Difference between revisions of "BE 150/Bi 250b Winter 2013"
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* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358362, 2006.  * [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358362, 2006.  
BE 150:  BE 150:  
−  * {{be150 pdfwi12caltech/bfsclass  +  * {{be150 pdfwi12caltech/bfsclassstochastic_05Jan13.pdfBFS, Ch 4}}: Stochastic behavior 
−  * {{be150 pdfwi12caltech/bfsclass  +  * {{be150 pdfwi12caltech/bfsclassrandom_05Jan13.pdfBFS, App B}}: Probability and random processes (optional) 
 rowspan=2  HW 5   rowspan=2  HW 5  
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* Note: these notes are being written and will be updated during the course  * Note: these notes are being written and will be updated during the course  
* The public version is missing some copyrighted figures. These are available in the class version.  * The public version is missing some copyrighted figures. These are available in the class version.  
−  * Class version (Caltech access only, 5 Jan 2013): {{be150 pdfwi13caltech/bfsclassfrontmatter_05Jan13.pdfTOC}}, {{be150 pdfwi13caltech/bfsclassintro_05Jan13.pdfCh 1}}, {{be150 pdfwi13caltech/bfsclasscoreproc_05Jan13.pdfCh 2}}, {{be150 pdfwi13caltech/bfsclassdynamics_05Jan13.pdfCh 3}}, {{be150 pdf  +  * Class version (Caltech access only, 5 Jan 2013): {{be150 pdfwi13caltech/bfsclassfrontmatter_05Jan13.pdfTOC}}, {{be150 pdfwi13caltech/bfsclassintro_05Jan13.pdfCh 1}}, {{be150 pdfwi13caltech/bfsclasscoreproc_05Jan13.pdfCh 2}}, {{be150 pdfwi13caltech/bfsclassdynamics_05Jan13.pdfCh 3}}, {{be150 pdfwi13caltech/bfsclassstochastic_05Jan13.pdfCh 4}}, {{be150 pdfwi13caltech/bfsclasschemotaxis_05Jan13.pdfSec 5.2}}, {{be150 pdfwi13caltech/bfsclassrandom_05Jan13.pdfApp B}}, {{be150 pdfwi13caltech/bfsclassbackmatter_05Jan13.pdfRefs}} 
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Revision as of 05:50, 4 February 2013
Systems Biology  
Instructors

Teaching Assistants


This is the course homepage for BE 150/Bi 250b for Winter 2013. This page contains all of the information about the material that will be covered in the class, as well as links to the homeworks and information about the course projects and grading. 
Lecture Schedule
There will be 23 onehour lectures each week, as well as occasional onehour tutorials, recitations or journal club.
Week  Date  Topic  Reading  Homework 
1 
7 Jan 9 Jan+ MBE/RMM 
Course overview, gene circuit dynamics
Recitation section:

Bi 250b:
BE 150: 
HW1 
2 
13 Jan 15 Jan MBE 
Circuit motifs
Recitation (17 Jan): sample problems

Bi 250b:
BE 150:

HW2 
3 
23 Jan* 25 Jan RMM 
Biological clocks: how to produce oscillations in cells
No recitation 
BE 150:

HW3 
4 
28 Jan 30 Jan RMM 
Robustness
Recitation (1 Feb): sensitivity analysis

BE 150:

HW4 
1 Feb  Course projects posted. Instructions:
 
5 
4 Feb 6 Feb MBE 
Noise

BE 150:

HW 5 
6 
11 Feb 13 Feb+ MBE 
Burstiness in gene expression and signalling

 
20 Feb+* 
Course project discussion with TAs  
7 
22 Feb* 25 Feb RMM 
Patterning


HW 6 
8 
27 Feb 1 Mar RMM 
Fine grain patterns

 
9 
4 Mar 6 Mar 8 Mar 
Project presentations  
10 
11 Mar 13 Mar 
Project presentations 
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.
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) 
The following additional texts and notes may be useful for some students:
[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. 
Course project
All students enrolled in the course will be expected to participate in a course project, which will be assigned after the fourth week of class. Course projects will generally consist of reviewing one or more papers on a topic that makes use principles and tools discussed in the course. Each project will be undertaking by two students (nominally one from BE 150, one from Bi 250). Topic suggestions are posted here. Students can also propose their own topic of student by preparing a 12 page proposal and submitting this to the instructors no later than 4 Feb for consideration.
Course project timeline:
 1 Feb (Fri): course projects posted on home page and announced in class
 4 Feb (Mon): course project preferences due
 6 Feb (Wed): project assignments available
 20 Feb (Wed): discussion of course projects with TAs and others
 413 Mar: course project presentations. 1520 minutes per project + 510 minutes questions.
Course preference instructions
 Each student should send email no later than 4 Feb (Mon) with the following information
 Course: (BE 150/Bi 250b/Audit)
 Up to three project preferences (use titles from project listings)
 Optional preferred partner (both students should email identical preferences)
 Students will work in pairs, with most teams consisting of a BE 150 student and a Bi 250b student
 To propose your own project, please email a 12 page proposal in addition to at least two project preferences selected from the list of course projects
Grading
The ﬁnal grade will be based on biweekly homework sets (75%) and a course project (25%). The homework will be due in class approximately 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. The class project will be assigned and the end of the 5th week of instruction and project presentations will be scheduled for the last two weeks of class.
Collaboration Policy
Collaboration on homework assignments and the course project 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. Your course project presentation to properly acknowledge all source materials.