2007-2008 Edition
It is the responsibility of those of us involved in today's biomedical research enterprise to translate the remarkable scientific innovations we are witnessing into health gains for the nation… At no other time has the need for a robust, bidirectional information flow between basic and translational scientists been so necessary.
– Elias A. Zerhouni, M.D.,
Director, National Institutes of Health
New England Journal of Medicine, 353:1621, 2005
Translational Bioinformatics is the development of analytic, storage, and interpretive methods to optimize the transformation of increasingly voluminous genetic, genomic, and biological data into diagnostics and therapeutics for medicine.
Topics covered in this course:
Also known as: Computer Science 275
Time: Winter Quarter 2007-2008, Monday and Wednesday 3:30 pm to 4:45 pm
First class: Wednesday, January 9, 2008
Location: Stanford Medical School, Alway M-104 (look for the Alway Building on this map)
Prerequisites: Programming ability at the level of cs106A and familiarity with statistics and biology, or approval of the instructor.
Grading: Grading will be based on four problem sets, midterm exam, final exam, and a final project.
Instructor: Atul Butte, MD, PhD, Assistant Professor of Medicine (Medical Informatics) and Pediatrics abutte@stanford.edu, and two time winner of the American Association for Clinical Chemistry Outstanding Speaker Award. Profile Lab
Teaching Assistants: Marina Sirota msirota@stanford.edu and David Chen dpchen@stanford.edu
Contact: Most questions should be posted to the wiki, on the Q&A page, so that all students can benefit from the answers. Other queries can be directed to biomedin217-win0708-staff@lists.stanford.edu biomedin217-win0708-staff@lists.stanford.edu. The professor or TA will respond as soon as possible.
Office Hours:
This course is designed for:
Required books: None (the course will be taught using recent publications)
Recommended books:
Students should use the Q&A page for discussion and posting questions/answers related to the course and to homeworks. We are experimenting with using this in lieu of a newsgroup.
Readings are linked from each lecture on the schedule page. Expect two to three readings per class as preparation.
Four problem sets: hands-on analysis of data, which start with reproducing the findings in one or two publications given their raw data, then adding a twist.
Problem set coding language policy: Please use the following languages for problem sets: R, MySQL.
Problem set collaboration policy: You can talk with others in the class about this problem set, but you must turn in your own individual work.
Problem set due dates: Problem sets are due at or before 5:00 PM on the due date.
In the second half of the quarter, the students will research, design, and implement a project of similar scope to one of the problem sets. Final presentations will be held on March 20 from 3:30 to 6:30 pm, in Wallenberg Learning Theatre.
Problem Set 1 Due: Fri, Jan 18, 5pm.
Problem Set 2 Due: Fri, Jan 25, 5pm.
Problem Set 3 Due: Fri, Feb 1, 5pm.
Problem Set 4 Due: Fri, Feb 15, 5pm.
Based on the lectures and the readings. Open book. To be held during a special evening session, to be determined.
Based on all the lectures and the readings. Open book. To be held during a class session, to be determined.
Midterms and finals may be graded on a curve. Final grades will be calculated:
| Component | Percent |
|---|---|
| Problem set 1 | 10% |
| Problem set 2 | 10% |
| Problem set 3 | 10% |
| Problem set 4 | 10% |
| Midterm exam | 15% |
| Final exam | 15% |
| Final project | 30% |
| Total | 100% |