Murray Wiki - User contributions [en]

Tal Danino, Jan 2011

2011-01-24T19:36:38Z

Elisa: /* Agenda */

Tal Danino will be visiting Caltech on 26 Jan 2011 (Wed). Sign up for a time to meet with him below.

=== Agenda ===

{{agenda begin}}
{{agenda item|10:00|Richard Murray, 109 Steele}}
{{agenda item|10:45|Elisa Franco}}
{{agenda item|11:30|Frances Arnold}}
{{agenda item|12:00p|Lunchtime seminar, 214 Steele}}
{{agenda item|1:30p|Niles Pierce, Broad}}
{{agenda item|2:00p|Rob Phillips, Broad}}
{{agenda item|2:30p|Open}}
{{agenda item|3:00p|CDS tea}}
{{agenda item|3:45p|Open}}
{{agenda item|4:30p|Open}}
{{agenda end}}

=== Talk ===

'''Synthetic gene oscillators and their applications'''

Wednesday, 26 January 2011<br>
12:00, 114 Steele (library)

The engineering of genetic circuits with predictive functionality in living cells represents a defining focus of the expanding field of synthetic biology. This focus was elegantly set in motion a decade ago with the design and construction of a genetic toggle switch and an oscillator, with subsequent highlights that have included circuits capable of pattern generation, noise shaping, edge detection and event counting. Here we describe an engineered gene network with global intercellular coupling that is capable of generating synchronized oscillations in a growing population of cells. Using microfluidic devices tailored for cellular populations at differing length scales, we investigate the collective synchronization properties along with spatiotemporal waves occurring at millimetre scales. We use computational modelling to describe quantitatively the period and amplitude of bulk oscillations. In addition to the work on the synchronized clock, we will discuss studies on synthetic gene oscillators using a high-throughput microfluidic platform that facilitates automated tracking in single-cells. We will describe the use of this device to chemically drive synthetic gene oscillators (analogous to the way circadian systems are driven by light) as well investigation into coupling of additional circuits to oscillators.

Group Schedule, Winter 2011

2011-01-10T22:53:46Z

Elisa: /* Group Meetings */

{{righttoc}}
This page contains information about various upcoming events that are of interest to the group.
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2010]]
|}

== Group Meetings ==
Group meetings are at noon in 114 Steele. Visitors are welcome (but be prepared to get signed up to give a talk!).
{| width=100% border=1
|- valign=top
|
{{agenda begin}}
{{agenda item|Date|Speaker}}
{{agenda item|5 Jan (Wed)|Shou}}
{{agenda item|13 Jan (Thu)|Dom}}
{{agenda item|21 Jan (Fri)|Elisa}}
{{agenda item|26 Jan (Wed)|Jun Liu}}
{{agenda end}}
|
{{agenda begin}}
{{agenda item|Date|Speaker}}
{{agenda item|4 Feb (Fri)|Ophelia}}
{{agenda item|11 Feb (Fri)|Hold}}
{{agenda item|16 Feb (Wed)|Edgar}}
{{agenda item|23 Feb (Wed)|Linlin}}
{{agenda end}}
|
{{agenda begin}}
{{agenda item|Date|Speaker}}
{{agenda item|2 Mar (Wed)|Dionysios}}
{{agenda item|9 Mar (Wed)|Hold}}
{{agenda item|14-18 Mar|No group meeting}}
{{agenda item|21-25 Mar|No group meeting}}
{{agenda end}}
|}

== Mini-group meetings ==

* Biocircuits: Mondays at 2 pm
* Robotics: Wednesdays at 4 pm
* NCS: Thursdays at 4 pm

All mini-group meetings are in 110 Steele.

