Systems Biology

Course Info

Course Number/Code: 9.531J (Fall 2004)
Course Title: Systems Biology
Course Level: Graduate
Offered By: Massachusetts Institute of Technology (MIT)
Department: Physics
Course Instructor(s): Prof. Alexander van Oudenaarden
Course Introduction:
Syllabus Help support MIT OpenCourseWare by shopping at! MIT OpenCourseWare offers direct links to to purchase the books cited in this course. Click on the Amazon logo to the left of any citation and purchase the book from, and MIT OpenCourseWare will receive up to 10% of all purchases you make. Your support will enable MIT to continue offering open access to MIT courses.Overview

The goal of this course is to help students develop a quantitative understanding of the biological function of genetic and biochemical networks. Students will be provided with the essential mathematical tools needed to model network modules, such as biological switches, oscillators, filters, amplifiers, etc. An array of example biological problems that can be successfully tackled with a systems biology approach will be introduced by discussing recent papers on the subject. The intrinsic challenge of this class is that students are coming in with wildly different backgrounds. Read up on your biology or math if needed. Use time in the recitations to help close some of the knowledge gaps and to help you prepare for the homework.

There are three levels of complexity to Systems Biology:

I Systems Microbiology (14 Lectures) 'The cell as a well-stirred biochemical reactor'II Systems Cell Biology (8 Lectures) 'The cell as a compartmentalized system with concentration gradients'III Systems Developmental Biology (3 Lectures) 'The cell in a social context communicating with neighboring cells'


The course notes serve as the text. For good biology reference texts, see:

Alberts, Bruce, et. al. Molecular Biology of the Cell. 4th ed. New York: Garland Science, 2002. ISBN: 9780815332183.

Lodish, Harvey, et al. Molecular Cell Biology. 5th ed. New York: W. H. Freeman and Company, 2003. ISBN: 9780716743668.

Assignments, Exams, and Grading

MATLAB® will be used intensively during the course. Make sure you know or learn how to use it as it is necessary for the problem sets.

There are 5 problem sets and one take home final for the course. The grading breakdown is as follows:

AssIGNMENTSPERCENTAGESProblem set 115%Problem set 215%Problem set 315%Problem set 415%Problem set 515%Final25%