Wednesday, August 22, 2012

Intro Bioinfo Theory Course Example Release 1


What is the purpose of this release?

It illustrates the kind of content I am releasing as open source course materials, to bootstrap an open source bioinformatics teaching materials consortium where instructors can selectively use, modify and share materials for their own teaching. If you're interested in using these materials or participating in such a consortium, I invite you to contribute your thoughts or feedback in the Comments section below, or by email to

What is this?

This is a snapshot of the reading, lectures, homework, projects, practice exams, and exams from my 2011 Bioinformatics Theory course offered separately as a CS undergrad course and Bioinformatics graduate course (different exams; separate graduate term project). The course uses a core set of simple genetics, sequence analysis and phylogeny problems to teach fundamental principles that arise in virtually all bioinformatics problems. This course is not for students who want to learn to use existing methods (e.g. BLAST) but rather for students who might in the future want to invent new bioinformatics analyses. It emphasizes statistical inference, graph models and computational complexity.

Note: this is not a standard lecture course; approximately half the class time was devoted to in-class concept tests, where the class was presented with a question that tests conceptual understanding. Students answered concept tests using an open-response (i.e. not multiple choice) in-class response system by typing answers on their laptops or smartphones. We then discussed our answers using Peer Instruction methods, and I analyzed all the individual students' answers in detail; at the subsequent class, I went through each of conceptual errors the students made for each question. I have written approximately 200 concept tests for a wide range of statistical and computational concepts relevant to bioinformatics, and a wide variety of "problems-to-work" (i.e. more conventional homework problems) covering the same material. I am making all of these materials and software available as open source; this is the first step in that release process.