based on the principle of information hiding~\citep{Parnas1972a}. This
principle supports design for change, because the ``secrets'' that each module
hides represent likely future changes. Design for change is valuable in SC,
where modifications are frequent, especially during initial development as the
solution space is explored.
Our design follows the rules layed out by \citet{ParnasEtAl1984}, as follows:
\begin{itemize}
\item System details that are likely to change independently should be the
secrets of separate modules.
\item Each data structure is used in only one module.
\item Any other program that requires information stored in a module's data
structures must obtain it by calling access programs belonging to that module.
\end{itemize}
After completing the first stage of the design, the Software Requirements
Specification (SRS), the Module Guide (MG) is developed~\citep{ParnasEtAl1984}. The MG
specifies the modular structure of the system and is intended to allow both
designers and maintainers to easily identify the parts of the software. The
potential readers of this document are as follows:
\begin{itemize}
\item New project members: This document can be a guide for a new project member
to easily understand the overall structure and quickly find the
relevant modules they are searching for.
\item Maintainers: The hierarchical structure of the module guide improves the
maintainers' understanding when they need to make changes to the system. It is
important for a maintainer to update the relevant sections of the document
after changes have been made.
\item Designers: Once the module guide has been written, it can be used to
check for consistency, feasibility and flexibility. Designers can verify the
system in various ways, such as consistency among modules, feasibility of the
decomposition, and flexibility of the design.
\end{itemize}
The rest of the document is organized as follows. Section
\ref{SecChange} lists the anticipated and unlikely changes of the software
requirements. Section \ref{SecMH} summarizes the module decomposition that
was constructed according to the likely changes. Section \ref{SecConnection}
specifies the connections between the software requirements and the
modules. Section \ref{SecMD} gives a detailed description of the
modules. Section \ref{SecTM} includes two traceability matrices. One checks
the completeness of the design against the requirements provided in the SRS. The
other shows the relation between anticipated changes and the modules. Section
\ref{SecUse} describes the use relation between modules.
\section{Anticipated and Unlikely Changes} \label{SecChange}
This section lists possible changes to the system. According to the likeliness
of the change, the possible changes are classified into two
categories. Anticipated changes are listed in Section \ref{SecAchange}, and
unlikely changes are listed in Section \ref{SecUchange}.
\subsection{Anticipated Changes} \label{SecAchange}
Anticipated changes are the source of the information that is to be hidden
inside the modules. Ideally, changing one of the anticipated changes will only
require changing the one module that hides the associated decision. The approach
adapted here is called design for
change.
\begin{description}
\item[\refstepcounter{acnum} \actheacnum \label{acHardware}:] The specific
hardware on which the software is running.
\item[\refstepcounter{acnum} \actheacnum \label{acInput}:] The format of the
initial input data.
\item ...
\end{description}
\subsection{Unlikely Changes} \label{SecUchange}
The module design should be as general as possible. However, a general system is
more complex. Sometimes this complexity is not necessary. Fixing some design
decisions at the system architecture stage can simplify the software design. If
these decision should later need to be changed, then many parts of the design
will potentially need to be modified. Hence, it is not intended that these
decisions will be changed.
\begin{description}
\item[\refstepcounter{ucnum} \uctheucnum \label{ucIO}:] Input/Output devices
(Input: File and/or Keyboard, Output: File, Memory, and/or Screen).
\item[\refstepcounter{ucnum} \uctheucnum \label{ucInput}:] There will always be
a source of input data external to the software.
\item ...
\end{description}
\section{Module Hierarchy} \label{SecMH}
This section provides an overview of the module design. Modules are summarized
in a hierarchy decomposed by secrets in Table \ref{TblMH}. The modules listed
below, which are leaves in the hierarchy tree, are the modules that will
actually be implemented.
\begin{description}
\item [\refstepcounter{mnum} \mthemnum \label{mHH}:] Hardware-Hiding Module
\item ...
\end{description}
\begin{table}[h!]
\centering
\begin{tabular}{p{0.3\textwidth} p{0.6\textwidth}}
\toprule
\textbf{Level 1} & \textbf{Level 2}\\
\midrule
{Hardware-Hiding Module} & ~ \\
\midrule
\multirow{7}{0.3\textwidth}{Behaviour-Hiding Module} & ?\\
& ?\\
& ?\\
& ?\\
& ?\\
& ?\\
& ?\\
& ?\\
\midrule
\multirow{3}{0.3\textwidth}{Software Decision Module} & {?}\\
& ?\\
& ?\\
\bottomrule
\end{tabular}
\caption{Module Hierarchy}
\label{TblMH}
\end{table}
\section{Connection Between Requirements and Design} \label{SecConnection}
The design of the system is intended to satisfy the requirements developed in
the SRS. In this stage, the system is decomposed into modules. The connection
between requirements and modules is listed in Table \ref{TblRT}.