== Events and talks ==

Group Schedule, Winter 2011

2011-01-02T09:21:54Z

Elisa: /* Group Meetings */

{{righttoc}}
This page contains information about various upcoming events that are of interest to the group.
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2010]]
|}

== Group Meetings ==
Group meetings are at noon in 114 Steele. Visitors are welcome (but be prepared to get signed up to give a talk!).
{| width=100% border=1
|- valign=top
|
{{agenda begin}}
{{agenda item|Date|Speaker}}
{{agenda item|5 Jan (Wed)|Dom}}
{{agenda item|12 Jan (Wed)|Shuo}}
{{agenda item|21 Jan (Fri)|Dionysios}}
{{agenda item|26 Jan (Wed)|Jun Liu}}
{{agenda end}}
|
{{agenda begin}}
{{agenda item|Date|Speaker}}
{{agenda item|4 Feb (Fri)|Ophelia}}
{{agenda item|11 Feb (Fri)|Hold}}
{{agenda item|16 Feb (Wed)|Edgar}}
{{agenda item|23 Feb (Wed)|Linlin}}
{{agenda end}}
|
{{agenda begin}}
{{agenda item|Date|Speaker}}
{{agenda item|2 Mar (Wed)|Elisa}}
{{agenda item|9 Mar (Wed)|Hold}}
{{agenda item|14-18 Mar|No group meeting}}
{{agenda item|21-25 Mar|No group meeting}}
{{agenda end}}
|}

== Mini-group meetings ==

* Biocircuits: Mondays at 2 pm
* Robotics: Wednesdays at 4 pm
* NCS: Thursdays at 4 pm

All mini-group meetings are in 110 Steele.

== Events and talks ==

Pablo Parrilo, Oct 2010

2010-10-24T23:42:26Z

Elisa:

Pablo Parrilo will be visiting Caltech on 25 Oct 2010 (Mon). Sign up for a time to meet with him below.

{{agenda begin}}
{{agenda item|10:30a|Javad Lavaei}}
{{agenda item|11:15a|Open}}
{{agenda item|12:00p|Lunch with Richard and John}}
{{agenda item|1:30p|Houman (Firestone 302)}}
{{agenda item|2:15p|Elisa Franco}}
{{agenda item|3:00p|Dennice Gayme}}
{{agenda item|4:00p|ACM seminar}}
{{agenda end}}

SoCal Control Workshop, Fall 2010

2010-10-04T16:32:29Z

Elisa: /* UCSB -> Pasadena */

This page has information on the Fall 2010 Southern California (Nonlinear) Control Workshop, which will be held at UCSB on 8 October (Fri).
* [http://www.ccec.ece.ucsb.edu/~teel/workshop/SoCal_Workshop.html Workshop agenda and information]

=== Carpooling ===

Use the table below to indicate if you are going to the workshop and whether you can drive/need a ride. Drivers: please contact everyone who signs up for a slot in your car and make arrangements on where to meet.

{| width=100% border=1
|- valign= top
| width=50% |
==== Pasadena -> UCSB ====
People with cars:
* Richard (leaving at 6:30 am): 3 passengers
** Marcella
** Scott Livingston
** Shuo
* Necmiye (leaving at 6:00 am): 3 passengers
** Elisa Franco
** Open
** Open
People who need a ride:
| width=50% |

==== UCSB -> Pasadena ====
People with cars:
* Richard (leaving at 12:45 pm): 3 passengers
** Marcella
** Elisa
** Open
* Necmiye (leaving at 5:45 pm): 3 passengers
** Shuo
** Open
** Open
People who need a ride:
|}

SoCal Control Workshop, Fall 2010

2010-10-04T16:32:20Z

Elisa: /* Pasadena -> UCSB */

This page has information on the Fall 2010 Southern California (Nonlinear) Control Workshop, which will be held at UCSB on 8 October (Fri).
* [http://www.ccec.ece.ucsb.edu/~teel/workshop/SoCal_Workshop.html Workshop agenda and information]

=== Carpooling ===

Use the table below to indicate if you are going to the workshop and whether you can drive/need a ride. Drivers: please contact everyone who signs up for a slot in your car and make arrangements on where to meet.

