Good enough practices in scientific computing

This course focuses on tools for collaborative scientific writing within the context of reproducible scientific articles. We, therefore, put you into an environment for scientific computing. While we don’t teach a programming language, the provided tools allow you to integrate programming languages such as R or Python within your writing.

The following paper provides recommendations for some of the practices we use in class and puts them into the context of organising research or academic work. It will help you build some of the foundational background knowledge.

  1. Use your browser, the Zotero Connector and Zotero to store the following paper in your personal Zotero library (My Library or a sub-folder at the top left): https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510.
  2. Read Wilson et al. (2017).
  3. Chose one of the recommended practices (Data Management, Software, Collaboration, Project organization, Keeping track of changes, Manuscripts), then:
  4. Come up with a real-world example or scenario where the recommended practice could be applied in your research or academic work.
  5. Be prepared to explain how the recommended practices would improve your research process. This will be in the class setting as part of small discussion group (max 3 people).

References

Wilson, Greg, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K. Teal. 2017. “Good Enough Practices in Scientific Computing.” PLOS Computational Biology 13 (6): e1005510. https://doi.org/10.1371/journal.pcbi.1005510.