Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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{{supheader|Biological Systems}}
 
{{supheader|Biological Systems}}
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<font size="+1">Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)</font>
  
Biological systems make use of feedback in an extraordinary number of ways, on scales ranging from molecules
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{{warning|This page is out of dateSee http://www.cds.caltech.edu/~murray/BFSwiki for the latest version}}
to cells to organisms to ecosystems.  This page collects information on the analysis of feedback systems in biologyWhat is currently connected here are working notes on the supplement and links to further information. This information is ''in progress''; comments and constructive suggestions are welcome and can be sent to [[User:murray|Richard Murray]].
+
  
== Molecular Biology (Del Vecchio and Murray) ==
+
__NOTOC__
 +
This textbook is intended for researchers interested in the application of feedback and control to biomolecular systems.  The material has been designed so that it can be used in parallel with ''Feedback Systems'' as part of a course on biomolecular feedback and control systems, or as a standalone reference for readers who have had a basic course in feedback and
 +
control theory.  This book is being written by [[http:www.mit.edu/~ddv/|Domitilla Del Vecchio]] and [[Richard Murray]] based on a variety of presentations, lectures and notes.
  
The text contains a number of examples and exercises related to some of the molecular mechanisms for feedback within cellsThese examples are being expanded into a set of notes by [http://www.eecs.umich.edu/~ddv/ Domitilla Del Vecchio] and [[User:Murray|Richard Murray]] based on a variety of presentations, lectures and notes.
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'''Note:''' These notes are in draft form and may contain errorsPermission is granted to download and print a copy for individual use, but this material may not be reproduced, in whole or in part, without written consent from the author.
  
'''Tentative outline'''
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<!-- {{BFS quick links}} -->
{|
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===== News ([[BFS:Archived news|archive]]) =====
 +
* 14 Sep 2014: The contents of this page have been moved to http://www.cds.caltech.edu/~murray/BFSwiki.
 +
* 19 Jan 2014: Updated chapters on circuits, modules and tradeoffs (Ch 5-7) + bibliography.  A {{BFS pdf|complete manuscript|bfs-public|19Jan14}} is also available.
 +
* 6 Jan 2014: Updated chapter on stochastic modeling and analysis (Ch 4)
 +
* 11 Dec 2013: Updated chapter on dynamic behavior (Ch 3)
 +
* 7 Dec 2013: Updated chapter on core processes (Ch 2)
 +
* 5 Dec 2013: Updated contents, preface, introduction (Ch 1) and references
 +
* 12 Jul 2012: Updated outline; new PDFs posted.  A {{BFS pdf|complete manuscript|bfs-public|11Jul12}} is also available.
 +
<p>
 +
 
 +
=== Contents ===
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{| width=100% border=1
 
|- valign=top
 
|- valign=top
 
| width=50% |
 
| width=50% |
<ol type="I">
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* {{BFS pdf|Preface and Contents|bfs-frontmatter|05Dec13}}
<li> Introduction</li>
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* Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|05Dec13}}
<li> Modeling  
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** Systems Biology: Modeling, Analysis and the Role of Feedback
* Review of cell biology basics
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** The Cell as a System
* Chemical kinetics, Michaelis-Menten, Hill functions
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** Control and Dynamical Systems Tools
* Signaling cascades
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** Input/Output Modeling
* Standard elements (repressor, activator, combinatorial promotors, etc)
+
** From Systems to Synthetic Biology
* Additional topics (time delays)
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* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|07Dec13}}
</li>
+
** Modeling Techniques
<li> Regulation in cells
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** Transcription and Translation
* Proportional control: activation and repression (+ demand theory)
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** Transcriptional Regulation
* Integral compensation (chemotaxis)
+
** Post-Transcriptional Regulation
* Allosteric regulation
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** Cellular Subsystems
</li>
+
* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|11Dec13}}
</ol>
+
** Analysis Near Equilibria
|  
+
** Robustness
<ol type="I" start=4>
+
** Oscillatory Behavior
<li> Robustness and limits of performance
+
** Bifurcations
* Autocatalysis and right half plane zeros
+
** Model Reduction Techniques
</li>
+
* Chapter 4: {{BFS pdf|Stochastic Modeling and Analysis|bfs-stochastic|06Jan14}}
<li> Biological switches and oscillators </li>
+
** Stochastic Modeling of Biochemical Systems
<li> Modularity and synthetic biology </li>
+
** Simulation of Stochastic Systems
</ol>
+
** Input/Output Linear Stochastic Systems
 +
<!--
 +
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
 +
** The ''lac'' Operon
 +
** Bacterial chemotaxis|bfs-chemotaxis
 +
-->
 +
| width=50% |
 +
* Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|19Jan14}}
 +
** Introduction to Biological Circuit Design
 +
** Negative Autoregulation
 +
** The Toggle Switch
 +
** The Repressilator
 +
** Activator-repressor Clock
 +
** An Incoherent Feedforward Loop (IFFL)
 +
** Bacterial Chemotaxis
 +
* Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|19Jan14}}
 +
** Input/Output Modeling and the Modularity Assumption
 +
** Introduction to Retroactivity
 +
** Retroactivity in Gene Circuits
 +
** Retroactivity in Signaling Systems
 +
** Insulation Devices: Retroactivity Attentuation
 +
** A Case Study on the Use of Insulation Devices
 +
* Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|19Jan14}}
 +
** Competition for Shared Cellular Resources
 +
** Stochastic Effects: Design Tradeoffs in Systems with Large Gains
 +
* Appendix A: A Primer on Control Theory
 +
<!--
 +
* Appendix A: Cell Biology Primer (from NCBI)
 +
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_cell.html What is a Cell]
 +
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html What is a Genome]
 +
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_molecular.html Molecular Genetics: Piecing It Together]
 +
** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]
 +
* Appendix C: {{BFS pdf|Random Processes|bfs-random|11Jul12}}
 +
** Random Variables
 +
** Continuous-State Random Processes
 +
** Discrete-State Random Processes
 +
-->
 +
* {{BFS pdf|Bibliography and Index|bfs-backmatter|19Jan14}}
 
|}
 
|}
 
Some of the examples for this material will be pulled from tutorial presentations on control given at systems biology workshops:
 
