BIOMEDIN 217 (otherwise known as Translational Bioinformatics, or CS 275) will be taught in person by
Dr. Butte for the 2012-2013 Spring Quarter.
Class meeting days/time/location: Monday/Wednesday, 2:15-3:30PM in Gates B03
Stanford students can register for the class using Axess (https://axess.stanford.edu). Remote SCPD students can register at http://scpd.stanford.edu or call SCPD at 650-725-3016 and ask for student services.
Lectures will be recorded and can be found in the following locations:
The TAs this year are Brian Maples firstname.lastname@example.org and Luke Yancy, Jr. email@example.com. If you are taking the class, be sure to sign up for Piazza (http://www.piazza.com), our Piazza site (http://piazza.com/class#spring2013/biomedin217), and subscribe to our blog (http://bmi217translationalbioinformatics.blogspot.com/).
The TAs will be offering one R/MySQL help-session:
R statistical language/MySQL TA session: Wednesday, April 3rd, 2:15-3:30, Gates B03 (normal class time/location)
TA Sessions will be recorded for SCPD students.
We will require four problem sets, one midterm exam, one final exam, and a final project.
Welcome to BMI 217! – Atul Butte
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: 2:15-3:30PM, Spring Quarter 2012-2013, lectures delivered live
First class: April 1, 2013
Location: Gates B03
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, Associate Professor of Pediatrics and, by courtesy, Medicine and Computer Science, and two time winner of the American Association for Clinical Chemistry Outstanding Speaker Award. Profile Lab
Contact: Most questions should be posted to the piazza group page, so that all students can benefit from the answers. Professor Butte or the TAs will respond as soon as possible. For private matters, you can contact us at firstname.lastname@example.org. Please do not email the TAs individually unless you specifically have a question for just one of them.
This course is designed for:
Required books: None (the course will be taught using recent publications)
Students should use the piazza group page. To access it, please first subscribe to the BIOMEDIN217 class in http://www.piazza.com. After that this link will direct you to the group. Use it for discussion and posting questions/answers related to the course and problem sets.
Readings are linked from each lecture on the schedule page. Expect two to three readings per video lecture 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: You must use R and/or MySQL for the problem sets.
Problem set collaboration policy: You cannot talk with others in the class about the problem sets, and you must turn in your own individual work.
Problem set due dates: Problem sets are due at or before 11:59 PM on the due date. You are allotted 4 free late days total this quarter, so use them wisely for the four problem sets. After that, 20% off your grade per day late. Not using all your late days may influence your final grade (bump up) if borderline.
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.
Based on the lectures and the readings. Open book.
Based on all the lectures and the readings. Open book.
Midterms and finals may be graded on a curve. Final grades will be calculated:
|Problem set 1||10%||Out April 3rd, Due April 10th 11:59 pm Pacific|
|Problem set 2||10%||Out April 10th, Due April 17th 11:59 pm Pacific|
|Problem set 3||10%||Out April 17th, Due April 24th 11:59 pm Pacific|
|Problem set 4||10%||Out May 1st, Due May 8th 11:59 pm Pacific|
|Midterm exam||15%||April 24th, 2:15 - 3:30 pm||Gates B03|
|Final exam||15%||June 5th, 2:15 - 3:30 pm||Gates B03|
|Final project proposal||5%||Due May 1, 2013 11:59 pm Pacific|
|Final project report||25%||Due June 11, 2013 11:59 pm Pacific|