best-practices-scientific-computing-2012.bib

% $Id: best-practices-scientific-computing-2012.bib 2995 2012-10-18 12:58:10Z gvw $

@string{adc2005         = "Proc.\ Agile Development Conference 2005"}
@string{cns		= "Proc.\ Canadian Nuclear Society Conference"}
@string{cse		= "Computing in Science \& Engineering"}
@string{hpca		= "International Journal of High Performance Computing Applications"}
@string{icassp2007	= "Proc.\ 32nd International Conference on Acoustics, Speech, and Signal Processing"}
@string{icse2007	= "Proc. \ 29th International Conference on Software Engineering"}
@string{icse2008	= "Proc.\ 30th International Conference on Software Engineering"}
@string{icse2009	= "Proc.\ 31st International Conference on Software Engineering"}
@string{esp1986		= "Proc.\ First Workshop on Empirical Studies of Programmers"}
@string{htos1999	= "Proc.\ 7th Workshop on Hot Topics in Operating Systems"}
@string{icpc2009	= "Proc.\ 2009 IEEE International Conference on Program Comprehension"}
@string{ieee-computer	= "IEEE Computer"}
@string{ieee-software	= "IEEE Software"}
@string{ieee-trans-se	= "IEEE Transactions on Software Engineering"}
@string{lanl		= "Los Alamos National Laboratory"}
@string{ms		= "Making Software: What Really Works, and Why We Believe It"}
@string{secse2008	= "Proc.\ First International Workshop on Software Engineering for Computational Science and Engineering"}
@string{secse2009	= "Proc.\ Second International Workshop on Software Engineering for Computational Science and Engineering"}
@string{secse2010	= "Proc.\ Third International Workshop on Software Engineering for Computational Science and Engineering"}
@string{secse2011	= "Proc.\ Fourth International Workshop on Software Engineering for Computational Science and Engineering"}
@string{sc2005		= "Proc.\ Supercomputing 2005"}
@string{sc2008		= "Proc.\ Supercomputing 2008"}
@string{sc2011          = "Proc.\ 24th ACM/IEEE Conference on High Performance Computing, Networking, Storage and Analysis"}

@article{hypertension2012,
	author = {Monica L. Bertoia and Molly E. Waring and Priya S. Gupta and Mary B. Roberts and Charles B. Eaton},
	title = "{Notice of Retraction}", 
	month = {Aug.},
	year = {2012}, 
	volume = {60},
	issue = {e29},
	doi = {10.1161/HYP.0b013e318269bc7a}, 
	howpublished = {http://hyper.ahajournals.org/content/early/2012/08/06/HYP.0b013e318269bc7a.1.short}, 
	eprint = {http://hyper.ahajournals.org/content/early/2012/08/06/HYP.0b013e318269bc7a.1.full.pdf+html}, 
	journal = {Hypertension} 
}

@misc{aranda2012,
	author = {Jorge Aranda},
	title = "{Software Carpentry Assessment Report}",
	year = {2012},
	type = {whitepaper},
	url = {http://software\-carpentry.org/bib/aranda\-assessment-2012-07.pdf}
}

@book{baddeley2009,
	author = {Alan Baddeley and Michael W. Eysenck and Michael C. Anderson},
	title = "{Memory}",
	publisher = {Psychology Press},
	year = {2009},
	isbn = {1848720017}
}

@inproceedings{binkley2009,
	author = {D. Binkley and M. Davis and D. Lawrie and C. Morrell},
	title = "{To CamelCase or Under\_score}",
	booktitle = icpc2009,
	year = {2009},
	pages = {158-167}
}

@incollection{brown2010,
	author = {C. Titus Brown and Rosangela Canino-Koning},
	title = "{Continuous Integration}",
	pages = {77-87},
	booktitle = "{The Architecture of Open Source Applications}",
	editor = {Amy Brown and Greg Wilson},
	publisher = {Lulu.com},
	year = {2010},
	isbn = {1257638017}
}

