Difference between revisions of "CDS 270-4, 2010: Bio-Control"

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| 9 April (F)
| 9 April (F)
| Modeling: Stochastic methods, Gillespie algorithm.  
| Modeling: Stochastic methods, Gillespie algorithm. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-2.pdf  Slides]
|  [http://pubs.acs.org/doi/pdf/10.1021/j100540a008 Gillespie's fundamental paper]
|  [http://pubs.acs.org/doi/pdf/10.1021/j100540a008 Gillespie's fundamental paper]
|  [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|  [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]

Revision as of 19:46, 10 April 2010

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Spring 2010

NOTE: The Friday lectures will include discussing a paper related to the week topic. Papers will be announced about a week prior to the discussion.

Course Schedule

Week Date Lecture Topic Papers considered in class BioControl Journal Club
1 Introduction, Modeling biological systems
29 March (M) Course overview and objectives, layers of control of gene expression. Slides Syllabus NA
2 April (F) Modeling: Ordinary Differential Equations. Slides Review on modeling genetic regulatory networks and Modeling the trp operon Model-based redesign of transcriptional networks
2 Building and analyzing models
6 April (T) CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. Slides Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems , Negative Autoregulation Speeds the Response Times of Transcription Networks NA
9 April (F) Modeling: Stochastic methods, Gillespie algorithm. Slides Gillespie's fundamental paper Defining bifurcations in stochastic systems

Course Administration

This course is a special topics course in which the lecture material has been prepared by a senior graduate student. The class is P/F only and there is no required homework and no midterm or final exam. Students will be required to work on an individual or team course project.

Course Project

Project proposals are due at 5pm on the last day of the Midterm examination period (May 4) and are due by 5pm on the last day of the final examination period (June 7). Project theme: select a cellular regulatory mechanism, define a list of important features of the system, come up with a modeling framework and carry out an analysis of its properties (e.g. stability, robustness, modularity...).