This is the material for the University of Arizona's BE434/535 "Biosystems Analytics" course taught be Dr. Bonnie Hurwitz and Ken Youens-Clark. The material is divided primarily into "lectures" which are covered in class and at home and "assignments" which are due weekly. Each assignment is provided a complete test suite so that you will know when you have achieved the correct result. The "bin" directory contains some handy programs, and the "data" directory is referenced by some of the programs. Under each "lecture" is an "examples" directory containing all the programs referenced in the text so that you can easily execute and copy code.
Essentially this course is most of what I do on a daily basis as professional programmer working in "bioinformatics." I try to cover all the essentials you would need to replace me. The programs are intended to be short and focused on a few ideas so that you can most easily comprehend and steal my code. Further, I provide a "common patterns" section for both bash and Python with just a few lines of code dedicated to some idea like "reading a file" or "sorting a dictionary by keys."
I write the lectures in Markdown format and use pandoc to convert to PDF and EPUB formats.
MIT (see LICENSE)
Ken Youens-Clark [email protected]