@inproceedings{carver2007,
	author = {Jeffrey C. Carver and Richard P. Kendall and Susan E. Squires and Douglass E. Post},
	title = "{Software Development Environments for Scientific and Engineering Software: A Series of Case Studies}",
	booktitle = icse2007,
	year = {2007},
	pages = {550-559},
	doi = {10.1109/ICSE.2007.77}
}

@article{chang2007,
	author = {Geoffrey Chang},
	title = "{Retraction of `Structure of MsbA from \emph{Vibrio cholera}: A Multidrug Resistance ABC Transporter Homolog in a Closed Conformation' [J. Mol. Biol. (2003) 330 419–430]}",
	journal = {Journal of Molecular Biology},
	volume = {369},
	number = {2},
	year = {2007}
}

@incollection{cohen2010,
	author = {Jason Cohen},
 	title = "{Modern Code Review}",
	pages = {329-336},
	booktitle = ms,
	editor = {Andy Oram and Greg Wilson},
	publisher = {O'Reilly},
	year = {2010},
	pages = {329-337},
	isbn = {0596808321}
}

@article{currie2007,
	author = {David Currie and Jeremy Kerr},
	title = "{Testing, as Opposed to Supporting, the Mid-Domain Hypothesis: a Response to Lees and Colwell (2007)}",
	journal = {Ecology Letters},
	volume = {10},
	number = {9},
	pages = {E9-E10},
	year = {2007}
}

@article{dubois2003a,
	author = {P. Dubois and J. Johnson},
	title = "{Issue Tracking}",
	journal = cse,
	volume = {5},
	number = {6},
	year = {2003},
	month = {Nov.-Dec.},
	pages = {71-77},
	doi = {10.1109/MCISE.2003.1238707}
}

@article{dubois2003b,
	author = {P. F. Dubois and T. Epperly and G. Kumfert},
	title = "{Why Johnny Can't Build (Portable Scientific Software)}",
	journal = cse,
	volume = {5},
	number = {5},
	pages = {83-88},
	year = {2003},
	doi = {10.1109/MCISE.2003.1225867}
}

@article{dubois2005,
	author = {P. F. Dubois},
	title = "{Maintaining Correctness in Scientific Programs}",
	journal = cse,
	volume = {7},
	number = {3},
	pages = {80-85},
	year = {2005},
	month = {May-June},
	doi = {10.1109/MCSE.2005.54}
}

@article{fagan1976,
	author = {Michael E. Fagan},
	title = "{Design and Code Inspections to Reduce Errors in Program Development}",
	journal = {IBM Systems Journal},
	volume = {15},
	number = {3},
	year = {1976},
	pages = {182-211}
}

@book{feathers2004,
	author = {Michael Feathers},
	title = "{Working Effectively with Legacy Code}",
	publisher = {Prentice Hall},
	year = {2004},
	isbn = {0131177052}
}

@article{ferrari2013,
	author = {F. Ferrari and Y. L. Jung and P. V. Kharchenko and A. Plachetka and A. A. Alekseyenko and M. I. Kuroda and P. J. Park},
	title = "{Comment on ``Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters''}",
	volume = {340},
	number = {6130},
	pages = {273},
	year = {2013},
	doi = {10.1126/science.1231815},
	url = {http://www.sciencemag.org/content/340/6130/273.3.abstract},
	journal = {Science}
}

@book{fogel2005,
	author = {Karl Fogel},
	title = "{Producing Open Source Software: How to Run a Successful Free Software Project}",
	publisher = {O'Reilly},
	year = {2005},
	isbn = {0596007590},
	url = {http://producingoss.com}
}

@inproceedings{fomel2007,
	author = {S. Fomel and G. Hennenfent},
	title = "{Reproducible Computational Experiments using SCons}",
	booktitle = icassp2007,
	volume = {IV},
	pages = {1257-1260},
	year = {2007}
}

@book{fowler1999,
	author = {Martin J. Fowler},
	title = "{Refactoring: Improving the Design of Existing Code}",
	publisher = {Addison-Wesley},
	year = {1999},
	isbn = {0201485672}
}

