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book.bib
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@comment{
Entries currently used in book.
Special characters *MUST* use LaTeX escapes, because BibTeX doesn't handle UTF-8 properly.
}
@inproceedings{Alme2017,
author = {Daniel A. Almeida and Gail C. Murphy and Greg Wilson and Mike Hoye},
title = {Do Software Developers Understand Open Source Licenses?},
booktitle = {Proceedings of the 25th International Conference on Program Comprehension},
year = {2017},
ISBN = {9781-538-6053-5-6},
pages = {1--11},
URL = {https://doi.org/10.1109/ICPC.2017.7},
DOI = {10.1109/ICPC.2017.7},
publisher = {{IEEE} Press},
note = {Found that developers understand single licenses well, but frequently misunderstand the interactions between multiple licenses.}
}
@book{Auro2018,
author = {Valerie Aurora and Mary Gardiner and Annalee {Flower Horne}},
title = {How to Respond to Code of Conduct Reports},
publisher = {Frame Shift Consulting},
year = {2018},
link = {https://frameshiftconsulting.com/code-of-conduct-book/},
note = {A practical step-by-step guide to handling code of conduct issues.}
}
@book{Auro2019,
author = {Valerie Aurora and Mary Gardiner},
title = {How to Respond to Code of Conduct Reports},
publisher = {Frame Shift Consulting LLC},
edition = {Version 1.1},
year = {2019},
isbn = {978-1386922575},
link = {https://files.frameshiftconsulting.com/books/cocguide.pdf},
note = {A short, practical guide to enforcing a Code of Conduct.}
}
@inproceedings{Bacc2013,
author = {Alberto Bacchelli and Christian Bird},
title = {Expectations, Outcomes, and Challenges of Modern Code Review},
booktitle = {Proc.\ International Conference on Software Engineering},
month = {May},
year = {2013},
url = {http://research.microsoft.com/apps/pubs/default.aspx?id=180283},
note = {FIXME}
}
@article{Beck2016,
author = {Brett A. Becker and Graham Glanville and Ricardo Iwashima and Claire McDonnell and Kyle Goslin and Catherine Mooney},
title = {Effective Compiler Error Message Enhancement for Novice Programming Students},
journal = {Computer Science Education},
volume = {26},
number = {2-3},
pages = {148--175},
year = {2016},
month = {Jul},
publisher = {Informa {UK} Limited},
doi = {10.1080/08993408.2016.1225464},
link = {https://doi.org/10.1080/08993408.2016.1225464},
local = {becker-2016-error-message-enhancement.pdf},
note = {Reports that improved error messages helped novices learn faster.}
}
@misc{Brai2018,
title = {On Testing Machine Learning Programs},
author = {Houssem Ben Braiek and Foutse Khomh},
year = {2018},
howpublished = {https://arxiv.org/abs/1812.02257},
note = {Looks at how developers (don't) test machine learning programs.}
}
@inproceedings{Beni2017,
author = {Gal Beniamini and Sarah Gingichashvili and Alon Klein Orbach and Dror G. Feitelson},
title = {Meaningful Identifier Names: The Case of Single-Letter Variables},
booktitle = {Proc.\ 2017 International Conference on Program Comprehension ({ICPC'17})},
year = {2017},
month = {May},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
doi = {10.1109/icpc.2017.18},
link = {https://doi.org/10.1109/icpc.2017.18},
local = {beniamini-2017-single-letter.pdf},
note = {Reports that use of single-letter variable names doesn't affect ability to modify code, and that some single-letter variable names have implicit types and meanings.}
}
@misc{Bern2018,
author = {Gary Bernhardt},
title = {A Case Study in Not Being a Jerk in Open Source},
howpublished = {https://www.destroyallsoftware.com/blog/2018/a-case-study-in-not-being-a-jerk-in-open-source},
year = {2018},
note = {Rewrites a typically abusive message by Linus Torvalds to be less repellant.}
}
@inproceedings{Bett2008,
author = {Nicolas Bettenburg and Sascha Just and Adrian Schr\"{o}ter and Cathrin Weiss and Rahul Premraj and Thomas Zimmermann},
title = {What makes a good bug report?},