\section{Module Decomposition} \label{SecMD}
Modules are decomposed according to the principle of ``information hiding''
proposed by \citet{ParnasEtAl1984}. The \emph{Secrets} field in a module
decomposition is a brief statement of the design decision hidden by the
module. The \emph{Services} field specifies \emph{what} the module will do
without documenting \emph{how} to do it. For each module, a suggestion for the
implementing software is given under the \emph{Implemented By} title. If the
entry is \emph{OS}, this means that the module is provided by the operating
system or by standard programming language libraries. Also indicate if the
module will be implemented specifically for the software.
Only the leaf modules in the
hierarchy have to be implemented. If a dash (\emph{--}) is shown, this means
that the module is not a leaf and will not have to be implemented. Whether or
not this module is implemented depends on the programming language
selected.
\subsection{Hardware Hiding Modules (\mref{mHH})}
\begin{description}
\item[Secrets:]The data structure and algorithm used to implement the virtual
hardware.
\item[Services:]Serves as a virtual hardware used by the rest of the
system. This module provides the interface between the hardware and the
software. So, the system can use it to display outputs or to accept inputs.
\item[Implemented By:] OS
\end{description}
\subsection{Behaviour-Hiding Module}
\begin{description}
\item[Secrets:]The contents of the required behaviours.
\item[Services:]Includes programs that provide externally visible behaviour of
the system as specified in the software requirements specification (SRS)
documents. This module serves as a communication layer between the
hardware-hiding module and the software decision module. The programs in this
module will need to change if there are changes in the SRS.
\item[Implemented By:] --
\end{description}
\subsubsection{Input Format Module (\mref{mInput})}
\begin{description}
\item[Secrets:]The format and structure of the input data.
\item[Services:]Converts the input data into the data structure used by the
input parameters module.
\item[Implemented By:] [Your Program Name Here]
\end{description}
\subsubsection{Etc.}
\subsection{Software Decision Module}
\begin{description}
\item[Secrets:] The design decision based on mathematical theorems, physical
facts, or programming considerations. The secrets of this module are
\emph{not} described in the SRS.
\item[Services:] Includes data structure and algorithms used in the system that
do not provide direct interaction with the user.
% Changes in these modules are more likely to be motivated by a desire to
% improve performance than by externally imposed changes.
\item[Implemented By:] --
\end{description}
\subsubsection{Etc.}
\section{Traceability Matrix} \label{SecTM}
This section shows two traceability matrices: between the modules and the
requirements and between the modules and the anticipated changes.
% the table should use mref, the requirements should be named, use something
% like fref
\begin{table}[H]
\centering
\begin{tabular}{p{0.2\textwidth} p{0.6\textwidth}}
\toprule
\textbf{Req.} & \textbf{Modules}\\
\midrule
R1 & \mref{mHH}, \mref{mInput}, \mref{mParams}, \mref{mControl}\\
R2 & \mref{mInput}, \mref{mParams}\\
R3 & \mref{mVerify}\\
R4 & \mref{mOutput}, \mref{mControl}\\
R5 & \mref{mOutput}, \mref{mODEs}, \mref{mControl}, \mref{mSeqDS}, \mref{mSolver}, \mref{mPlot}\\
R6 & \mref{mOutput}, \mref{mODEs}, \mref{mControl}, \mref{mSeqDS}, \mref{mSolver}, \mref{mPlot}\\
R7 & \mref{mOutput}, \mref{mEnergy}, \mref{mControl}, \mref{mSeqDS}, \mref{mPlot}\\
R8 & \mref{mOutput}, \mref{mEnergy}, \mref{mControl}, \mref{mSeqDS}, \mref{mPlot}\\
R9 & \mref{mVerifyOut}\\
R10 & \mref{mOutput}, \mref{mODEs}, \mref{mControl}\\
R11 & \mref{mOutput}, \mref{mODEs}, \mref{mEnergy}, \mref{mControl}\\
\bottomrule
\end{tabular}
\caption{Trace Between Requirements and Modules}
\label{TblRT}
\end{table}
\begin{table}[H]
\centering
\begin{tabular}{p{0.2\textwidth} p{0.6\textwidth}}
\toprule
\textbf{AC} & \textbf{Modules}\\
\midrule
\acref{acHardware} & \mref{mHH}\\
\acref{acInput} & \mref{mInput}\\
\acref{acParams} & \mref{mParams}\\
\acref{acVerify} & \mref{mVerify}\\
\acref{acOutput} & \mref{mOutput}\\
\acref{acVerifyOut} & \mref{mVerifyOut}\\
\acref{acODEs} & \mref{mODEs}\\
