Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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{{supheader|Biological Systems}}
 
{{supheader|Biological Systems}}
 
<font size="+1">Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)</font>
 
<font size="+1">Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)</font>
 +
 +
{{warning|This page is out of date.  See http://www.cds.caltech.edu/~murray/BFSwiki for the latest version}}
  
 
__NOTOC__
 
__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
 
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.  The supplement is being written by [[http:www.mit.edu/~ddv/|Domitilla Del Vecchio]] and [[Richard Murray]] based on a variety of presentations, lectures and notes.
+
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.
  
 
'''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.
 
'''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.
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<!-- {{BFS quick links}} -->
 
<!-- {{BFS quick links}} -->
 
===== News ([[BFS:Archived news|archive]]) =====
 
===== News ([[BFS:Archived news|archive]]) =====
* 20 Jul 2013: Updated outline and new PDFs are being posted over the next month.
+
* 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.
 
* 12 Jul 2012: Updated outline; new PDFs posted.  A {{BFS pdf|complete manuscript|bfs-public|11Jul12}} is also available.
* 16 Jan 2012: Updated outline; new PDFs for all chapters and appendices (coming later today)
 
 
<p>
 
<p>
  
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** Input/Output Modeling
 
** Input/Output Modeling
 
** From Systems to Synthetic Biology
 
** From Systems to Synthetic Biology
* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|01Jan11}}
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* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|07Dec13}}
 
** Modeling Techniques
 
** Modeling Techniques
 
** Transcription and Translation
 
** Transcription and Translation
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** Post-Transcriptional Regulation
 
** Post-Transcriptional Regulation
 
** Cellular Subsystems
 
** Cellular Subsystems
* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|11Jul12}}
+
* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|11Dec13}}
** Input/Output Modeling
+
 
** Analysis Near Equilibria
 
** Analysis Near Equilibria
 
** Robustness
 
** Robustness
** Analysis of Reaction Rate Equations
 
 
** Oscillatory Behavior
 
** Oscillatory Behavior
 
** Bifurcations
 
** Bifurcations
 
** Model Reduction Techniques
 
** Model Reduction Techniques
* Chapter 4: {{BFS pdf|Stochastic Behavior|bfs-stochastic|11Jul12}}
+
* Chapter 4: {{BFS pdf|Stochastic Modeling and Analysis|bfs-stochastic|06Jan14}}
 
** Stochastic Modeling of Biochemical Systems
 
** Stochastic Modeling of Biochemical Systems
 
** Simulation of Stochastic Systems
 
** Simulation of Stochastic Systems
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| width=50% |
 
| width=50% |
* Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|11Jul12}}
+
* Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|19Jan14}}
 
** Introduction to Biological Circuit Design
 
** Introduction to Biological Circuit Design
 
** Negative Autoregulation
 
** Negative Autoregulation
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** Activator-repressor Clock
 
** Activator-repressor Clock
 
** An Incoherent Feedforward Loop (IFFL)
 
** An Incoherent Feedforward Loop (IFFL)
* Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|11Jul12}}
+
** Bacterial Chemotaxis
 +
* Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|19Jan14}}
 
** Input/Output Modeling and the Modularity Assumption
 
** Input/Output Modeling and the Modularity Assumption
 
** Introduction to Retroactivity
 
** Introduction to Retroactivity
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** Retroactivity in Signaling Systems
 
** Retroactivity in Signaling Systems
 
** Insulation Devices: Retroactivity Attentuation  
 
** Insulation Devices: Retroactivity Attentuation  
* Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|11Jul12}}
+
** A Case Study on the Use of Insulation Devices
** Metabolic Burden
+
* Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|19Jan14}}
** Stochastic Effects: Design Tradeoffs between Retroactivity and Noise
+
** Competition for Shared Cellular Resources
* Appendix A: Control Systems Primer
+
** Stochastic Effects: Design Tradeoffs in Systems with Large Gains
 +
* Appendix A: A Primer on Control Theory
 
<!--
 
<!--
 
* Appendix A: Cell Biology Primer (from NCBI)
 
* Appendix A: Cell Biology Primer (from NCBI)
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** Discrete-State Random Processes
 
** Discrete-State Random Processes
 
-->
 
-->
* {{BFS pdf|Bibliography and Index|bfs-backmatter|05Dec13}}
+
* {{BFS pdf|Bibliography and Index|bfs-backmatter|19Jan14}}
 
|}
 
|}
 
=== Additional Information ===
 
 
* [[ASCC 2009 Workshop]] - Analysis and Design of Biomolecular Feedback Systems
 
* [http://meetings.cshl.edu/meetings/engine08.shtml Engineering Principles in Biological Systems]: 10-12 December 2008, Cold Spring Harbor Laboratory
 
* [http://www.ima.umn.edu/2007-2008/W4.21-25.08/ Design Principles in Biological Systems]: 24-28 April 2008, Institute for Mathematics and Its Applications (IMA)
 
* [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)