@book{grubb2003,
	author = {Penny Grubb and Armstrong A. Takang},
	title = "{Software Maintenance: Concepts and Practice}",
	edition = {2nd},
	publisher = {World Scientific},
	year = {2003},
	isbn = {981238426X}
}

@book{haddock2010,
	author = {Steven Haddock and Casey Dunn},
	title = "{Practical Computing for Biologists}",
	publisher = {Sinauer Associates},
	year = {2010},
	isbn = {0878933913}
}

@inproceedings{hannay2008,
	author = {Jo Erskine Hannay and Hans Petter Langtangen and Carolyn MacLeod and Dietmar Pfahl and Janice Singer and Greg Wilson},
	title = "{How Do Scientists Develop and Use Scientific Software?}",
	booktitle = secse2009,
	year = {2009},
	pages = {1-8}
}

@article{hatton1994,
	author = {L. Hatton and A. Roberts},
	title = "{How Accurate is Scientific Software?}",
	journal = ieee-trans-se,
	volume = {20},
	number = {10},
	pages = {785-797},
	year = {1994}
}

@article{hatton1997,
	author = {L. Hatton},
	title = "{The {T} Experiments: Errors in Scientific Software}",
	journal = {Computational Science \& Engineering},
	volume = {4},
	number = {2},
	pages = {27-38},
	year = {1997}
}

@misc{herndon2013,
	author = {T. Herndon and M. Ash and R. Pollin},
	title = "{Does High Public Debt Consistently Stifle Economic Growth? A Critique of Reinhart and Rogoff}",
	month = {April},
	year = {2013},
	howpublished = {Working Paper, Political Economy Research Institute},
	url = {http://www.peri.umass.edu/fileadmin/pdf/working\_papers/working\_papers\_301\-350/WP322.pdf}
}

@inproceedings{heroux2009,
	author = {Michael A. Heroux and James M. Willenbring},
	title = "{Barely-Sufficient Software Engineering: 10 Practices to Improve Your {CSE} Software}",
	booktitle = secse2009,
	pages = {15-21},
	year = {2009}
}

@book{hock2008,
	author = {Roger R. Hock},
	title = "{Forty Studies That Changed Psychology: Explorations into the History of Psychological Research}",
	edition = {6th},
	publisher = {Prentice Hall},
	year = {2008},
	isbn = {013603599X}
}

@inproceedings{hook2009,
	author = {Daniel Hook and Diane Kelly},
	title = "{Testing for Trustworthiness in Scientific Software}",
	booktitle = secse2009,
	year = {2009},
	month = {May},
	pages = {59-64}
}

@book{hunt1999,
	author = {Andrew Hunt and David Thomas},
	title = "{The Pragmatic Programmer: From Journeyman to Master}",
	publisher = {Addison-Wesley},
	year = {1999},
	isbn = {020161622X}
}

@inproceedings{jones1999,
	author = {Michael B. Jones and John Regehr},
	title = "{The Problems You're Having May Not Be the Problems You Think You're Having: Results from a Latency Study of Windows NT}",
	booktitle = htos1999,
	year = {1999},
	pages = {96-101}
}

@book{jones2008,
	author = {Capers Jones},
	title = "{Applied Software Measurement: Global Analysis of Productivity and Quality}",
	publisher = {McGraw-Hill Osborne Media},
	year = {2008},
	isbn = {0071502440}
}

@article{jaccretract2013,
	author = {Anon},
	title = "{Retraction Notice to ``Plasma PCSK9 Levels and Clinical Outcomes in the TNT (Treating to New Targets) Trial'' [J Am Coll Cardiol 2012;59:1778–1784]}",
	journal = {Journal of the American College of Cardiology},
	volume = {61},
	number = {16},
	pages = {1751},
	year = {2013},
	doi = {10.1016/j.jacc.2013.04.002},
}