booktitle = {Proc.\ 16th {ACM} {SIGSOFT} International Symposium on Foundations of Software Engineering - ({SIGSOFT}'08/{FSE}'16)},
year = {2008},
publisher = {{ACM} Press},
doi = {10.1145/1453101.1453146},
note = {Reports a survey of developers on what makes for a good bug report.}
}
@article{Bink2012,
author = {Dave Binkley and Marcia Davis and Dawn Lawrie and Jonathan I. Maletic and Christopher Morrell and Bonita Sharif},
title = {The Impact of Identifier Style on Effort and Comprehension},
journal = {Empirical Software Engineering},
volume = {18},
number = {2},
pages = {219--276},
year = {2012},
month = {May},
publisher = {Springer Nature},
doi = {10.1007/s10664-012-9201-4},
link = {https://doi.org/10.1007/s10664-012-9201-4},
note = {Reports that reading and understanding code is fundamentally different from reading prose, and that experienced developers are relatively unaffected by identifier style, but beginners benefit from the use of camel case (versus pothole case).}
}
@book{Boll2014,
author = {David Bollier},
title = {Think Like a Commoner: A Short Introduction to the Life of the Commons},
year = {2014},
publisher = {New Society Publishers},
isbn = {0865717680},
link = {https://isbndb.com/book/0865717680},
note = {A short introduction to a widely-used model of governance.}
}
@misc{Borw2013,
author = {Jonathan Borwein and David H. Bailey},
title = {The Reinhart-Rogoff Error---Or, How not to Excel at Economics},
howpublished = {https://theconversation.com/the-reinhart-rogoff-error-or-how-not-to-excel-at-economics-13646},
year = {2013},
note = {Summarizes the now-infamous Reinhart--Rogoff spreadsheet.}
}
@book{Bran1995,
author = {Stewart Brand},
title = {How Buildings Learn: What Happens After They're Built},
publisher = {Penguin USA},
year = {1995},
isbn = {0140139966},
note = {FIXME}
}
@misc{Broc2019,
author = {Jon Brock},
title = {"A love letter to your future self": What scientists need to know about FAIR data},
howpublished = {https://www.natureindex.com/news-blog/what-scientists-need-to-know-about-fair-data},
note = {Accessed November 2019}
}
@book{Broo2016,
author = {Stephen D. Brookfield and Stephen Preskill},
title = {The Discussion Book: 50 Great Ways to Get People Talking},
publisher = {Jossey-Bass},
year = {2016},
isbn = {978-1119049715},
note = {Describes fifty different ways to get groups talking productively.}
}
@book{Brow2007,
author = {Michael Jacoby Brown},
title = {Building Powerful Community Organizations: A Personal Guide to Creating Groups that Can Solve Problems and Change the World},
publisher = {Long Haul Press},
year = {2007},
isbn = {978-0977151806},
note = {A practical guide to creating effective organizations in and for communities.}
}
@article{Brow2018,
doi = {10.1371/journal.pcbi.1006023},
url = {https://doi.org/10.1371/journal.pcbi.1006023},
year = {2018},
month = {Apr},
publisher = {{PLoS}},
volume = {14},
number = {4},
author = {Neil C.C. Brown and Greg Wilson},
title = {Ten Quick Tips for Teaching Programming},
journal = {{PLOS} Computational Biology}
}
@misc{Brown2017,
author = {Titus Brown},
title = {How I learned to stop worrying and love the coming archivability crisis in scientific software},
howpublished = {http://ivory.idyll.org/blog/tag/futurepaper.html},
year = {2017}
}
@incollection{Buck1995,
author = {Jonathan B. Buckheit and David L. Donoho},
title = {{WaveLab} and Reproducible Research},
booktitle = {Wavelets and Statistics},
publisher = {Springer New York},
year = {1995},
pages = {55--81},
doi = {10.1007/978-1-4612-2544-7_5},
note = {An early and influential discussion of reproducible research.}
}
@article{Carr2014,
author = {John Carroll},
title = {Creating Minimalist Instruction},
journal = {International Journal of Designs for Learning},
volume = {5},
number = {2},
year = {2014},
month = {Nov},
publisher = {IUScholarWorks},
doi = {10.14434/ijdl.v5i2.12887},
link = {https://doi.org/10.14434/ijdl.v5i2.12887},
local = {carroll-2014-creating-minimalist.pdf},
