This is the GitHub website for the course Practical Computing Skills for Biologists, a 2-credit online-only course at Ohio State University during the Spring semester of 2021. The course is taught as a section of Current Topics in Plant Pathology (PLNTPTH8300) by Jelmer Poelstra from the MCIC.
As datasets have rapidly grown larger in biology, coding has been recognized as an increasingly important skill for biologists. Yet in fact, basic coding skills and “computational thinking” are highly beneficial for any scientist, paving the way for more efficient, robust, and reproducible research.
In this course, students will gain hands-on experience with a set of general and versatile tools for day-to-day work with data sets small and large alike. The course’s focus is on foundational skills such as working in the Unix shell, coding in Python, organizing, documenting, version-controlling and sharing research, submitting jobs to a compute cluster, and building flexible workflows. Taken together, this will allow students to reproduce their own work, and have others reproduce their work, with as little as a single command.
See also the page Practical course information and the full syllabus (PDF).
Primary: Allesina S, Wilmes M (2019). Computing Skills for Biologists. Princeton UP.
Secondary: Buffalo V (2015). Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. O’Reilly Media, Inc.
If you are a student in this course, you should also refer to the CarmenCanvas site for this course.1
You can always find the link to the CarmenCanvas site in the top-right corner of this site by clicking on the graduation cap icon.↩︎
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".