8.591J | Fall 2004 | Graduate

Systems Biology


Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session


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:

Problem set 1 15%
Problem set 2 15%
Problem set 3 15%
Problem set 4 15%
Problem set 5 15%
Final 25%

Course Info

As Taught In
Fall 2004
Learning Resource Types
Lecture Notes
Problem Sets