note = {A look back on the author's work on minimalist instruction.}
}
@incollection{Cohe2010,
author = {Jason Cohen},
title = {Modern Code Review},
booktitle = {Making Software},
editor = {Andy Oram and Greg Wilson},
publisher = {O'Reilly},
year = {2010},
isbn = {978-0596808327},
note = {FIXME}
}
@book{Cone2016,
author = {Rob Conery},
title = {The Imposter's Handbook},
publisher = {Big Machine, Inc.},
year = {2016},
isbn = {978-0692933039},
note = {FIXME}
}
@book{Csik1991,
author = {Mihaly Csikszentmihalyi},
title = {Flow: The Psychology of Optimal Experience},
publisher = {Harper Perennial Modern Classics},
year = {2008},
isbn = {978-0061339202},
note = {FIXME}
}
@misc{Dieh2018,
author = {Jan Diehm and Amber Thomas},
title = {Pockets},
howpublished = {https://pudding.cool/2018/08/pockets/},
note = {Accessed November 2019}
}
@article{Denn2017,
author = {Peter J. Denning},
title = {Remaining Trouble Spots with Computational Thinking},
journal = {Communications of the {ACM}},
volume = {60},
number = {6},
year = {2017},
month = {May},
pages = {33--39},
doi = {10.1145/2998438},
note = {FIXME}
}
@article{Deve2018,
doi = {10.1371/journal.pcbi.1005963},
url = {https://doi.org/10.1371/journal.pcbi.1005963},
year = {2018},
month = {Mar},
publisher = {{PLoS}},
volume = {14},
number = {3},
author = {Gabriel A. Devenyi and Rémi Emonet and Rayna M. Harris and Kate L. Hertweck and Damien Irving and Ian Milligan and Greg Wilson},
title = {Ten Simple Rules for Collaborative Lesson Development},
journal = {{PLOS} Computational Biology}
}
@article{Dobz1973,
author = {Theodosius Dobzhansky},
title = {Nothing in biology makes sense except in the light of evolution},
journal = {The American Biology Teacher},
month = {Mar},
year = {1973},
link = {https://en.wikipedia.org/wiki/Nothing_in_Biology_Makes_Sense_Except_in_the_Light_of_Evolution},
note = {A forceful statement of the central unifying theme of modern biology.}
}
@article{Faga1976,
author = {Michael E. Fagan},
title = {Design and Code Inspections to Reduce Errors in Program Development},
journal = {IBM Systems Journal},
volume = {15},
number = {3},
pages = {182-211},
year = {1976},
doi = {10.1147/sj.153.0182},
note = {FIXME}
}
@article{Faga1986,
author = {Michael E. Fagan},
title = {Advances in Software Inspections},
journal = {IEEE Transactions on Software Engineering},
volume = {12},
number = {7},
pages = {744-751},
month = {Jul},
year = {1986},
doi = {10.1109/TSE.1986.6312976},
note = {FIXME}
}
@book{Foge2005,
author = {Karl Fogel},
title = {Producing Open Source Software: How to Run a Successful Free Software Project},
year = {2005},
publisher = {O'Reilly Media},
isbn = {0596007590},
link = {http://producingoss.com/},
note = {The definite guide to managing open source software development projects.}
}
@article{Free1972,
author = {Jo Freeman},
title = {The Tyranny of Structurelessness},
journal = {The Second Wave},
volume = {2},
number = {1},
year = {1972},
local = {freeman-1972-tyranny-structurelessness.pdf},
link = {https://www.jofreeman.com/joreen/tyranny.htm},
note = {Points out that every organization has a power structure: the only question is whether it's accountable or not.}
}
@inproceedings{Fucc2016,
author = {Davide Fucci and Giuseppe Scanniello and Simone Romano and Martin Shepperd and Boyce Sigweni and Fernando Uyaguari and Burak Turhan and Natalia Juristo and Markku Oivo},
title = {An External Replication on the Effects of Test-driven Development Using a Multi-site Blind Analysis Approach},
booktitle = {Proc.\ 10th {ACM}/{IEEE} International Symposium on Empirical Software Engineering and Measurement ({ESEM'16})},
year = {2016},
publisher = {{ACM} Press},
doi = {10.1145/2961111.2962592},
link = {https://doi.org/10.1145/2961111.2962592},
note = {The latest in a long line to find that test-driven development (TDD) has little or no impact on development time or code quality.}
}
@article{Fucc2017,