{| width=100% border=1
|- valign= top
| width=50% |
==== Pasadena -> UCSB ====
People with cars:
* Richard (leaving at 6:30 am): 3 passengers
** Marcella
** Scott Livingston
** Shuo
* Necmiye (leaving at 6:00 am): 3 passengers
** Elisa Franco
** Open
** Open
People who need a ride:
| width=50% |

==== UCSB -> Pasadena ====
People with cars:
* Richard (leaving at 12:45 pm): 3 passengers
** Marcella
** Open
** Open
* Necmiye (leaving at 5:45 pm): 3 passengers
** Shuo
** Open
** Open
People who need a ride:
|}

CDS 270-4, 2010: Bio-Control

2010-05-23T19:22:09Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''System identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
| [http://www.nature.com/nature/journal/v407/n6804/abs/407651a0.html Large-scale metabolic network organization], [http://chaos.aip.org/chaoeh/v11/i1/p142_s1?isAuthorized=no Genetic modules design principles]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties, [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-2.pdf Slides]
|[http://www.nature.com/nrg/journal/v8/n6/abs/nrg2102.html Review on network motifs, theory and experiments]
|NA
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| CANCELED
|
|NA
|-
| 14 May (F)
| RNA-based control and ultrasensitivity [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week7-2.pdf Slides]
|[http://www.nature.com/nbt/journal/v24/n5/full/nbt1208.html RNA synthetic biology, review], [http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050229 sRNA-based regulation], [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Ultrasensitive response in protein interactions]
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Introduction: robustness in control theory vs biology [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week8-1.pdf Slides]
| [http://www.cell.com/retrieve/pii/S0092867404008402 Review on robustness of cellular functions], [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549435/ Heat shock response in E. coli], [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/18/2415 Model checking for robust biological networks]
|NA
|-
| 21 May (F)
| Chemotaxis: robust perfect adaptation [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week8-2.pdf Slides]
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 26 May (W)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-05-18T20:03:38Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''System identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
| [http://www.nature.com/nature/journal/v407/n6804/abs/407651a0.html Large-scale metabolic network organization], [http://chaos.aip.org/chaoeh/v11/i1/p142_s1?isAuthorized=no Genetic modules design principles]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties, [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-2.pdf Slides]
|[http://www.nature.com/nrg/journal/v8/n6/abs/nrg2102.html Review on network motifs, theory and experiments]
|NA
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| CANCELED
|
|NA
|-
| 14 May (F)
| RNA-based control and ultrasensitivity [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week7-2.pdf Slides]
|[http://www.nature.com/nbt/journal/v24/n5/full/nbt1208.html RNA synthetic biology, review], [http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050229 sRNA-based regulation], [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Ultrasensitive response in protein interactions]
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Introduction: robustness in control theory vs biology [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week8-1.pdf Slides]
| [http://www.cell.com/retrieve/pii/S0092867404008402 Review on robustness of cellular functions], [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549435/ Heat shock response in E. coli], [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/18/2415 Model checking for robust biological networks]
|NA
|-
| 21 May (F)
| Chemotaxis
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-05-18T19:59:33Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''System identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
| [http://www.nature.com/nature/journal/v407/n6804/abs/407651a0.html Large-scale metabolic network organization], [http://chaos.aip.org/chaoeh/v11/i1/p142_s1?isAuthorized=no Genetic modules design principles]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties, [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-2.pdf Slides]
|[http://www.nature.com/nrg/journal/v8/n6/abs/nrg2102.html Review on network motifs, theory and experiments]
|NA
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| CANCELED
|
|NA
|-
| 14 May (F)
| RNA-based control and ultrasensitivity [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week7-2.pdf Slides]
|[http://www.nature.com/nbt/journal/v24/n5/full/nbt1208.html RNA synthetic biology, review], [http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050229 sRNA-based regulation], [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Ultrasensitive response in protein interactions]
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Introduction: robustness in control theory vs biology [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week8-1.pdf Slides]
|NA
|-
| 21 May (F)
| Chemotaxis
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-05-18T19:56:52Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''System identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
| [http://www.nature.com/nature/journal/v407/n6804/abs/407651a0.html Large-scale metabolic network organization], [http://chaos.aip.org/chaoeh/v11/i1/p142_s1?isAuthorized=no Genetic modules design principles]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties, [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-2.pdf Slides]
|[http://www.nature.com/nrg/journal/v8/n6/abs/nrg2102.html Review on network motifs, theory and experiments]
|NA
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| CANCELED
|
|NA
|-
| 14 May (F)
| RNA-based control and ultrasensitivity [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week7-2.pdf Slides]
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Introduction: robustness in control theory vs biology [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week8-1.pdf Slides]
|NA
|-
| 21 May (F)
| Chemotaxis
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-05-08T01:22:12Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
| [http://www.nature.com/nature/journal/v407/n6804/abs/407651a0.html Large-scale metabolic network organization], [http://chaos.aip.org/chaoeh/v11/i1/p142_s1?isAuthorized=no Genetic modules design principles]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties, [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-2.pdf Slides]
|[http://www.nature.com/nrg/journal/v8/n6/abs/nrg2102.html Review on network motifs, theory and experiments]
|NA
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-05-04T22:06:25Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression[http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
| [http://www.nature.com/nature/journal/v407/n6804/abs/407651a0.html Large-scale metabolic network organization], [http://chaos.aip.org/chaoeh/v11/i1/p142_s1?isAuthorized=no Genetic modules design principles]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-05-04T22:01:34Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides], [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2-KGalloway.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|[http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week6-1.pdf Slides]
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-30T23:53:11Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-2.pdf Slides]
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-29T22:24:37Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway.
| [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-29T22:23:58Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
| [http://arxiv.org/abs/math/0206133 Monotone Control Systems]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway.
|
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.] [http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.7404 Oscillations in I/O Monotone Systems Under Negative FeedbackOscillations in I/O Monotone Systems Under Negative Feedback]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-29T22:20:14Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
|
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway.
|
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-29T22:19:46Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
| [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week5-1.pdf Slides]
|NA
|-
| 30 April (F)
| Predicting oscillations; monotonicity in CRNs. The MAPK pathway.
|
| [http://www.math.rutgers.edu/~sontag/PUBDIR/FTP_DIR/angeli_leenheer_sontag_graph_theoretic_monotone_journal_math_biology_online2009.pdf Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates.]
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