@inproceedings{kane2003,
	author = {David Kane},
	title = "{Introducing Agile Development into Bioinformatics: An Experience Report}",
	booktitle = adc2005,
	pages = {132-139},
	year = {2005}
}

@article{kane2006,
	author = {David Kane and Moses Hohman and Ethan Cerami and Michael McCormick and Karl Kuhlmman and Jeff Byrd},
	title = "{Agile Methods in Biomedical Software Development: a Multi-Site Experience Report}",
	journal = {BMC Bioinformatics},
	volume = {7},
	number = {1},
	pages = {273},
	year = {2006},
	issn = {1471-2105},
	doi = {10.1186/1471-2105-7-273},
	url = {http://www.biomedcentral.com/1471-2105/7/273}
}

@inproceedings{kelly2008,
	author = {Diane Kelly and Rebecca Sanders},
	title = "{Assessing the Quality of Scientific Software}",
	booktitle = secse2008,
	year = {2008},
	month = {May}
}

@article{kelly2009,
	author = {Diane Kelly and Daniel Hook and Rebecca Sanders},
	title = "{Five Recommended Practices for Computational Scientists Who Write Software}",
	journal = cse,
	volume = {11},
	number = {5},
	pages = {48-53},
	year = {2009},
	doi = {10.1109/MCSE.2009.139}
}

@book{kerievsky2004,
	author = {Joshua Kerievsky},
	title = "{Refactoring to Patterns}",
	publisher = {Addison-Wesley},
	year = {2004},
	isbn = {0321213351}
}

@book{kernighan1976,
	author = {Brian W. Kernighan and P. J. Plauger},
	title = "{Software Tools}",
	publisher = {Addison-Wesley},
	year = {1976},
	isbn = {020103669X}
}

@book{kernighan1984,
	author = {Brian W. Kernighan and Rob Pike},
	title = "{The Unix Programming Environment}",
	publisher = {Prentice Hall},
	year = {1984},
	isbn = {013937681X}
}

@article{killcoyne2009,
	author = {Sarah Killcoyne and John Boyle},
	title = "{Managing Chaos: Lessons Learned Developing Software in the Life Sciences}",
	journal = cse,
	volume = {11},
	number = {6},
	pages = {20-29},
	year = {2009},
	doi = {10.1109/MCSE.2009.198}
}

@book{kniberg2007,
	author = {Henrik Kniberg},
	title = "{Scrum and XP from the Trenches}",
	publisher = {Lulu.com},
	year = {2007},
	isbn = {978-1430322641}
}

@techreport{kumfert2002,
	author = {G. Kumfert and T. Epperly},
	title = "{Software in the {DOE}: The Hidden Overhead of ``The Build''}",
	number = {UCRL-ID-147343},
	year = {2002},
	month = {February},
	institution = {Lawrence Livermore National Lab.},
	doi = {10.2172/15005938}
}

@article{ince2012,
	author = {Darrel C. Ince and Leslie Hatton and John Graham-Cumming},
	title = "{The Case for Open Computer Programs}",
	journal = {Nature},
	volume = {482},
	pages = {485-488},
	month = {February},
	year = {2012},
	doi = {doi:10.1038/nature10836},
}

@inproceedings{juergens2009,
	author = {Elmar Juergens and Florian Deissenboeck and Benjamin Hummel and Stefan Wagner},
	title = "{Do Code Clones Matter?}",
	booktitle = icse2009,
	year = {2009},
	pages = {485-495}
}

@article{kelt2008,
	author = {Douglas A. Kelt and James A. Wilson and Eddy S. Konno and Jessica D. Braswell and Douglas Deutschman},
	title = "{Differential Responses of Two Species of Kangaroo Rat (\emph{Dipodomys}) to Heavy Rains: A Humbling Reappraisal}",
	journal = {Journal of Mammalogy},
	volume = {89},
	number = {1},
	pages = {252-254},
	year = {2008}
}