author = {Davide Fucci and Hakan Erdogmus and Burak Turhan and Markku Oivo and Natalia Juristo},
title = {A Dissection of the Test-Driven Development Process: Does It Really Matter to Test-First or to Test-Last?},
journal = {{IEEE} Transactions on Software Engineering},
volume = {43},
number = {7},
month = {Jul},
year = {2017},
doi = {10.1109/tse.2016.2616877},
note = {FIXME}
}
@article{Gawa2007,
author = {Atul Gawande},
title = {The Checklist},
journal = {The New Yorker},
year = {2007},
month = {Dec},
day = {10},
link = {https://www.newyorker.com/magazine/2007/12/10/the-checklist},
nolocal = {true},
note = {Describes the life-saving effects of simple checklists.}
}
@article{Gil2016,
author = {Gil, Yolanda and David, C{\'{e}}dric H. and Demir, Ibrahim and Essawy, Bakinam T. and Fulweiler, Robinson W. and Goodall, Jonathan L. and Karlstrom, Leif and Lee, Huikyo and Mills, Heath J. and Oh, Ji-Hyun and Pierce, Suzanne A. and Pope, Allen and Tzeng, Mimi W. and Villamizar, Sandra R. and Yu, Xuan},
doi = {10.1002/2015EA000136},
journal = {Earth and Space Science},
pages = {388--415},
title = {{Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance}},
url = {http://doi.wiley.com/10.1002/2015EA000136},
volume = {3},
year = {2016}
}
@article{Gold1991,
author = {David Goldberg},
title = {What Every Computer Scientist Should Know About Floating-Point Arithmetic},
journal = {{ACM} Computing Surveys},
year = {1991},
month = {Mar},
publisher = {Association for Computing Machinery ({ACM})},
volume = {23},
number = {1},
doi = {10.1145/103162.103163},
link = {https://doi.org/10.1145/103162.103163},
note = {FIXME}
}
@article{Good2014,
doi = {10.1371/journal.pcbi.1003542},
url = {https://doi.org/10.1371/journal.pcbi.1003542},
year = {2014},
month = {Apr},
publisher = {Public Library of Science ({PLoS})},
volume = {10},
number = {4},
pages = {e1003542},
author = {Alyssa Goodman and Alberto Pepe and Alexander W. Blocker and Christine L. Borgman and Kyle Cranmer and Merce Crosas and Rosanne Di Stefano and Yolanda Gil and Paul Groth and Margaret Hedstrom and David W. Hogg and Vinay Kashyap and Ashish Mahabal and Aneta Siemiginowska and Aleksandra Slavkovic},
title = {Ten Simple Rules for the Care and Feeding of Scientific Data},
journal = {{PLoS} Computational Biology}
}
@book{Gore2014,
author = {Micha Gorelick and Ian Ozsvald},
title = {High Performance Python},
publisher = {O'Reilly Media},
year = {2014},
isbn = {978-1449361594},
note = {A guide to writing efficient numerical code in Python.}
}
@book{Goyv2012,
author = {Jan Goyvaerts and Steven Levithan},
title = {Regular Expressions Cookbook},
edition = {2nd},
publisher = {O'Reilly Media},
year = {2012},
isbn = {978-1449327453},
note = {An exhaustive collection of useful regular expressions in several programming languages}
}
@book{Grue2015,
author = {Steve Gruenert and Todd Whitaker},
title = {School Culture Rewired: How to Define, Assess, and Transform It},
publisher = {ASCD},
year = {2015},
isbn = {978-1416619901},
note = {The source of a much-quoted observation on culture.}
}
@book{Hadd2010,
author = {Steven Haddock and Casey Dunn},
title = {Practical Computing for Biologists},
publisher = {Sinauer Associates},
year = {2010},
isbn = {978-0878933914},
note = {FIXME}
}
@inproceedings{Hann2018,
author = {Christoph Hannebauer and Marc Hesenius and Volker Gruhn},
title = {Does Syntax Highlighting Help Programming Novices?},
booktitle = {Proc.\ 2018 International Conference on Software Engineering ({ICSE'18})},
year = {2018},
publisher = {{ACM} Press},
doi = {10.1145/3180155.3182554},
note = {FIXME}
}
@article{Hart2016,
doi = {10.1371/journal.pcbi.1005097},
url = {https://doi.org/10.1371/journal.pcbi.1005097},
year = {2016},
month = {Oct},
publisher = {Public Library of Science ({PLoS})},
volume = {12},
number = {10},
pages = {e1005097},
author = {Edmund M. Hart and Pauline Barmby and David LeBauer and Fran{\c{c}}ois Michonneau and Sarah Mount and Patrick Mulrooney and Timoth{\'{e}}e Poisot and Kara H. Woo and Naupaka B. Zimmerman and Jeffrey W. Hollister},