Summer 2010 Murray Group Trip

2010-04-29T17:44:28Z

Elisa: /* Tentative itinerary */

Elisa and Sawyer are organizing the 2010 Summer Murray group trip. The votes have been tallied, and we will be going to '''Montana de Oro on June 18-20''' this year!

This trip will be pretty free-form -- we will have some planned activities, but you will be in a central location from which you will have freedom to do any sort of play you want. (For instance, if you'd like to lie on the beach and explore tidepools the whole weekend, it's very possible!)

= Details =

[[File:Cfiles13761.jpg]]

We will be camping in Montana de Oro state park, 3.5 hours north by car from Los Angeles, on the ocean. Montana de Oro is one of California's largest state parks, and comes with rocky coastlines, tidepools, giant sand dunes and beaches. We will be staying at the Montana de Oro state park campground.

=== Costs per Person (rough) ===

$30 for gas, $10 for camp site, $15 for sleeping bag/tent rental, $15-35 for kayak, $55-65 for horseback riding. We will calculate food after the fact, but probably less than $50 for communal food, not including anything you buy for yourself (eg., in restaurants).

=== Tentative itinerary ===

* Friday, June 18
** early afternoon, before LA traffic: drive to Montana de Oro and set up camp. Short walk to beach, time permitting. Dinner at camp.
* Saturday, June 19
** morning: your choice of activity. Maybe a trip to the dunes or swim or surf, conditions permitting.
** afternoon: [http://www.kayakhorizons.com/ kayaking] out to sandspit in Morro Bay, perhaps dinner there and kayak back in the twilight?
* Sunday, June 20
** morning: horseback riding.
** afternoon: hike the loop trail (surfing if possible?) including Oats Peak and possibly Valencia Peak and the shoreline.
** evening: return by car to Los Angeles

'''Possible activities'''
* Walk to coralina cove tidepools (30 min walk each way)
* Watch sunset on bluffs
* Sandboarding on sand dunes (10 minute drive, 30 min walk)
* Surfing (wave size permitting. Sawyer will look at the forecast and rent boards accordingly. if you're interested and possibly want a board, let him know ($20) -- tips for catching a wave happily offered)
* Hike up valencia peak (1-2 hrs each way)
* Hacky-sacking
* Read a book on the beach