@article{lees2007,
	author = {David C. Lees and Robert K. Colwell},
	title = "{A Strong Madagascan Rainforest MDE and No Equatorward Increase in Species Richness: Re-Analysis of 'The Missing Madagascan Mid-Domain Effect', by Kerr J.T., Perring M. \& Currie D.J. (Ecology Letters 9:149–159, 2006)}",
	journal = {Ecology Letters},
	volume = {10},
	number = {9},
	pages = {E4-E8},
	year = {2007}
}

@article{leveque2012,
	author = {Randall LeVeque and Ian M. Mitchell and Victoria Stodden},
	title = "{Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture}",
	journal = cse,
	year = 2012,
	volume = 14,
	number = 4,
	pages = {13-17},
	doi = {10.1109/MCSE.2012.38}
}

@inproceedings{letovsky1986,
	author = {S. Letovsky},
	title = "{Cognitive Processes in Program Comprehension}",
	booktitle = esp1986,
	year = {1986},
	isbn = {0-89391-388-X},
	pages = {58-79}
}

@article{ma2007,
	author = {Che Ma and Geoffrey Chang}, 
	title = "{Retraction for Ma and Chang, Structure of the Multidrug Resistance Efflux Transporter EmrE from \emph{Escherichia coli}}", 
	volume = {104}, 
	number = {9}, 
	pages = {3668}, 
	year = {2007},
	journal = {Proceedings of the National Academy of Sciences} 
}

@book{martin2002,
	author = {Robert C. Martin},
	title = "{Agile Software Development, Principles, Patterns, and Practices}",
	publisher = {Prentice Hall},
	year = {2002},
	isbn = {0135974445}
}

@book{martin2008,
	author = {Robert C. Martin},
	title = "{Clean Code: A Handbook of Agile Software Craftsmanship}",
	publisher = {Prentice Hall},
	year = {2008},
	isbn = {0132350882}
}

@article{matthews2008,
	author = {David Matthews and Greg Wilson and Steve Easterbrook},
	title = "{Configuration Management for Large-Scale Scientific Computing at the {UK Met Office}}",
	journal = cse,
	year = {2008},
	month = {Nov.-Dec.},
	pages = {56-64}
}

@book{mcconnell2004,
	author = {Steve McConnell},
	title = "{Code Complete: A Practical Handbook of Software Construction}",
	edition = {2nd},
	publisher = {Microsoft Press},
	year = {2004},
	isbn = {0735619670}
}

@article{merali2010,
	author = {Zeeya Merali},
	title = "{Error: Why Scientific Programming Does Not Compute}",
	journal = {Nature},
	volume = {467},
	pages = {775-777},
	year = {2010},
	url = {http://www.nature.com/news/2010/101013/full/467775a.html}
}

@book{meszaros2007,
	author = {Gerard Meszaros},
	title = "{xUnit Test Patterns: Refactoring Test Code}",
	publisher = {Addison-Wesley},
	year = {2007},
	isbn = {0131495054}
}

@article{miller2006,
	author = {Greg Miller},
	title = "{A Scientist's Nightmare: Software Problem Leads to Five Retractions}",
	journal = {Science},
	volume = {314},
	number = {5807},
	pages = {1856-1857},
	month = {Dec.},
	year = {2006},
	doi = {10.1126/science.314.5807.1856}
}

@article{noble2009,
	author = {William Stafford Noble},
	title = "{A Quick Guide to Organizing Computational Biology Projects}",
	journal = {PLoS Computational Biology},
	volume = {5},
	number = {7},
	article = {e1000424},
	year = {2009},
	doi = {10.1371/journal.pcbi.1000424}
}

@book{oberkampf2010,
	author = {William L. Oberkampf and Christopher J. Roy},
	title = "{Verification and Validation in Scientific Computing}",
	publisher = {Cambridge University Press},
	year = {2010},
	isbn = {0521113601}
}