title = {Ten Simple Rules for Digital Data Storage},
journal = {{PLOS} Computational Biology}
}
@article{Hekm2017,
author = {David R. Hekman and Stefanie K. Johnson and Maw-Der Foo and Wei Yang},
title = {Does Diversity-Valuing Behavior Result in Diminished Performance Ratings for Non-White and Female Leaders?},
journal = {Academy of Management Journal},
year = {2017},
month = {Apr},
publisher = {Academy of Management},
volume = {60},
number = {2},
pages = {771--797},
doi = {10.5465/amj.2014.0538},
link = {https://doi.org/10.5465/amj.2014.0538},
note = {FIXME}
}
@book{Hock2004,
author = {Roger R. Hock},
title = {Forty Studies that Changed Psychology},
publisher = {Prentice Hall},
year = {2004},
isbn = {978-0131147294},
note = {FIXME}
}
@book{Jans2014,
author = {Jeroen Janssens},
title = {Data Science at the Command Line},
publisher = {O'Reilly Media},
year = {2014},
isbn = {978-1491947852},
note = {How to process data using the Unix shell.}
}
@book{Kern1978,
author = {Brian W. Kernighan and P. J. Plauger},
title = {The Elements of Programming Style},
edition = {Second},
year = {1978},
publisher = {McGraw-Hill},
isbn = {0070342075},
link = {https://isbndb.com/book/0070342075},
note = {An influential early book on how (rather than what) to program.}
}
@book{Kern1981,
author = {Brian W. Kernighan and P. J. Plauger},
title = {Software Tools in Pascal},
publisher = {Addison-Wesley Professional},
year = {1981},
isbn = {978-0201103427},
note = {An early and influential description of tool-based programming.}
}
@book{Kern1983,
author = {Brian W. Kernighan and Rob Pike},
title = {The Unix Programming Environment},
year = {1983},
publisher = {Prentice-Hall},
isbn = {013937681X},
link = {https://isbndb.com/book/013937681X},
note = {An influential early description of Unix.}
}
@book{Kern1988,
author = {Brian W. Kernighan and Dennis M. Ritchie},
title = {The C Programming Language},
edition = {Second},
year = {1988},
publisher = {Prentice-Hall},
isbn = {0131103628},
link = {https://isbndb.com/book/0131103628},
note = {The book that made C a popular programming language.}
}
@book{Kern1999,
author = {Brian W. Kernighan and Rob Pike},
title = {The Practice of Programming},
year = {1999},
publisher = {Addison-Wesley},
isbn = {9788177582482},
link = {https://isbndb.com/book/9788177582482},
note = {A programming style manual written by two of the creators of modern computing.}
}
@book{Lana2017,
author = {Gabriele Lanaro},
title = {Python High Performance},
edition = {2nd},
publisher = {Packt},
year = {2017},
isbn = {978-1787282896},
note = {A guide to writing efficient numerical code in Python.}
}
@book{Lee1962,
author = {Stan Lee},
title = {Amazing Fantasy \#15},
publisher = {Marvel},
year = {1962},
note = {Popularized the phrase, "With great power comes great responsibility."}
}
@book{Lind2008,
author = {Van Lindberg},
title = {Intellectual Property and Open Source: A Practical Guide to Protecting Code},
publisher = {O'Reilly Media},
isbn = {978-0596517960},
year = {2008},
note = {A thorough dive into intellectual property issues related to open source software}
}
@book{Lyon2018,
author = {Dan Lyons},
title = {Lab Rats: How Silicon Valley Made Work Miserable for the Rest of Us},
publisher = {Hachette Books},
year = {2018},
isbn = {978-0316561860},
note = {FIXME}
}
@misc{Maju2019,
title = {Why Software Projects need Heroes (Lessons Learned from 1000+ Projects)},
author = {Suvodeep Majumder and Joymallya Chakraborty and Amritanshu Agrawal and Tim Menzies},
year = {2019},
howpublished = {https://arxiv.org/abs/1904.09954},
note = {FIXME}
}
@book{Mak2006,
author = {Ronald Mak},
title = {The Martian Principles},
publisher = {Wiley},
year = {2006},
isbn = {0471789658},
note = {A short, enjoyable guide to software architecture from someone whose code had to deal with Mars.}
}
@article{Marw2018,