\acref{acEnergy} & \mref{mEnergy}\\
\acref{acControl} & \mref{mControl}\\
\acref{acSeqDS} & \mref{mSeqDS}\\
\acref{acSolver} & \mref{mSolver}\\
\acref{acPlot} & \mref{mPlot}\\
\bottomrule
\end{tabular}
\caption{Trace Between Anticipated Changes and Modules}
\label{TblACT}
\end{table}
\section{Use Hierarchy Between Modules} \label{SecUse}
In this section, the uses hierarchy between modules is
provided. \citet{Parnas1978} said of two programs A and B that A {\em uses} B if
correct execution of B may be necessary for A to complete the task described in
its specification. That is, A {\em uses} B if there exist situations in which
the correct functioning of A depends upon the availability of a correct
implementation of B. Figure \ref{FigUH} illustrates the use relation between
the modules. It can be seen that the graph is a directed acyclic graph
(DAG). Each level of the hierarchy offers a testable and usable subset of the
system, and modules in the higher level of the hierarchy are essentially simpler
because they use modules from the lower levels.
\begin{figure}[H]
\centering
%\includegraphics[width=0.7\textwidth]{UsesHierarchy.png}
\caption{Use hierarchy among modules}
\label{FigUH}
\end{figure}
%\section*{References}
\bibliographystyle {plainnat}
\bibliography{../../../ReferenceMaterial/References}
\end{document}
\ No newline at end of file
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# Makefile
# From https://danielkaes.wordpress.com/2009/03/14/compiling-latex-documents-using-makefiles/
PROJECT=MG
TEX=pdflatex
BIBTEX=bibtex
BUILDTEX=$(TEX) $(PROJECT).tex
all:
$(BUILDTEX)
$(BIBTEX) $(PROJECT)
$(BUILDTEX)
$(BUILDTEX)
clean-all:
rm -f *.dvi *.log *.bak *.aux *.bbl *.blg *.idx *.ps *.eps *.pdf *.toc *.out *~
clean:
rm -f *.log *.bak *.aux *.bbl *.blg *.idx *.toc *.out *.lof *.lot *~
\ No newline at end of file
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# Module Guide
The folders and files for the module guide.
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\documentclass[12pt, titlepage]{article}
\usepackage{amsmath, mathtools}
\usepackage[round]{natbib}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{graphicx}
\usepackage{colortbl}
\usepackage{xr}
\usepackage{hyperref}
\usepackage{longtable}
\usepackage{xfrac}
\usepackage{tabularx}
\usepackage{float}
\usepackage{siunitx}
\usepackage{booktabs}
\usepackage{multirow}
\usepackage[section]{placeins}
\usepackage{caption}
\usepackage{fullpage}
\hypersetup{
bookmarks=true, % show bookmarks bar?
colorlinks=true, % false: boxed links; true: colored links
linkcolor=red, % color of internal links (change box color with linkbordercolor)
citecolor=blue, % color of links to bibliography
filecolor=magenta, % color of file links
urlcolor=cyan % color of external links
}
\usepackage{array}
\externaldocument{../../SRS/SRS}
\input{../../Comments}
\newcommand{\progname}{Program Name}
\begin{document}
\title{Module Interface Specification for ...}
\author{Author Name}
\date{\today}
\maketitle
\pagenumbering{roman}
\section{Revision History}
\begin{tabularx}{\textwidth}{p{3cm}p{2cm}X}
\toprule {\bf Date} & {\bf Version} & {\bf Notes}\\
\midrule
Date 1 & 1.0 & Notes\\
Date 2 & 1.1 & Notes\\
\bottomrule
\end{tabularx}
~\newpage
\section{Symbols, Abbreviations and Acronyms}
See SRS Documentation at \wss{give url}
\wss{Also add any additional symbols, abbreviations or acronyms}
\newpage
\tableofcontents
\newpage
\pagenumbering{arabic}
\section{Introduction}
The following document details the Module Interface Specifications for
\wss{Fill in your project name and description}
Complementary documents include the System Requirement Specifications
and Module Guide. The full documentation and implementation can be
found at \url{...}. \wss{provide the url for your repo}
\section{Notation}
\wss{You should describe your notation. You can use what is below as
a starting point.}
The structure of the MIS for modules comes from \citet{HoffmanAndStrooper1995},
with the addition that template modules have been adapted from
\cite{GhezziEtAl2003}. The mathematical notation comes from Chapter 3 of
\citet{HoffmanAndStrooper1995}. For instance, the symbol := is used for a
multiple assignment statement and conditional rules follow the form $(c_1
\Rightarrow r_1 | c_2 \Rightarrow r_2 | ... | c_n \Rightarrow r_n )$.
