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

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(Course Schedule)
(Course Schedule)
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| Week || Date || Lecture Topic || Additional Material || Journal Club
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| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
 
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| align=center rowspan=3 | 1  
 
| align=center rowspan=3 | 1  
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| 2 April (F)
 
| 2 April (F)
 
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf  Slides]   
 
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf  Slides]   
| Suggested papers: [http://www.liebertonline.com/doi/pdf/10.1089/10665270252833208 Review on modeling genetic regulatory networks] and  [http://www.pnas.org/content/98/4/1364.full Modeling the trp operon]
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| [http://www.liebertonline.com/doi/pdf/10.1089/10665270252833208 Review on modeling genetic regulatory networks] and  [http://www.pnas.org/content/98/4/1364.full Modeling the trp operon]
 
|[http://nar.oxfordjournals.org/cgi/content/short/37/5/e38  Model-based redesign of transcriptional networks]
 
|[http://nar.oxfordjournals.org/cgi/content/short/37/5/e38  Model-based redesign of transcriptional networks]
 
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| 6 April (T)
 
| 6 April (T)
 
| Review of CDS methods for stability and periodic behaviors.
 
| Review of CDS methods for stability and periodic behaviors.
| Suggested papers: [http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Angeli et al. ]
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|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Angeli et al. ]
 
|NA
 
|NA
 
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| 9 April (F)
 
| 9 April (F)
 
| Modeling: Stochastic methods, Gillespie algorithm.  
 
| Modeling: Stochastic methods, Gillespie algorithm.  
| Suggested papers: [http://pubs.acs.org/doi/pdf/10.1021/j100540a008 Gillespie's fundamental paper]
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| [http://pubs.acs.org/doi/pdf/10.1021/j100540a008 Gillespie's fundamental paper]
| BioControl Reading: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
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| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
 
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Revision as of 17:00, 5 April 2010

CaltechLogoPrimaryOrangeCropped.gif Bio-Control Cdslogo.png
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) Review of CDS methods for stability and periodic behaviors. Angeli et al. NA
9 April (F) Modeling: Stochastic methods, Gillespie algorithm. 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...).