good-enough-practices-for-scientific-computing.bib

@misc{raj2016,
	author = {Arjun Raj},
	title = {From over-reproducibility to a reproducibility wish-list},
	month = {March},
	year = {2016},
	url = {http://rajlaboratory.blogspot.ca/2016/03/from-over-reproducibility-to.html}
}

@misc{brown2015,
	author = {C. Titus Brown},
	title = {How to grow a sustainable software development process},
	month = {June},
	year = {2015},
	url = {http://ivory.idyll.org/blog/2015-growing\--sustainable\--software\--development-process.html}
}

@misc{ffIllinois,
	author = {University of Illinois Library},
	title = {File Formats and Organization},
	url = {http://www.library.illinois.edu/sc/services/data\_management/file\_formats.html}
}

@book{gawande2011,
	author = {Atul Gawande},
	title = {The Checklist Manifesto: How to Get Things Right},
	year = {2011},
	publisher = {Picador},
	isbn = {0312430000}
}

@misc{gentzkow2014,
	author = {Matthew Gentzkow and Jesse M. Shapiro},
	title = {Code and Data for the Social Sciences: A Practitioner's Guide},
	month = {January},
	year = {2014},
	url = {http://web.stanford.edu/~gentzkow/research/CodeAndData.pdf}
}

@article{hart2016,
	author = {Edmund M. Hart and Pauline Barmby and David LeBauer and François Michonneau and Sarah Mount and Patrick Mulrooney and Timothée Poisot and Kara H. Woo and Naupaka Zimmerman and Jeffrey W. Hollister},
	title = {Ten simple rules for digital data storage},
	journal = {PLoS Computational Biology},
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}

@book{hunt1999,
	author = {Andrew Hunt and David Thomas},
	title = {The Pragmatic Programmer},
	publisher = {Addison-Wesley},
	year = {1999},
	isbn = {978-0201616224}
}

@misc{kitzes2016,
	author = {Justin Kitzes},
	title = {Reproducible Workflows},
	year = {2016},
	url = {http://datasci.kitzes.com/lessons/python/\-reproducible\_workflow.html}
}

@book{laurent2004,
	author = {Andrew M. {St.~Laurent}},
	title = {Understanding Open Source and Free Software Licensing},
	publisher = {O'Reilly Media},
	year = {2004},
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	chapter = {2},
	url = {http://www.oreilly.com/openbook/osfreesoft/book/}
}

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

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

@article{miller1956,
	author = {G. A. Miller},
	title = {The Magical Number Seven, Plus or Minus Two: Some Limits on Our Capacity for Processing Information},
	journal = {Psychological Review},
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	number = {2},
	pages = {81–97},
	year = {1956},
	doi = {doi:10.1037/h0043158m}
}

@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}
}

@inproceedings{petre2014,
	author = {Marian Petre and Greg Wilson},
	title = {Code Review For and By Scientists},
	booktitle = {Proc.\ WSSSPE 2014},
	editor = {Daniel Katz},
	year = {2014}
}

@article{sandve2013,
	author = {G. K. Sandve and A. Nekrutenko and J. Taylor and E. Hovig},
	title = {Ten Simple Rules for Reproducible Computational Research},
	journal = {PLoS Computational Biology},
	volume = {9},
	number = {10},
	year = {2013},
	doi = {doi:10.1371/journal.pcbi.1003285}
}

@article{shade2015,
	author = {Ashley Shade and Tracy K. Teal},
	title = {Computing Workflows for Biologists: A Roadmap},
	journal = {PLoS Biology},
	year = {2015},
	month = {November},
	doi = {doi:10.1371/journal.pbio.1002303}
}

@article{steinmacher2015,
	author = {Igor Steinmacher and {Marco Aur{\eacute}lio} {Graciotto Silva} and {Marco Aur{\acute}lio} Gerosa and David F. Redmiles},
	title = {A Systematic Literature Review on the Barriers Faced by Newcomers to Open Source Software Projects},
	journal = {Information and Software Technology},
	volume = {59},
	number = {C},
	month = {March},
	year = {2015},
	doi = {10.1016/j.infsof.2014.11.001}
}

@article{white2013,
	author = {E. P. White and E. Baldridge and Z. T. Brym and K. J. Locey and D. J. McGlinn and S. R. Supp},
	title = {Nine Simple Ways to Make It Easier to (Re)use Your Data},
	journal = {Ideas in Ecology and Evolution},
	volume = {6},
	number = {2},
	year = {2013},
	doi = {doi:10.4033/iee.2013.6b.6.f}
}

@misc{wickes2015,
	author = {Elizabeth Wickes},
	title = {Comment on "Metadata"},
	month = {November},
	year = {2015},
	url = {https://github.com/swcarpentry/good\--enough\--practices\--in\--scientific\--computing/issues/3\#issuecomment-157410442}
}

@article{wickham2014,
	author = {Hadley  Wickham},
	title = {Tidy Data},
	journal = {Journal of Statistical Software},
	volume = {59},
	number = {1},
	year = {2014},
	issn = {1548-7660},
	pages = {1--23},
	doi = {10.18637/jss.v059.i10},
	url = {https://www.jstatsoft.org/index.php/jss/article/view/v059i10}
}

@article{wilson2014,
	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 = {January},
	volume = {12},
	pages = {e1001745},
	number = {1},
	doi = {10.1371/journal.pbio.1001745}
}