BE 150/Bi 250b Winter 2012
Systems Biology  
Instructors

Teaching Assistants

Course Description
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.
BE 150: Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higherlevel circuit properties such as robustness. Organization of transcriptional and proteinprotein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.
Bi 250b: The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higherlevel circuit properties such as robustness. The course will also consider the organization of transcriptional and proteinprotein interaction networks at the genomic scale.
Announcements
 11 Dec 2011: updated syllabus (should be final now)
 19 Nov 2011: added TAs; updated schedule
 2 Oct 2011: web page creation
Textbook
The primary text for the BE 150 and Bi 250b is
[Alon]  U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press, 2006. 
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
[BFS]  D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS. 
The following additional texts and notes may be useful for some students:
[FBS]  K. J. Astrom and R. M. Murray, Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki. 
[Klipp]  Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, Systems biology: A textbook. Wiley, 2009. 
[Strogatz]  Steven Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering. Westview Press, 2001. 
Grading
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.
Collaboration Policy
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.
Lecture Schedule
There will be two 1hour lectures each week, as well as a 1hour recitation section.
Week  Date  Topic  Reading  Homework 
1 
4 Jan 6 Jan MBE/RMM 
Course overview
Recitation section:


2 
9 Jan 11 Jan+ MBE 
Gene circuit dynamics
Recitation sections:


HW #1 
3 
18 Jan* 20 Jan* RMM 
Circuit motifs


HW #2 
4 
23 Jan 25 Jan MBE 
Biological clocks: how to produce oscillations in cells
Background slides on modeling and stability 

HW #3 
5 
30 Jan 1 Feb RMM 
Robustness


HW #4 
6 
6 Feb* 8 Feb RMM 
Noise


HW #5 
7 
13 Feb+ 15 Feb MBE 
Burstiness in gene expression and signalling


HW #6 
8 
22 Feb 24 Feb RMM 
Patterning


HW #7 
9 
27 Feb 29 Feb*+ MBK 
Modeling of complex biological networks (Mary Kennedy) 


10 
5 Mar 7 Mar MBE 
Fine grain patterns


HW #8 