The following table summarizes the primitive data types used by \progname.
\begin{center}
\renewcommand{\arraystretch}{1.2}
\noindent
\begin{tabular}{l l p{7.5cm}}
\toprule
\textbf{Data Type} & \textbf{Notation} & \textbf{Description}\\
\midrule
character & char & a single symbol or digit\\
integer & $\mathbb{Z}$ & a number without a fractional component in (-$\infty$, $\infty$) \\
natural number & $\mathbb{N}$ & a number without a fractional component in [1, $\infty$) \\
real & $\mathbb{R}$ & any number in (-$\infty$, $\infty$)\\
\bottomrule
\end{tabular}
\end{center}
\noindent
The specification of \progname \ uses some derived data types: sequences, strings, and
tuples. Sequences are lists filled with elements of the same data type. Strings
are sequences of characters. Tuples contain a list of values, potentially of
different types. In addition, \progname \ uses functions, which
are defined by the data types of their inputs and outputs. Local functions are
described by giving their type signature followed by their specification.
\section{Module Decomposition}
The following table is taken directly from the Module Guide document for this project.
\begin{table}[h!]
\centering
\begin{tabular}{p{0.3\textwidth} p{0.6\textwidth}}
\toprule
\textbf{Level 1} & \textbf{Level 2}\\
\midrule
{Hardware-Hiding} & ~ \\
\midrule
\multirow{7}{0.3\textwidth}{Behaviour-Hiding} & Input Parameters\\
& Output Format\\
& Output Verification\\
& Temperature ODEs\\
& Energy Equations\\
& Control Module\\
& Specification Parameters Module\\
\midrule
\multirow{3}{0.3\textwidth}{Software Decision} & {Sequence Data Structure}\\
& ODE Solver\\
& Plotting\\
\bottomrule
\end{tabular}
\caption{Module Hierarchy}
\label{TblMH}
\end{table}
\newpage
~\newpage
\section{MIS of \wss{Module Name}} \label{Module} \wss{Use labels for
cross-referencing}
\wss{You can reference SRS labels, such as R\ref{R_Inputs}.}
\wss{It is also possible to use \LaTeX for hypperlinks to external documents.}
\subsection{Module}
\wss{Short name for the module}
\subsection{Uses}
\subsection{Syntax}
\subsubsection{Exported Access Programs}
\begin{center}
\begin{tabular}{p{2cm} p{4cm} p{4cm} p{2cm}}
\hline
\textbf{Name} & \textbf{In} & \textbf{Out} & \textbf{Exceptions} \\
\hline
\wss{accessProg} & - & - & - \\
\hline
\end{tabular}
\end{center}
\subsection{Semantics}
\subsubsection{State Variables}
\subsubsection{Access Routine Semantics}
\noindent \wss{accessProg}():
\begin{itemize}
\item transition: \wss{if appropriate}
\item output: \wss{if appropriate}
\item exception: \wss{if appropriate}
\end{itemize}
\newpage
\bibliographystyle {plainnat}
\bibliography {../../../ReferenceMaterial/References}
\newpage
\section{Appendix} \label{Appendix}
\wss{Extra information if required}
\end{document}
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# Makefile
# From https://danielkaes.wordpress.com/2009/03/14/compiling-latex-documents-using-makefiles/
PROJECT=MIS
TEX=pdflatex
BIBTEX=bibtex
BUILDTEX=$(TEX) $(PROJECT).tex
all:
$(BUILDTEX)
$(BIBTEX) $(PROJECT)
$(BUILDTEX)
$(BUILDTEX)
clean-all:
rm -f *.dvi *.log *.bak *.aux *.bbl *.blg *.idx *.ps *.eps *.pdf *.toc *.out *~
clean:
rm -f *.log *.bak *.aux *.bbl *.blg *.idx *.toc *.out *~
\ No newline at end of file
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# Module Interface Specification #
Suggest following something like the example used in Lab 11 (Box 3D).