''' Horseback riding '''
* Sunday, June 20th, morning. We will have to split in two groups of max 8 people each. The first ride will depart at 10am, the second around 11.30 am. We will rent horses from [http://www.caladventures.com/jjriding.htm this place], the cost is $55 per person.
* This will be a beginner ride, so don't worry if you have never done this before.
* Gear: closed toe shoes and long pants. The saddle leather can bruise the skin of your legs if they are not properly covered; I do not recommend heavy jeans, but a lot of people are fine with that. Make sure you wear comfortable clothes that you are not afraid of staining or ruining. Also, note that you might want to change after the ride...

= Participants =

* Andrea Censi - Central Coast, any date ('''confirmed, +1 guest, needs bag pad tent space needed''')
* Dionysios Barmpoutis - San Gorgonio, 21-23 May only
* Elisa Franco - any, any ('''confirmed +1 guest?''')
* Floris van Breugel - any, prefers June 19
* Francisco Zabala - Central Coast, any date
* Mumu Xu - Central Coast, June 19 only
* Nok Wongpiromsarn - ('''confirmed, pad and tent space needed''')
* Ophelia Venturelli - Central Coast, June 19 best ('''confirmed + 1, both need bag, pad, tent''')
* Richard Murray - any, any ('''confirmed, coming from SF area, somebody needs to pick up his bag/pad/tent''')
* Sawyer Fuller - any, any ('''confirmed''')
* Shuo Han - Central Coast, June only ('''confirmed, bag pad tent space needed''')
* Tim Chung - interested, unknown travel schedule could have conflicts ('''confirmed, nothing needed''')
* Ufuk Topcu - Central Coast, June only ('''confirmed +1 guest, bags pads tent space needed''')
* Vanessa Jonsson - any, any

= Old stuff =

Dates: Richard's availability is for the following week-ends (Both possible trips involve leaving some time during the day on Friday, either morning or afternoon).

* (14-16 May is now out)
* 21-23 May
* 4-6 June
* 18-20 June

Destinations:

'''Option 1.''' Backpacking in San Gorgonio wilderness (with option of climbing to the top of [http://en.wikipedia.org/wiki/San_Gorgonio_Mountain San Gorgonio ], Southern California's highest peak).
** This will be a 2-night, 3-day backpacking trip. Don't worry if you haven't done this before. We'll make sure you have the right gear (we will rent from the Caltech Y) and we'll plan the hikes so that everyone can enjoy them.
[[File:Drylake.jpg]]

'''Option 2.''' Camping near the ocean in Montana de Oro state park, near Morro bay (Central Coast): [http://www.trails.com/activity.aspx?area=15068 hiking ], [http://www.kayakhorizons.com/ kayaking ], surfing (including lessons from Sawyer if conditions are reasonable), and [http://www.caladventures.com/jjriding.htm horseback riding ] on the beach.
** This will be a more leisurely option with little mandatory hiking. We will do the various activities as excursions from our campsite.

Apr 2010 meetings

2010-04-26T16:39:45Z

Elisa: /* 30 Apr (Fri) */

The list below has times that I am available to meet on 28-30 Apr.
* One-on-one meetings: Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and see if you can switch).

<br>
<table width=100% border=1>
<tr valign=top><td width=30%>
==== 28 Apr (Wed) ====
{{agenda begin}}
{{agenda begin}}
{{agenda item|9:30a|Open - 45m}}
{{agenda item|10:15a|Vanessa - 45m}}
{{agenda item|11:00a|Pete - 60m}}
{{agenda item||}}
{{agenda item|1:30p|Open - 60m}}
{{agenda item|2:30p|Open - 30m}}
{{agenda item|3:00p|CDS tea}}
{{agenda item|3:30p|Open - 60m}}
{{agenda item|4:30p|Open - 60m}}
{{agenda item|5:30p|Open - 60m}}
{{agenda end}}

