Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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{{supheader|Biological Systems}}
 
{{supheader|Biological Systems}}
<font size="+1">Domitilla Del Vecchio (U. Mich) and Richard M. Murray (Caltech)</font>
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<font size="+1">Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)</font>
  
{{righttoc}}
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{{warning|This page is out of dateSee http://www.cds.caltech.edu/~murray/BFSwiki for the latest version}}
This supplement is intended for researchers interested in the application of feedback and control to biomolecular systemsThe material has been designed so that it can be used in parallel with {\em 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
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control theory.  The supplement is being written 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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<font color=red>This page contains working notes for the material that is being prepared for the supplementWe anticipate that a preliminary version of the notes will be available by July 2009.</font>
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__NOTOC__
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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
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control theoryThis 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.
  
=== Outline ===
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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.
The current plan for the supplement is based on the following draft outlineComments are welcome on topics that are missing.
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{|
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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
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* 12 Jul 2012: Updated outline; new PDFs posted.  A {{BFS pdf|complete manuscript|bfs-public|11Jul12}} is also available.
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<p>
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=== 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> Review of Core Processes
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* Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|05Dec13}}
* Modeling of transcription and translation
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** Systems Biology: Modeling, Analysis and the Role of Feedback
** ODE models (coming from chemical reactions and thermodynamics)
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** The Cell as a System
** time constants
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** Control and Dynamical Systems Tools
** cell affects (dilution, degradation)
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** Input/Output Modeling
* Transcriptional Regulation
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** From Systems to Synthetic Biology
** repression
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* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|07Dec13}}
** activation
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** Modeling Techniques
** (Thermodynamics &rarr; chemical kinetics &rarr;Hill functions, Michaelis-Menten)
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** Transcription and Translation
* Intracellular sensing
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** Transcriptional Regulation
* Intracellular communication
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** Post-Transcriptional Regulation
* Intracellular computation
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** Cellular Subsystems
</li>
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* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|11Dec13}}
<li> Dynamic behavior
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** Analysis Near Equilibria
* Steady state analysis (log/log diagrams)
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** Robustness
* Phase plane analysis
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** Oscillatory Behavior
* Time response
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** Bifurcations
* Limit cycles
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** Model Reduction Techniques
</li>
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* Chapter 4: {{BFS pdf|Stochastic Modeling and Analysis|bfs-stochastic|06Jan14}}
<li> Feedback examples
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** Stochastic Modeling of Biochemical Systems
* Lactose metabolism
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** Simulation of Stochastic Systems
* Heat shock
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** Input/Output Linear Stochastic Systems
* Chemotaxis
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<!--
</li>
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* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
</ol>
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** The ''lac'' Operon
|  
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** Bacterial chemotaxis|bfs-chemotaxis
<ol type="I" start=4>
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-->
<li> Stochastic behavior 
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| width=50% |
* Noise modeling (intrinsic/extrinsic), spectrum
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* Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|19Jan14}}
* Stochastic simulation analysis (SSA)  
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** Introduction to Biological Circuit Design
* Markov modeling and analysis
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** Negative Autoregulation
* Linearized modeling and analysis: include disturbance attenuation in freq domain (?)
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** The Toggle Switch
</li>
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** The Repressilator
<li> Biological  circuit design
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** Activator-repressor Clock
* DNA-protein, vs protein-protein, etc.
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** An Incoherent Feedforward Loop (IFFL)
* Feedforward loops
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** Bacterial Chemotaxis
* PID in biocircuits
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* Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|19Jan14}}
* Activation vs repression (demand theory)  
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** Input/Output Modeling and the Modularity Assumption
* Modularity and retroactivity
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** Introduction to Retroactivity
* Logical functions: AND, switches, inverters, toggles, etc.  
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** Retroactivity in Gene Circuits
</li>
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** Retroactivity in Signaling Systems
<li> Design examples
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** Insulation Devices: Retroactivity Attentuation
</li>
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** A Case Study on the Use of Insulation Devices
<li> Robustness and evolvability
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* Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|19Jan14}}
</li>
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** Competition for Shared Cellular Resources
<li> Multicellular systems
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** Stochastic Effects: Design Tradeoffs in Systems with Large Gains
* Additional core processes
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* Appendix A: A Primer on Control Theory
* Quorum Sensing
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<!--
* Development
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* Appendix A: Cell Biology Primer (from NCBI)
</li>
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** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_cell.html What is a Cell]
</ol>
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** [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]
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** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]
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* Appendix C: {{BFS pdf|Random Processes|bfs-random|11Jul12}}
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** Random Variables
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** Continuous-State Random Processes
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** Discrete-State Random Processes
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-->
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* {{BFS pdf|Bibliography and Index|bfs-backmatter|19Jan14}}
 
|}
 
|}
 
=== Examples ===
 
 
=== Additional Information ===
 
 
* [http://meetings.cshl.edu/meetings/engine06.shtml Engineering Principles in Biological Systems]: 6-8 December 2006, 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)
 

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)