Bio 698: Microbiome Bioinformatics with QIIME 2 (Spring 2017)

Professor: Greg Caporaso (

Course website:

Class sessions: Wednesdays 4:00-5:15pm (1 credit hour) in Biology 419

Office hours: see course website

Course schedule: Linked from the course website, this will be updated throughout the semester as we identify areas where we want to focus more or less.

Course Description

This seminar will introduce students to the QIIME 2 microbiome bioinformatics platform, and the daily topics will be driven by student interest. On the first day of the semester, we will discuss what students want to achieve in this seminar, and the course will be structured to meet those goals as much as possible. This can include spending time on the theory of microbiome analysis; working with real data sets on the monsoon cluster to gain experience with QIIME 2; or even developing plugins for QIIME 2 to implement new microbiome analysis methods.

Student Learning Expectations/Outcomes for this Course

After taking this course, students should be comfortable applying QIIME 2 to perform microbiome analysis, and interpreting the results of microbiome analysis.

Course Structure/Approach

This course will be focused on lectures and hands-on work. The specific details will be determined as we define goals for the course.

Required Materials

A computer: You will need access to a computer that can run Google Chrome (or another modern web browser) for this course. If you have a laptop, please get in the habit of bringing it to class.

Course Schedule:

A tentative course schedule is provided at the link above. The schedule will change over the course of the semester as we identify certain areas that we want to spend additional time on. For that reason the outline is provided in a dynamic format. The spreadsheet at the above link will always be the definitive source for the outline, reading assignments, and homework assignments. Check this link regularly!

Assessment of Student Learning Outcomes

You must attend at least fourteen of the seventeen class sessions to pass this seminar. It is expected that you engage in discussion and in-class exercises.

Grading System

Grading Scale: Pass/Fail.

Course Policy

University Policies

The Safe Environment, Students with Disabilities, Institutional Review Board, Academic Integrity, Academic Contact Hour, Classroom Management and Professional Ethics and Code of Conduct policies are available at Students are responsible for reviewing and understanding these policies.