Bio 450/CS 499: Fundamentals of Bioinformatics (Spring 2018)

Instructor: Arron Shiffer (

Office hours: see course website

Tues/Thurs 9:35-10:50 am (3 credit hours) in HEALTH & LEARNING CTR, RM 3102

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 Prerequisites (Bio/CS 499): Bio 181/181L, or instructor consent.

Course Description

Teaches computer scientists and biologists the fundamentals of bioinformatics. This course will introduce important tools and algorithms used in bioinformatics and several topics in detail with the aim of teaching students how to use and evaluate bioinformatics tools, and develop their own bioinformatics pipelines to address biological questions.  

Topics covered will include biological sequence alignment, phylogeny reconstruction, sequence clustering, working with “Next Generation” (i.e., 454 and Illumina) DNA sequencing data, cloud computing, microbial ecology, and human genome analysis. Students will learn to use tools including BLAST, muscle, FastTree, scikit-bio, QIIME, and QIIME2.

Student Learning Expectations/Outcomes for this Course

After taking this course, students should be comfortable with bioinformatics algorithms for database searching, sequence alignment, sequence clustering and phylogenetic reconstruction. Students will have experience with software tools that are used in real-world bioinformatics, will understand how to initiate, perform, carry out and present a bioinformatics experiment, and will understand how to evaluate new bioinformatics tools.

Course Structure/Approach

This course will be focused on lectures, five projects, group presentations, seven brief quizzes, and a final project. Regular in-class time will be scheduled for hands-on work, such as interacting with the IPython interpreter to accomplish computational tasks, identifying the source of erroneous sequence reads from “next-generation” DNA sequencers, and reconstructing phylogeny from sequence data. Projects and reading should be completed by the due date provided on the course schedule.

There will be regular quizzes throughout the semester. These will cover material that was recently presented, and should not be difficult if you are attending class and doing the readings. Quizzing on the homework and reading assignments due the same day is fair game.

This course covers a lot of diverse material, and office hours are your chance to directly interact with the instructors to ensure that you understand the concepts being covered in class. Coming to office hours is also a great way to boost your class participation score.

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, 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 will be assessed primarily through graded material (see Grading System). A small portion of your assessment will be based on participation. This allows us to determine if you understand the material well enough to ask questions and engage in discussion in class and in office hours. We will strive to return all graded materials within seven days. Under some circumstances we may need a little more time. Check with us at any time during the semester on your current participation score.

Grading System

Grading Scale: A: 90-100; B: 80-89; C: 70-79; D: 60-69; F: 0-59. A curve may be applied at the discretion of the instructor.

Late Work: Late assignments will be penalized at -10% per day.

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.