Practical Computing Skills for Biologists: a graduate-level course in SP21

Nov. 12, 2020
A skilled Bobolink


Spring 2021 PLNTPTH 8300 – Current Topics in Plant Pathology
Practical Computing Skills for Biologists

  • Instructor: Dr. Jelmer Poelstra (, Molecular and Cellular Imaging Center, Wooster campus
  • 14-week course; 2 credits. 
  • Online, but class meets synchronously via Zoom, TuTh 3:55 PM - 4:50 PM.
  • Sign up for Class number 35953 (Current Topics in Plant Pathology).
  • This is a graduate-level course. Undergraduates who wish to take this course should contact the instructor for permission to enroll in PLNTPTH 4193 - Individual Studies, Class number 35954.
  • Class capacity: 15.
  • Full syllabus (PDF, last updated 2020-12-22)

Course structure: The first Zoom session of each week will generally contain a lecture and the second session will be a coding lab. We will do participatory live coding across both sessions and will occasionally have short student presentations and discussions of assignments.

Course description: As datasets have rapidly grown larger in biology, coding has become an increasingly important skill for biologists. Often overlooked, however, is that basic coding skills and "computational thinking" are highly beneficial for any scientist, as they pave the way for more efficient and reproducible research. In this course, you will gain hands-on experience with a set of general and versatile tools that I think everyone should be using in their day-to-day work, with data sets small and large alike.

You will work at the command line in the UNIX shell and with Python, learn to use version control with git and to share your (home)work through Github, and finally, to build workflows that reproduce a complex analysis — not quite with the click of a mouse, but by typing a single command.

Prerequisites / co-requisites / exclusions: None. No prior coding experience is needed for this course. If you have never opened a terminal before, or never coded in any language, I recommend but do not require that you start reading or practising a bit before the course starts. A good place to start is the textbooks listed in the class syllabus, which are available online in the OSU Library Catalog. Don't hesitate to contact me if you have any questions.

For more information, have a look at the syllabus or contact Jelmer Poelstra.