</td><td width=30%>

==== 29 Apr (Thu) ====
{{agenda begin}}
{{agenda item|9:30a|Busy - 45m}}
{{agenda item|10:15a|Open - 45m}}
{{agenda item|11:00a|Javad & Somayeh - 60m}}
{{agenda item||}}
{{agenda item|1:30p|Busy - 90m}}
{{agenda item|3:00p|Open - 30m}}
{{agenda item|3:30p|Open - 30m}}
{{agenda item|4:00p|Open - 60m}}
{{agenda item|5:00p|iGEM - 60m}}
{{agenda item|6:00p|Open - 60m}}
{{agenda end}}
</td><td width=30%>

==== 30 Apr (Fri) ====
{{agenda begin}}
{{agenda item|9:30a|Open - 45m}}
{{agenda item|10:15a|Open - 45m}}
{{agenda item|11:00a|Open - 30m}}
{{agenda item|11:30a|Exam - 60m}}
{{agenda item||}}
{{agenda item|1:30p|Open - 60m}}
{{agenda item|2:30p|Elisa - 60m}}
{{agenda item|3:30p|Open - 60m}}
{{agenda item|4:30p|cisco - 60m}}
{{agenda item|5:30p|Open - 60m}}
{{agenda end}}
</td></tr>
</table>

CDS 270-4, 2010: Bio-Control

2010-04-24T20:40:12Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|[http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-24T20:39:44Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-2.pdf Slides]
|
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|- [http://www.jeremy-gunawardena.com/papers/crnt.pdf Chemical Reaction Network Theory for In Silico Biologists]
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-21T05:39:15Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem
|
|[http://www.sciencemag.org/cgi/content/abstract/327/5971/1389 Structural Sources of Robustness in Biochemical Reaction Networks, Shinar & Feinberg]
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-21T05:37:36Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/ M. Feinberg, original notes ], [http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf H. Othmer, Theory of Complex Reaction Networks ]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem
|
|
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-21T05:37:04Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples. Structural properties of CRNs. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf Slides]
|[M. Feinberg, original notes http://www.che.eng.ohio-state.edu/~FEINBERG/LecturesOnReactionNetworks/], [H. Othmer, Theory of Complex Reaction Networks http://www.math.leidenuniv.nl/~verduyn/Hans.Othmer_course_notes.pdf]
|NA
|-
| 23 April (F)
| Proof of the Deficiency Zero Theorem
|
|
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-17T19:46:31Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-2.pdf Slides]
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples
|
|NA
|-
| 23 April (F)
| Deficiency theory
|
|
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-16T02:40:26Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|NA
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples
|
|NA
|-
| 23 April (F)
| Deficiency theory
|
|
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-16T02:40:02Z

Elisa: /* Course Schedule */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> [[Image:CaltechLogoPrimaryOrangeCropped.gif|75px]]</td>
<td align=center><font color='orange' size='+3'>BioControl</font></td>
<td rowspan=2 align=center> [[Image:cdslogo.png|90px]]</td></tr>
<tr valign=top><td align=center><font color='orange' size='+2'>Spring 2010</font></td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>

* 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.
* ===>>NEW: [http://listserv.cds.caltech.edu/mailman/listinfo/cds-270-4 Mailing list] <<===

== Course Objectives: Biology and Control Theory ==

Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.

The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.

