References.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for Spencer Smith at 2017-11-23 11:56:51 -0500 


%% Saved with string encoding Unicode (UTF-8) 



@unpublished{SmithEtAl2017,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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@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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@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{ParnasEtAl1984,
	Author = {D.L. Parnas and P.C. Clement and D. M. Weiss},
	Booktitle = {International Conference on Software Engineering},
	Date-Added = {2017-10-23 20:16:11 +0000},
	Date-Modified = {2017-10-23 20:16:11 +0000},
	Pages = {408-419},
	Title = {The modular structure of complex systems},
	Year = {1984},
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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},
	Bdsk-File-1 = {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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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@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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@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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@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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	Bdsk-Url-1 = {http://doi.ieeecomputersociety.org/10.1109/ICSR.1998.685727}}

@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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	Bdsk-Url-1 = {citeseer.ist.psu.edu/13585.html}}

@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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	Bdsk-Url-1 = {http://www.research.avayalabs.com/user/weiss/Publications.html}}

@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},
	Bdsk-File-1 = {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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},
	Bdsk-File-1 = {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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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	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-15187-3_8}}

@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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	Bdsk-Url-1 = {http://dx.doi.org/10.1109/MCSE.2009.193}}

@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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@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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@inbook{RobertsonAndRobertson2012,
	Author = {James Robertson and Suzanne Robertson},
	Date-Added = {2017-09-07 18:01:08 +0000},
	Date-Modified = {2017-09-07 18:01:08 +0000},
	Editor = {16},
	Publisher = {Atlantic Systems Guild Limited},
	Title = {Volere Requirements Specification Template},
	Year = {2012},
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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{Parnas1972a,
	Author = {David L. Parnas},
	Date-Added = {2017-09-07 18:01:00 +0000},
	Date-Modified = {2017-09-07 18:01:00 +0000},
	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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@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},