author = {Ben Marwick and Carl Boettiger and Lincoln Mullen},
title = {Packaging data analytical work reproducibly using R (and friends)},
journal = {PeerJ Preprints},
year = {2018},
volume = {6},
doit = {10.7287/peerj.preprints.3192v2},
note = {Describes a simpler project layout scheme.}
}
@misc{Meil2015,
doi = {10.3886/E17507V2},
url = {http://www.openicpsr.org/openicpsr/project/100049/version/V2/view},
author = {Stephen Meili},
title = {Do Human Rights Treaties Help Asylum-Seekers: Findings from the U.K.},
publisher = {ICPSR - Interuniversity Consortium for Political and Social Research},
year = {2016}
}
@article{Mich2015,
doi = {10.1371/journal.pcbi.1004525},
url = {https://doi.org/10.1371/journal.pcbi.1004525},
year = {2015},
month = {Oct},
publisher = {Public Library of Science ({PLoS})},
volume = {11},
number = {10},
pages = {e1004525},
author = {William K. Michener},
title = {Ten Simple Rules for Creating a Good Data Management Plan},
journal = {{PLOS} Computational Biology}
}
@article{Mill1956,
author = {George A. Miller},
title = {The Magical Number Seven, Plus or Minus Two: Some Limits on Our Capacity for Processing Information},
journal = {Psychological Review},
volume = {63},
number = {2},
pages = {81--97},
year = {1956},
publisher = {American Psychological Association ({APA})},
doi = {10.1037/h0043158},
note = {FIXME}
}
@article{Miller2006,
author = {Miller, Greg},
doi = {10.1126/science.314.5807.1856},
journal = {Science},
number = {5807},
pages = {1856--1857},
title = {{A scientist's nightmare: Software problem leads to five retractions}},
volume = {314},
year = {2006}
}
@article{Mina1986,
author = {Anne Minahan},
title = {Martha's Rules},
journal = {Affilia},
volume = {1},
number = {2},
pages = {53--56},
month = {Jun},
year = {1986},
publisher = {{SAGE} Publications},
doi = {10.1177/088610998600100206},
note = {Describes a lightweight set of rules for consensus-based decision making.}
}
@article{Moreno2016,
author = {Moreno-S{\'{a}}nchez, Isabel and Font-Clos, Francesc and Corral, {\'{A}}lvaro},
title = {{Large-scale analysis of Zipf's Law in english texts}},
journal = {{PLoS ONE}},
volume = {11},
number = {1},
pages = {e0147073},
month = {Jan},
year = {2016},
doi = {10.1371/journal.pone.0147073},
link = {https://dx.plos.org/10.1371/journal.pone.0147073}
}
@article{Mori2012,
author = {Andrew Morin and Jennifer Urban and Piotr Sliz},
journal = {{PLoS} Computational Biology},
publisher = {Public Library of Science ({PLoS})},
title = {A Quick Guide to Software Licensing for the Scientist-Programmer},
year = {2012},
month = {Jul},
volume = {8},
number = {7},
link = {https://doi.org/10.1371/journal.pcbi.1002598},
doi = {10.1371/journal.pcbi.1002598},
note = {A short introduction to software licensing for non-specialists.}
}
@article{Nath2003,
author = {Mitchell J. Nathan and Anthony Petrosino},
title = {Expert Blind Spot Among Preservice Teachers},
journal = {American Educational Research Journal},
volume = {40},
number = {4},
pages = {905--928},
month = {Jan},
year = {2003},
doi = {10.3102/00028312040004905},
note = {FIXME}
}
@article{Nobl2009,
author = {William Stafford Noble},
title = {A Quick Guide to Organizing Computational Biology Projects},
journal = {{PLoS} Computational Biology},
volume = {5},
number = {7},
month = {Jul},
year = {2009},
doi = {10.1371/journal.pcbi.1000424},
link = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424},
note = {How to organize a small to medium-sized bioinformatics project.}
}
@article{Nust2020,
author = {Daniel N{\"u}st and Vanessa Sochat and Ben Marwick and Stephen Eglen and Tim Head and Tony Hirst and Benjamin Evans},
title = {Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science},
year = {2020},
doi = {10.31219/osf.io/fsd7t},
publisher = {OSF Preprints}
}
@article{Patil2016,
author = {Prasad Patil and Roger D. Peng and Jeffrey T. Leek},
title = {A statistical definition for reproducibility and replicability},
