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Computational Systems Biology
BME 211, Spring 2012

Home | Office Hours | Schedule | Assignments | DREAM | IMPROVER

Course Information

Location/Time: PSB 305 , Tues/Thurs: 8-9:45 am

Information and Handouts

·        Office Hours

·        Schedule of lectures

·        Homework assignments

·        Dialogue in Reverse Engineering Assessment and Methods (DREAM) Challenge

·        Frequently Asked Questions

Course Description & Objectives

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:

A key component of the course is participation in the DREAM or IMPROVER 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 ONE). You will form a team to either implement an existing winning method or develop your own method


BME 100


Grades are based on 2 (or 3) homework assignments (30%), a review of a winning algorithm from the DREAM competition (10%), a mid-term exam (20%), a final exam (20%), and a final project (20%). The homework assignments require some programming.


Review of Prior Art

You'll be responsible for hosting a 20-minute presentation covering a leading algorithm (i.e. in the top 5) submitted to the DREAM competition. In your review, you will be evaluated on your ability to clearly describe the mathematical and/or computational formulation that distinguish the winning algorithm. 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 may work with a partner. 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.

DREAM Projects

You may work in teams of 1-3 people on the final programming project. You will compete in a gene function prediction challenge. Each team will create a program that assigns gene function categories to genes with associated molecular fingerprints. Programming projects will be graded on a ~5 page writeup of the methods, if the code executes properly and performs competitively, and a 20 minute oral presentation that describes the team's unique approach.


Working in Groups

You may also work with your teammates on homework assignments.  Please include the names of all teammates 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.

Late Policy

Each student can use a total of 7 late days on all homework assignments. A maximum of 3 late days can be used on any one assignment. No late days can be used for the mid-term, final, topical presentations, or final programming projects.


Extra Credit

Eextra credit is available for scribing lectures. You can earn as much as 5% extra credit. The amount depends on the quality of the scribed notes. Notes should be written in LaTeX, contain relevant figures from the lecture, and follow the instructions on the Scribing Instructions page



We strongly encourage students to come to office hours.

Please do not e-mail the instructors with grading questions. If you want us to explain why we took points off, you can talk to us after class or during office hours. If you want a re-grade, please write an explanation and hand the homework and the explanation to one of the instructors during office hours or after class.

If you qualify for classroom accommodations because of a disability, please get an Accommodation Authorization from the Disability Resource Center (DRC) and submit it to me in person outside of class (e.g., office hours) within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY), or the DRC website for more information on the requirements and/or process.


Textbook Information

There are no required textbooks this year.

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