== Course Schedule ==

{| border=1 width=100%
|-
| Week || Date || Lecture Topic || Papers considered in class || BioControl Journal Club
|-
| align=center rowspan=3 | 1
| colspan=4 | '''Introduction, Modeling biological systems'''
|- valign=top
| 29 March (M)
| Course overview and objectives, layers of control of gene expression. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-1.pdf Slides]
| [[Media:CDS270-4SyllabusSpring10.pdf |Syllabus]]
|NA
|-
| 2 April (F)
| Modeling: Ordinary Differential Equations. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week1-2.pdf Slides]
| [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]
|-
| align=center rowspan=3 | 2
| colspan=4 | '''Deterministic and stochastic modeling'''
|- valign=top
| 6 April (T)
| CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week2-1.pdf Slides]
|[http://www.math.rutgers.edu/~sontag/FTP_DIR/angeli_ferrell_sontag_pnas04_paper_and_supplementary.pdf Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems ], [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-473N66C-3&_user=10&_coverDate=11%2F08%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=217ba83086d0bb64f7bbd513445a7627 Negative Autoregulation Speeds the Response Times of Transcription Networks]
|NA
|-
| 9 April (F)
| 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832680/ Defining bifurcations in stochastic systems]
|-
|-
| align=center rowspan=3 | 3
| colspan=4 | '''Model identification in biology'''
|- valign=top
| 13 April (T)
| Overview of system identification methods. [http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week3-1.pdf Slides]
|
|NA
|-
| 16 April (F)
| Experimental approaches to identification of biological networks
|[http://www.nature.com/msb/journal/v5/n1/full/msb200975.html Using noise for parameter identification], [http://stke.sciencemag.org/cgi/content/abstract/pnas;99/20/12841 Identification of network connectivity], [http://www.nature.com/ncb/journal/v9/n3/abs/ncb1543.html Experimental identification of network topologies], [http://www.nature.com/ng/journal/v40/n12/abs/ng.281.html Using dynamic correlation to reveal regulatory activity]
|
|-
|-
| align=center rowspan=3 | 4
| colspan=4 | '''Theory of Chemical Reaction Networks'''
|- valign=top
| 20 April (T)
| General introduction and examples
|
|NA
|-
| 23 April (F)
| Deficiency theory
|
|
|-
|-
| align=center rowspan=3 | 5
| colspan=4 | '''Monotone systems'''
|- valign=top
| 27 April (T)
| Definitions and basic theorems
|
|NA
|-
| 30 April (F)
| Applications, predicting oscillations
|
|
|-
|-
| align=center rowspan=3 | 6
| colspan=4 | '''Synthetic biology: design principles '''
|- valign=top
| 4 May (T)
| Design of molecular control systems and demand for gene expression
|
|NA
|-
| 7 May (F)
| Network motifs, structural and dynamical properties
|
|
|-
|-
| align=center rowspan=3 | 7
| colspan=4 | ''' Synthetic biology: design principles '''
|- valign=top
| 11 May (T)
| Transcriptional and translational control
|
|NA
|-
| 14 May (F)
| Ultrasensitivity
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Robustness '''
|- valign=top
| 18 May (T)
| Theoretical aspects of robustness
|
|NA
|-
| 21 May (F)
| Robustness in experimental biology
|
|
|-
|-
| align=center rowspan=3 | 8
| colspan=4 | ''' Modularity in control theory and biology '''
|- valign=top
| 25 May (T)
| Time-scale separation principle and dynamical systems approaches to modularity
|
|NA
|-
| 28 May (F)
| Modularity in experimental biology
|
|
|-
|}

== 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...).

CDS 270-4, 2010: Bio-Control

2010-04-14T06:25:41Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-14T03:44:08Z

Elisa:

CDS 270-4, 2010: Bio-Control

2010-04-10T20:11:46Z

Elisa:

CDS 270-4, 2010: Bio-Control

2010-04-10T20:10:56Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-10T20:09:41Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-10T20:01:25Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-10T19:56:18Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-10T19:53:56Z

Elisa:

CDS 270-4, 2010: Bio-Control

2010-04-10T19:52:49Z

Elisa:

CDS 270-4, 2010: Bio-Control

2010-04-10T19:46:48Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-07T16:31:04Z

Elisa:

CDS 270-4, 2010: Bio-Control

2010-04-07T16:30:42Z

Elisa:

CDS 270-4, 2010: Bio-Control

2010-04-07T07:03:09Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-05T17:01:53Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-05T17:00:02Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-05T16:57:15Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-05T16:57:01Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-05T16:56:39Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-05T16:56:14Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-04T04:54:56Z

Elisa: /* Course Administration */

CDS 270-4, 2010: Bio-Control

2010-04-04T00:54:49Z

Elisa: /* Course Schedule */

CDS 270-4, 2010: Bio-Control

2010-04-04T00:54:13Z

Elisa: /* Course Schedule */