View source for CDS 270-4, 2010: Bio-Control

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<td align=center><font color='orange' size='+3'>Bio-Control</font></td>
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<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
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* Instructor: [https://www.cds.caltech.edu/~elisa Elisa Franco]
* Faculty sponsor: [[User:Murray|Richard M. Murray]]
* Lectures: Tuesday 11-12PM, Friday 1-2PM, 110 Steele.
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 ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Additional Material
|-
| align=center rowspan=5 | 1 
| colspan=3 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [[ Media:CDS270-4-2010-Week1-1.pdf | Slides]] 
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [[Media:CDS270-4-2010-Week1-2.pdf | Slides]] 
| Papers: [http://www.pnas.org/content/98/4/1364.full Modeling the trp operon] and [http://nar.oxfordjournals.org/cgi/content/short/37/5/e38  Model-based redesign of transcriptional networks]
|-
| colspan=3 | '''Building and analyzing models'''
| align=center rowspan=3 | 2
|- valign=top
| 6 April (T)
| Review of CDS methods for stability and periodic behaviors. [[  | Slides]] 
| [[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Angeli et al. ]]
|-
| 9 April (F)
| Modeling: Stochastic methods, Gillespie algorithm. [[ | Slides]] 
| [[ Papers: [http://pubs.acs.org/doi/pdf/10.1021/j100540a008 Gillespie's fundamental paper] [Journal Club: TBD] ]]
|}

== Course Administration ==

This course is a special topics course in which much of 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...).

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