* [http://www.ima.umn.edu/2007-2008/W4.21-25.08/activities/Murray-Richard/ima_fbktut-21apr08_s.pdf Tutorial on control theory], IMA workshop on Design Principles in Biological Systems, 21 April 2008.
 
 
== Microbial Ecosystems ==
 
 
== Integrative Biology ==
 
 
=== Locomotion ===
 
 
Summarize work of Full, Holmes et al showing role of dynamics and feedback in insect locomotion.
 
* Low order models to describe locomotion
 
* Bifurcations of stable gates, neural pattern generator
 
* [http://epubs.siam.org/SIREV/volume-48/art_44513.html The Dynamics of Legged Locomotion: Models, Analyses, and Challenges], Philip Holmes, Robert J. Full, Dan Koditschek, John Guckenheimer.  ''SIAM Review'', 48(2):207-304, 2006.  (requires subscription)
 
 
=== Insect Flight ===
 
 
Summarize work of Dickinson, Srinivasan et al show mechanisms for visual sensoring processing and sensor fusion in insect flight.
 
 
== Motor Control Systems ==
 
 
Summarize work on Massaquoi from CSHL course.
 
 
== Additional Information ==
 
* [http://meetings.cshl.edu/meetings/engine06.shtml Engineering Principles in Biological Systems]: 6-8 December 2006, Cold Spring Harbor Laboratory
 

Latest revision as of 22:01, 14 September 2014

Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)

WARNING: This page is out of date. See http://www.cds.caltech.edu/~murray/BFSwiki for the latest version


This textbook is intended for researchers interested in the application of feedback and control to biomolecular systems. The material has been designed so that it can be used in parallel with Feedback Systems as part of a course on biomolecular feedback and control systems, or as a standalone reference for readers who have had a basic course in feedback and control theory. This book is being written by Domitilla Del Vecchio and Richard Murray based on a variety of presentations, lectures and notes.

Note: These notes are in draft form and may contain errors. Permission is granted to download and print a copy for individual use, but this material may not be reproduced, in whole or in part, without written consent from the author.

News (archive)
  • 14 Sep 2014: The contents of this page have been moved to http://www.cds.caltech.edu/~murray/BFSwiki.
  • 19 Jan 2014: Updated chapters on circuits, modules and tradeoffs (Ch 5-7) + bibliography. A complete manuscript (PDF) is also available.
  • 6 Jan 2014: Updated chapter on stochastic modeling and analysis (Ch 4)
  • 11 Dec 2013: Updated chapter on dynamic behavior (Ch 3)
  • 7 Dec 2013: Updated chapter on core processes (Ch 2)
  • 5 Dec 2013: Updated contents, preface, introduction (Ch 1) and references
  • 12 Jul 2012: Updated outline; new PDFs posted. A complete manuscript (PDF) is also available.

Contents

  • Preface and Contents (PDF)
  • Chapter 1: Introductory Concepts (PDF)
    • Systems Biology: Modeling, Analysis and the Role of Feedback
    • The Cell as a System
    • Control and Dynamical Systems Tools
    • Input/Output Modeling
    • From Systems to Synthetic Biology
  • Chapter 2: Core Processes (PDF)
    • Modeling Techniques
    • Transcription and Translation
    • Transcriptional Regulation
    • Post-Transcriptional Regulation
    • Cellular Subsystems
  • Chapter 3: Dynamic Behavior (PDF)
    • Analysis Near Equilibria
    • Robustness
    • Oscillatory Behavior
    • Bifurcations
    • Model Reduction Techniques
  • Chapter 4: Stochastic Modeling and Analysis (PDF)
    • Stochastic Modeling of Biochemical Systems
    • Simulation of Stochastic Systems
    • Input/Output Linear Stochastic Systems
  • Chapter 5: Biological Circuit Components (PDF)
    • Introduction to Biological Circuit Design
    • Negative Autoregulation
    • The Toggle Switch
    • The Repressilator
    • Activator-repressor Clock
    • An Incoherent Feedforward Loop (IFFL)
    • Bacterial Chemotaxis
  • Chapter 6: Interconnecting Components (PDF)
    • Input/Output Modeling and the Modularity Assumption
    • Introduction to Retroactivity
    • Retroactivity in Gene Circuits
    • Retroactivity in Signaling Systems
    • Insulation Devices: Retroactivity Attentuation
    • A Case Study on the Use of Insulation Devices
  • Chapter 7: Design Tradeoffs (PDF)
    • Competition for Shared Cellular Resources
    • Stochastic Effects: Design Tradeoffs in Systems with Large Gains
  • Appendix A: A Primer on Control Theory
  • Bibliography and Index (PDF)