Reading Material
Books
Practical Computing for Biologists
aims to teach scientists of all types essential computational
skills for data analysis. It assumes no pre-requisites other than
motivation, features the most useful tools that can benefit
researchers almost immediately, and explains how to use these
tools together. With a background level of comfort, researchers
can then go on to reap even more benefit from Software Carpentry
and other educational sites and courses.
Contact:
Steve Haddock
Effective Computation in
Physics is a manual of programming and software skills aimed at
researchers in the physical sciences and engineering. This field guide to
effective scientific computing in Python covers: programming in Python,
important Python packages such as NumPy and Pandas, interaction with the
command line, software testing, version control, build systems,
documentation, publishing using LaTeX, how to manage collaborative
software development with GitHub, and even how to license your software.
Contact:
Katy Huff, Anthony Scopatz
Papers
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Jorge Aranda: "Software Carpentry Assessment Report", July 2012.
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John D. Blischak, Emily R. Davenport, and Greg Wilson: "A Quick Introduction to Version Control with Git and GitHub" PLoS Computational Biology, 2016.
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Beth Duckles: "Value of Software Carpentry to Instructors", 2016
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Beth Duckles: "Non-Teaching Instructor Report", 2016
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Belinda Weaver: "*The efficacy and usefulness of Software Carpentry training: a follow-up cohort study.* MPhil Thesis, School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Australia.", 2020
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Matthew Gentzkow and Jesse Shapiro: "Code and Data for the Social Sciences: A Practitioner's Guide.", 2014.
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Jo Erskine Hannay, Hans Petter Langtangen, Carolyn MacLeod, Dietmar Pfahl, Janice Singer, and Greg Wilson: "How Do Scientists Develop and Use Scientific Software?" Proc. 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering, 2009.
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Edmund Hart, Pauline Barmby, David LeBauer, François Michonneau, Sarah Mount, Timothée Poisot, Kara H. Woo, Naupaka Zimmerman, and Jeffrey W Hollister: "Ten Simple Rules for Digital Data Storage" PeerJ PrePrints, 2015.
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Damien Irving: "A minimum standard for publishing computational results in the weather and climate sciences", 2015.
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Christian T. Jacobs, Gerard J. Gorman, and Lorraine Craig: "Experiences with efficient methodologies for teaching computer programming to geoscientists", 2015.
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Julie Libarkin: "Software Carpentry Workshop Evaluation", June 2012.
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William Stafford Noble: "A Quick Guide to Organizing Computational Biology Projects." PLoS Computational Biology, 2009.
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Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin and Juan Antonio Vizcaíno: "Ten Simple Rules for Taking Advantage of Git and GitHub" PLoS Comput Biol 12(7): e1004947, 2016.
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Marian Petre and Greg Wilson: "Code Review For and By Scientists" Proc. 2nd Workshop on Sustainable Software for Science: Practice and Experience, 2014.
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Jory Schossau and Greg Wilson: "Which Sustainable Software Practices Do Scientists Find Most Useful?" Proc. 2nd Workshop on Sustainable Software for Science: Practice and Experience, 2014.
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Ashley Shade and Tracy K. Teal: "Computing Workflows for Biologists: A Roadmap" PLoS Biology, 2015.
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Alexandra Simperler and Greg Wilson "Software Carpentry: Get More Done in Less Time" 2015.
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Tracy K. Teal, Karen A. Cranston, Hilmar Lapp, Ethan White, Greg Wilson, Karthik Ram, and Aleksandra Pawlik: "Data Carpentry: Workshops to Increase Data Literacy for Researchers" International Journal of Digital Curation, 2015.
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Ethan P. White, Elita Baldridge, Zachary T. Brym, Kenneth J. Locey, Daniel J. McGlinn, and Sarah R. Supp: "Nine Simple Ways to Make It Easier to (Re)use Your Data" PeerJ PrePrints, 2013.
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Hadley Wickham: "Tidy Data" Journal of Statistical Software, 2013.
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Greg Wilson, D. A. Aruliah, C. Titus Brown, Neil P. Chue Hong, Matt Davis, Richard T. Guy, Steven H. D. Haddock, Kathryn D. Huff, Ian M. Mitchell, Mark D. Plumbley, Ben Waugh, Ethan P. White, and Paul Wilson: "Best Practices for Scientific Computing" PLoS Biology, 2014.
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Greg Wilson: "Software Carpentry: Lessons Learned" F1000 Research, 2014.