Use doxygen (or equivalent) to document the interface for your modules.
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# Design Documentation
The folders and files for this folder are as follows:
Describe ...
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\documentclass{article}
\usepackage{booktabs}
\usepackage{tabularx}
\title{SE 3XA3: Development Plan\\Title of Project}
\author{Team \#, Team Name
\\ Student 1 name and macid
\\ Student 2 name and macid
\\ Student 3 name and macid
}
\date{}
\input{../Comments}
\begin{document}
\begin{table}[hp]
\caption{Revision History} \label{TblRevisionHistory}
\begin{tabularx}{\textwidth}{llX}
\toprule
\textbf{Date} & \textbf{Developer(s)} & \textbf{Change}\\
\midrule
Date1 & Name(s) & Description of changes\\
Date2 & Name(s) & Description of changes\\
... & ... & ...\\
\bottomrule
\end{tabularx}
\end{table}
\newpage
\maketitle
Put your introductory blurb here.
\section{Team Meeting Plan}
\section{Team Communication Plan}
\section{Team Member Roles}
\section{Git Workflow Plan}
\section{Proof of Concept Demonstration Plan}
\section{Technology}
\section{Coding Style}
\section{Project Schedule}
Provide a pointer to your Gantt Chart.
\section{Project Review}
\end{document}
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# Makefile
# From https://danielkaes.wordpress.com/2009/03/14/compiling-latex-documents-using-makefiles/
PROJECT=DevelopmentPlan
TEX=pdflatex
BIBTEX=bibtex
BUILDTEX=$(TEX) $(PROJECT).tex
all:
$(BUILDTEX)
# $(BIBTEX) $(PROJECT)
# $(BUILDTEX)
$(BUILDTEX)
clean-all:
rm -f *.dvi *.log *.bak *.aux *.bbl *.blg *.idx *.ps *.eps *.pdf *.toc *.out *~
clean:
rm -f *.log *.bak *.aux *.bbl *.blg *.idx *.toc *.out *~
\ No newline at end of file
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# Development Plan
The folders and files for this folder are as follows:
Describe ...
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# Makefile
.PHONY: SRS
all: SRS MG MIS PS SVnVP UVnVP SVnVR UVnVR
SRS:
cd SRS && make && cd ..
MG:
cd Design/MG && make && cd ../..
MIS:
cd Design/MIS && make && cd ../..
PS:
cd ProblemStatement && make && cd ..
SVnVP:
cd VnVPlan/SystVnVPlan && make && cd ../..
UVnVP:
cd VnVPlan/UnitVnVPlan && make && cd ../..
SVnVR:
cd VnVReport/SystVnVReport && make && cd ../..
UVnVR:
cd VnVReport/UnitVnVReport && make && cd ../..
clean: cleanSRS cleanMG cleanMIS cleanPS cleanSVnVP cleanUVnVP cleanSVnVR cleanUVnVR
cleanPS:
cd ProblemStatement && make clean && cd ..
cleanSRS:
cd SRS && make clean && cd ..
cleanMG:
cd Design/MG && make clean && cd ..
cleanMIS:
cd Design/MIS && make clean && cd ..
cleanSVnVP:
cd VnVPlan/SystVnVPlan && make clean && cd ..
cleanUVnVP:
cd VnVPlan/UnitVnVPlan && make clean && cd ..
cleanSVnVR:
cd VnVReport/SystVnVReport && make clean && cd ..
cleanUVnVR:
cd VnVReport/UnitVnVReport && make clean && cd ..
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# Makefile
# From https://danielkaes.wordpress.com/2009/03/14/compiling-latex-documents-using-makefiles/
PROJECT=ProblemStatement
TEX=pdflatex
BIBTEX=bibtex
BUILDTEX=$(TEX) $(PROJECT).tex
all:
$(BUILDTEX)
# $(BIBTEX) $(PROJECT)
# $(BUILDTEX)
$(BUILDTEX)
clean-all:
rm -f *.dvi *.log *.bak *.aux *.bbl *.blg *.idx *.ps *.eps *.pdf *.toc *.out *~
clean:
rm -f *.log *.bak *.aux *.bbl *.blg *.idx *.toc *.out *~
\ No newline at end of file