@techreport{openprovenance,
	key = {Open Provenance},
	author = {Luc Moreau and Juliana Freire and Joe Futrelle and Robert E. McGrath and Jim Myers and Patrick Paulson},
	title = {The Open Provenance Model (v1.00)},
	month = {Dec.},
	year = {2007},
	institution = {University of Southampton},
	howpublished = {http://openprovenance.org},
	note = {Viewed Sept. 2013}
}

@book{oram2010,
	title = ms,
	editor = {Andy Oram and Greg Wilson},
	publisher = {O'Reilly},
	year = {2010},
	isbn = {0596808321}
}

@book{osherove2009,
	author = {Roy Osherove},
	title = "{The Art of Unit Testing: With Examples in .NET}",
	publisher = {Manning},
	year = {2009},
	isbn = {1933988274}
}

@Article{perez2007,
	author = {Fernando P\'erez and Brian E. Granger},
	title = {{IP}ython: a {S}ystem for {I}nteractive {S}cientific {C}omputing},
	journal = cse,
	volume = {9},
	number = {3},
	pages = {21-29},
	month = {May},
	year = {2007},
	url = {http://ipython.org}
}

@article{pitt-francis2008,
	author = {Joe Pitt-Francis and Miguel O. Bernabeu and Jonathan Cooper and Alan Garny and Lee Momtahan and James Osborne and Pras Pathmanathan and Blanca Rodriguez and Jonathan P. Whiteley and David J. Gavaghan},
	title = "{Chaste: Using Agile Programming Techniques to Develop Computational Biology Software}",
	journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
	volume = {366},
	number = {1878},
	pages = {3111-3136},
	year = {2008},
	month = {Sept.},
	doi = {10.1098/rsta.2008.0096}
}

@article{pouillon2010,
	author = {Yann Pouillon and Jean-Michel Beuken and Thierry Deutsch and Marc Torrent and Xavier Gonze},
	title = "{Organizing Software Growth and Distributed Development: The Case of {Abinit}}",
	journal = cse,
	volume = {13},
	number = {1},
	pages = {62-69},
	year = {2011},
	doi = {10.1109/MCSE.2011.13}
}

@inproceedings{prabhu2011,
	author = {Prakash Prabhu and Thomas B. Jablin and Arun Raman and Yun Zhang and Jialu Huang and Hanjun Kim and Nick P. Johnson and Feng Liu and Soumyadeep Ghosh and Stephen Beard and Taewook Oh and Matthew Zoufaly and David Walker and David I. August},
	title = "{A Survey of the Practice of Computational Science}",
	booktitle = sc2011,
	year = {2011},
	pages = {19:1-19:12},
	doi = {doi.acm.org/10.1145/2063348.2063374},
}

@incollection{prechelt2010,
	author = {Lutz Prechelt},
 	title = "{Two Comparisons of Programming Languages}",
	booktitle = ms,
	editor = {Andy Oram and Greg Wilson},
	publisher = {O'Reilly},
	year = {2010},
	pages = {239-258},
	isbn = {0596808321}
}

@book{ray2009,
	author = {Deborah S. Ray and Eric J. Ray},
	title = "{Unix and Linux: Visual QuickStart Guide}",
	edition = {4th},
	publisher = {Peachpit Press},
	year = {2009},
	isbn = {0321636783}
}

@misc{robinson2005,
	author = {Evan Robinson},
	title = "{Why Crunch Mode Doesn't Work: Six Lessons}",
	year = {2005},
	howpublished = {http://www.igda.org/why-crunch-modes-doesnt-work-six-lessons},
	note = {Viewed Sept. 2013 (diagram labelled ``productivity graph'' not displaying correctly at that time)}
}

@article{sanders2008,
	author = {R. Sanders and D. Kelly},
	title = "{Dealing with Risk in Scientific Software Development}",
	journal = ieee-software,
	volume = {25},
	number = {4},
	pages = {21-28},
	year = {2008},
	month = {July-Aug.}
}

@article{segal2005,
	author = {Judith Segal},
	title = "{When Software Engineers Met Research Scientists: A Case Study}",
	journal = {Empirical Software Engineering},
	volume = {10},
	number = {4},
	pages = {517-536},
	year = {2005}
}