year = {2016},
month = {Jul},
doi = {10.1101/066803},
publisher = {Cold Spring Harbor Laboratory},
}
@article{Pea1986,
author = {Roy D. Pea},
title = {Language-Independent Conceptual ``Bugs'' in Novice Programming},
journal = {Journal of Educational Computing Research},
volume = {2},
number = {1},
pages = {25--36},
year = {1986},
month = {Feb},
publisher = {{SAGE} Publications},
doi = {10.2190/689t-1r2a-x4w4-29j2},
note = {FIXME}
}
@inproceedings{Pere2013,
author = {Santiago {Perez De Rosso} and Daniel Jackson},
title = {What's Wrong With Git?},
booktitle = {Proc.\ 2013 {ACM} International Symposium on New Ideas, New Paradigms, and Reflections on Programming and Software ({Onward!'13})},
year = {2013},
doi = {10.1145/2509578.2509584},
note = {The first in a series exploring what's wrong with Git.}
}
@inproceedings{Pere2016,
author = {Santiago {Perez De Rosso} and Daniel Jackson},
title = {Purposes, Concepts, Misfits, and a Redesign of Git},
booktitle = {Proc.\ 2016 {ACM} {SIGPLAN} International Conference on Object-Oriented Programming, Systems, Languages, and Applications ({OOPSLA'2016})},
year = {2016},
doi = {10.1145/2983990.2984018},
note = {The second in a series exploring what's wrong with Git.}
}
@inproceedings{Petr2014,
author = {Marian Petre and Greg Wilson},
title = {Code Review For and By Scientists},
booktitle = {Proc.\ Second Workshop on Sustainable Software for Science: Practice and Experience},
year = {2014},
doi = {arXiv:1407.5648},
note = {FIXME}
}
@misc{Quen2018,
author = {Joël Quenneville},
title = {Code Review},
howpublished = {https://github.com/thoughtbot/guides/tree/master/code-review},
year = {2018},
note = {Guidelines for code review}
}
@book{Ray2014,
author = {Eric J. Ray and Deborah S. Ray},
title = {Unix and Linux: Visual QuickStart Guide},
publisher = {Peachpit Press},
year = {2014},
isbn = {978-0321997548},
note = {An excellent general introduction to all things Unix.}
}
@misc{Robi2005,
author = {Evan Robinson},
title = {Why Crunch Mode Doesn't Work: 6 Lessons},
year = {2005},
publisher = {International Game Developers Association ({IGDA})},
howpublished = {http://www.igda.org/articles/erobinson\_crunch.php},
note = {Summarizes research on the effects of overwork and sleep deprivation.}
}
@misc{Sank2018,
author = {Sandya Sankarram},
title = {Unlearning toxic behaviors in a code review culture},
howpublished = {https://medium.freecodecamp.org/unlearning-toxic-behaviors-in-a-code-review-culture-b7c295452a3c},
year = {2018},
note = {What \emph{not} to do in code review.}
}
@inproceedings{Scha2018,
doi = {10.1145/3196321.3196332},
url = {https://doi.org/10.1145/3196321.3196332},
year = {2018},
publisher = {{ACM} Press},
author = {Andrea Schankin and Annika Berger and Daniel V. Holt and Johannes C. Hofmeister and Till Riedel and Michael Beigl},
title = {Descriptive compound identifier names improve source code comprehension},
booktitle = {Proc.\ 26th Conference on Program Comprehension (ICPC'18)}
}
@book{Scop2015,
author = {Anthony Scopatz and Kathryn D. Huff},
title = {Effective Computation in Physics},
publisher = {O'Reilly Media},
year = {2015},
isbn = {978-1491901533},
note = {A comprehensive introduction to scientific computing in Python}
}
@article{Sega2005,
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},
doi = {10.1007/s10664-005-3865-y},
note = {FIXME}
}
@article{Shol2019,
doi = {10.1371/journal.pcbi.1007296},
url = {https://doi.org/10.1371/journal.pcbi.1007296},
year = {2019},
month = {Sep},
publisher = {Public Library of Science ({PLoS})},
volume = {15},
number = {9},
pages = {e1007296},
author = {Dan Sholler and Igor Steinmacher and Denae Ford and Mara Averick and Mike Hoye and Greg Wilson},
editor = {Scott Markel},
title = {Ten simple rules for helping newcomers become contributors to open projects},
journal = {{PLOS} Computational Biology}
}
@book{Smit2011,
author = {Peter Smith},
