This is a short series of interactive lessons introducing Python, with a focus on genomics applications. It is intended for complete beginners -- no prior programming experience is assumed.
The main goal of these lessons is to introduce the bare minimum amount of programming needed to perform common data analysis tasks in genomics (particularly text file parsing). I initially designed these lessons for an introductory genomics course at Penn, where I was limited to only four 50-minute class periods to convey the material. We settled on a format where the students went over the main lesson notebooks at their own pace at home, and then completed the exercises in class with support from the TAs. Some additional material (concepts that are useful but not strictly necessary) was included in a set of "extra material" notebooks for the more motivated students.
I'm providing these notebooks here in the hope that they might be useful for other instructors looking for a way to include an introduction to programming in their course (without taking up half a semester!), as well as individual biologists looking for a quick way to get up and running with writing scripts to process text files.
If you use these notebooks for your class, I'd love to hear about it! Send me an email at sarahmid@mail.med.upenn.edu
For a slightly more in-depth introduction to Python, see my Programming Bootcamp materials.