BME 211: Computational Systems Biology

Course Overview

The course will cover machine-learning methods relevant for the analysis of molecular biology experiments. The exercises and examples are motivated from problems that arise during the analysis of high-throughput, genome-wide or genome-scale studies. Therefore, you should be fluent in a programming language and have taken basic molecular biology courses. The course involves the following major components:

  • Analyzing high-throughput datasets
  • Implementing and evaluating unsupervised, supervised, and semi-supervised algorithms.
  • Implementing a method to participate in a DREAM competition.
  • Presenting the results of the team project in a 5 page Methods paper and a two 15-minute presentations describing the results and details of the method.
A key component of the course is participation in the DREAM challenge. The Dialogue on Reverse Engineering Assessment and Methods (DREAM) is a ~yearly conference posts challenges for bioinformatics researchers to try to solve. Every year, teams compete in a double-blinded fashion and their performance is ranked. Winners are invited to submit manuscripts describing their approach in a special journal issue (e.g. PLoS or Nat Biotech). You will form a team to either implement an existing method or develop your own.


BME 205; Undergraduates may take course if they have completed BME 205, Computer Science 101 and any upper-division molecular biology or biochemistry course, such as Biochemistry 100 or 100A. 


Grades are based on 2 homework assignments (30%), two quizzes (20%), a DREAM abstract (5%), a DREAM background presentation (15%), a DREAM final results presentation (15%), and a final methods writeup (15%). The homework and DREAM project require some programming.


DREAM Projects

You may work in teams of 1-3 people on the final programming project. Each team will create a program to compete in the DREAM competition. Programming projects will be graded on a 5 page writeup of the methods, and a final presentation after submitting to a round of evaluation.

You'll be responsible for giving a 15-minute presentation covering a leading algorithm you are considering implementing for the DREAM competition. In your review, you will be evaluated on your ability to clearly describe the mathematical and/or computational formulation. You will also be graded on how well you answer questions, promote discussion, your overall organization, and how well you participate in asking questions when others are presenting. You will present with your selected team. You will be required to turn in any visual aids you can (e.g. powerpoint slides). If you give a "chalk-talk," you will need to provide handouts that include an outline and any equations you present. 

Working with Partners

You may work with a partner on homework assignments.  Please include the name of your partner on all documents that you turn in. (Note: If you do not have much programming experience, team up with someone who does!). If you work in a team, please provide a short paragraph outlining the contributions of each member. 

Classroom accommodations for disabilities

"UC Santa Cruz is committed to creating an academic environment that supports its diverse student body. If you are a student with a disability who requires accommodations to achieve equal access in this course, please submit your Accommodation Authorization Letter from the Disability Resource Center (DRC) to me privately during my office hours or by appointment, preferably within the first two weeks of the quarter. At this time, we would also like us to discuss ways we can ensure your full participation in the course. We encourage all students who may benefit from learning more about DRC services to contact DRC by phone at 831-459-2089 or by email at"

Late Policy

Each student can use a total of 3 late days on homework or the final 5 page report. After that, 10% is taken off for each day. 0% if the work is turned in more than a week late.