title = {Software Build Systems: Principles and Experience},
publisher = {Addison-Wesley Professional},
year = {2011},
isbn = {978-0321717283},
note = {A thorough, readable exploration of how software build systems and tools work.}
}
@inproceedings{Stei2014,
author = {Igor Steinmacher and Igor Scaliante Wiese and Tayana Conte and Marco Aur{\'{e}}lio Gerosa and David Redmiles},
title = {The Hard Life of Open Source Software Project Newcomers},
booktitle = {Proc.\ 7th International Workshop on Cooperative and Human Aspects of Software Engineering ({CHASE}/14)},
year = {2014},
doi = {10.1145/2593702.2593704},
note = {FIXME}
}
@article{Tasc2017,
author = {Morgan Taschuk and Greg Wilson},
title = {Ten Simple Rules for Making Research Software More Robust},
journal = {{PLoS} Computational Biology},
publisher = {Public Library of Science ({PLoS})},
volume = {13},
number = {4},
month = {Apr},
year = {2017},
doi = {10.1371/journal.pcbi.1005412},
link = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005412},
note = {A short guide to making research software usable by other people.}
}
@misc{Tier2020,
title = {A Realistic Guide to Making Data Available Alongside Code to Improve Reproducibility},
author = {Nicholas J Tierney and Karthik Ram},
year = {2020},
howpublished = {https://arxiv.org/abs/2002.11626},
note = {FIXME}
}
@article{Trav2010,
author = {V. Javier Traver},
title = {On Compiler Error Messages: What They Say and What They Mean},
journal = {Advances in Human-Computer Interaction},
volume = {2010},
pages = {1--26},
year = {2010},
publisher = {Hindawi Limited},
doi = {10.1155/2010/602570},
note = {FIXME}
}
@misc{Udel2011,
author = {Jon Udell},
title = {Seven Ways to Think Like the Web},
year = {2011},
howpublished = {http://blog.jonudell.net/2011/01/24/seven-ways-to-think-like-the-web/},
note = {FIXME}
}
@techreport{Wald1994,
author = {Jim Waldo and Geoff Wyant and Ann Wollrath and Sam Kendall},
title = {A Note on Distributed Computing},
institution = {IEEE Micro},
year = {1994},
note = {FIXME}
}
@book{Whit1958,
author = {Alfred North Whitehead},
title = {An Introduction to Mathematics},
publisher = {Oxford University Press},
year = {1958},
isbn = {978-0195002119},
note = {FIXME}
}
@misc{Wick2016,
author = {Elizabeth Wickes and Ayla Stein},
title = {Data Documentation Material},
howpublished = {http://hdl.handle.net/2142/91611},
year = {2016}
}
@article{Wick2014,
author = {Hadley Wickham},
title = {Tidy Data},
journal = {Journal of Statistical Software},
volume = {59},
number = {10},
year = {2014},
publisher = {Foundation for Open Access Statistics},
doi = {10.18637/jss.v059.i10},
link = {https://doi.org/10.18637/jss.v059.i10},
note = {The defining paper on tidy data.}
}
@book{Wick2014b,
author = {Hadley Wickham},
title = {Advanced R},
publisher = {Chapman \& Hall/CRC},
year = {2014},
isbn = {978-1466586963},
note = {A deep dive into the R programming language.}
}
@article{Wils2014,
author = {Greg Wilson and D. A. Aruliah and C. Titus Brown and Neil P. Chue Hong and Matt Davis and Richard T. Guy and Steven H. D. Haddock and Kathryn D. Huff and Ian M. Mitchell and Mark D. Plumbley and Ben Waugh and Ethan P. White and Paul Wilson},
journal = {{PLoS} Biology},
publisher = {Public Library of Science},
title = {Best Practices for Scientific Computing},
year = {2014},
month = {Jan},
volume = {12},
number = {1},
doi = {10.1371/journal.pbio.1001745},
link = {https://doi.org/10.1371/journal.pbio.1001745},
note = {Outlines what a mature research software project should look like.}
}
@article{Wils2017,
author = {Greg Wilson and Jennifer Bryan and Karen Cranston and Justin Kitzes and Lex Nederbragt and Tracy K. Teal},
journal = {{PLoS} Computational Biology},
publisher = {Public Library of Science},
title = {Good Enough Practices in Scientific Computing},
year = {2017},
month = {Jun},
volume = {13},
number = {6},
doi = {10.1371/journal.pcbi.1005510},
link = {https://doi.org/10.1371/journal.pcbi.1005510},