BIOMEDIN 217 (otherwise known as Translational Bioinformatics, or CS 275) will be taught virtually by
Dr. Butte for the 2014-2015 Winter Quarter. There are no in-person lectures this year.
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.
The video lectures for this year will be those given during the 2013-2014 academic year (January to March 2014).
Lectures can be found in the following locations:
The TAs this year are Emily Tsang, Daniel Kim, and Peyton Greenside. If you are taking the class, be sure to sign up for Piazza (http://www.piazza.com) and our Piazza site (http://www.piazza.com/stanford/winter2015/biomedin217).
The TAs will be offering one R/MySQL help session: Friday, January 9th, 1-2PM, LKSC 306
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: Lectures delivered virtually, no in-class sessions
First class: Lectures delivered virtually, no in-class sessions
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.
Biomedin 218: This 2-unit option is intended for medical students who wish to gain familiarity with bioinformatics but do not have enough credit hours to take Biomedin 217. To receive credit for Biomedin 218, students watch the lectures, do the required readings, and write up a title, aims, and abstract for the final project that they present to the class. They do not complete the homeworks or the exams. Biomedin 218 must be taken for credit/no credit and cannot be taken for a letter grade.
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. Students are expected to participate by answering questions posted by their peers. Professor Butte and the TAs will monitor the Piazza forum regularly. For private matters, you can contact us at email@example.com. 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. It will be considered a violation of the Honor Code to share code with other students. This includes posting code on Piazza or hosting code in a public repository (e.g. Github).
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. If you submit after the deadline, you are only allowed one late submission - do not resubmit multiple times!
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 January 7th, Due January 16th 11:59 pm Pacific|
|Problem set 2||10%||Out January 14th, Due January 21nd 11:59 pm Pacific|
|Problem set 3||10%||Out January 21nd, Due January 28th 11:59 pm Pacific|
|Problem set 4||10%||Out February 4th, Due February 11th 11:59 pm Pacific|
|Midterm exam||15%||February 2nd, 6:00 - 7:15 pm||Alway M114|
|Final exam||15%||March 16th, 12:15 - 1:45 pm||Alway M106|
|Final project proposal||5%||Due February 4th, 2015 11:59 pm Pacific|
|Final project report||25%||Due March 13, 2015 11:59 pm Pacific|