@inproceedings{segal2008a,
	author = {J. Segal},
	title = "{Models of Scientific Software Development}",
	booktitle = secse2008,
	month = {May},
	year = {2008}
}

@article{segal2008b,
	author = {J. Segal and C. Morris},
	title = "{Developing Scientific Software}",
	journal = ieee-software,
	volume = {25},
	number = {4},
	pages = {18-20},
	year = {2008}
}

@book{sink2011,
	author = {Erik Sink},
	title = "{Version Control by Example}",
	publisher = {Pyrenean Gold Press},
	year = {2011},
	isbn = {978-0-9835079-1-8}
}

@book{smith2011,
	author = {Peter Smith},
	title = "{Software Build Systems: Principles and Experience}",
	publisher = {Addison-Wesley},
	year = {2011},
	isbn = {0321717287}
}

@misc{spolsky2000,
	author = {Joel Spolsky},
	title = "{The Joel Test: 12 Steps to Better Code}",
	howpublished = {http://www.joelonsoftware.com/articles/fog0000000043.html},
	year = {2000},
	note = {Viewed Sept. 2013}
}

@incollection{turhan2010,
	author = {Burak Turhan and Lucas Layman and Madeline Diep and Hakan Erdogmus and Forrest Shull},
	title = "{How Effective is Test-Driven Development?}",
	pages = {207-217},
	booktitle = ms,
	editor = {Andy Oram and Greg Wilson},
	publisher = {O'Reilly},
	year = {2010},
	isbn = {0596808321}
}

@article{vardi2010,
	author = {Moshe Vardi},
	title = "{Science Has Only Two Legs}",
	journal = {Communications of the ACM},
	volume = {53},
	number = {9},
	month = {Sept.},
	pages = {5},
	year = {2010}
}

@article{chang2006,
	author = {Geoffrey Chang and Christopher B. Roth and Christopher L. Reyes and Owen Pornillos and Yen-Ju Chen and Andy P. Chen}, 
	title = "{Retraction}",
	journal = {Science},
	volume = {314}, 
	number = {5807}, 
	pages = {1875}, 
	year = {2006}, 
}

@incollection{williams2010,
	author = {Laurie Williams},
 	title = "{Pair Programming}",
	pages = {311-322},
	booktitle = ms,
	editor = {Andy Oram and Greg Wilson},
	publisher = {O'Reilly},
	year = {2010},
	isbn = {0596808321}
}

@article{wilson2006a,
	author = {Greg Wilson},
	title = "{Where's the Real Bottleneck in Scientific Computing?}",
	journal = {American Scientist},
	year = {2006},
	month = {January-February},
	pages = {5-6}
}

@article{wilson2006b,
	author = {Greg Wilson},
	title = "{Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive}",
	journal = cse,
	year = {2006},
	month = {Nov.-Dec.},
	pages = {66-69}
}

@misc{wilson2013,
	author = {Greg Wilson},
	title = "{Software Carpentry: Lessons Learned}",
	version = {1},
	journal = {Arxiv preprint},
	year = {2013},
	howpublished = {arXiv:1307.5448},
	url = {http://arxiv.org/abs/1307.5448}
}

@misc{xunit,
	key = {xUnit},
	title = "{List of Unit Testing Frameworks}",
	howpublished = {http://en.wikipedia.org/wiki/List\_of\_unit\_\-testing\_frameworks},
	note = {Viewed Sept. 2013}
}

@misc{xie2013knitr,
	author = {Yihui Xie},
	title = {knitr: A General-Purpose Tool for Dynamic Report Generation in R},
	howpublished = {R package version 0.9},
	year = {2013},
	url = {http://yihui.name/knitr/}
}

@book{zeller2009,
	author = {Andreas Zeller},
	title = "{Why Programs Fail: A Guide to Systematic Debugging}",
	publisher = {Morgan Kaufmann},
	year = {2009},
	isbn = {0123745152}
}