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<font color='blue' size='+2'>Biomolecular Feedback Systems</font></td></tr>
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<tr><td align=center height="40"><font size='+1'>[[Domitilla Del Vecchio]] and [[Richard M. Murray]]</font></td></tr>
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</table> __NOTOC__
  
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Welcome to {{SITENAME}}. This is the wiki for the text ''Biomolecular Feedback Systems'' by Domitilla Del Vecchio and Richard M. Murray.  On this site you will find the {{current version|complete text}} of the book as well as additional materials associated with the text.
  
== Getting started ==
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Copyright in this book is held by Princeton University Press, who have kindly agreed to allow us to keep the book available on the web.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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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 control theory.
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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===== News ([[Archived news|archive]]) =====
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* 14 Sep 2014: PDFs posted for [[Version 1.1b]]
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* 10 Sep 2014: new web site set up
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=== Contents ===
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|- valign=top bgcolor=lightyellow
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| width=50% |
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* '''{{BFS pdf|Preface and Contents|bfs-frontmatter|14Sep14}}'''
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* '''Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|14Sep14}}'''
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** Systems Biology: Modeling, Analysis and the Role of Feedback
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** The Cell as a System
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** Control and Dynamical Systems Tools
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** Input/Output Modeling
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** From Systems to Synthetic Biology
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* '''Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|14Sep14}}'''
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** Modeling Techniques
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** Transcription and Translation
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** Transcriptional Regulation
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** Post-Transcriptional Regulation
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** Cellular Subsystems
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* '''Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|14Sep14}}'''
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** Analysis Near Equilibria
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** Robustness
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** Oscillatory Behavior
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** Bifurcations
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** Model Reduction Techniques
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* '''Chapter 4: {{BFS pdf|Stochastic Modeling and Analysis|bfs-stochastic|14Sep14}}'''
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** Stochastic Modeling of Biochemical Systems
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** Simulation of Stochastic Systems
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** Input/Output Linear Stochastic Systems
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* '''Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|14Sep14}}'''
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** Introduction to Biological Circuit Design
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** Negative Autoregulation
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** The Toggle Switch
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** The Repressilator
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** Activator-repressor Clock
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** An Incoherent Feedforward Loop (IFFL)
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** Bacterial Chemotaxis
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* '''Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|14Sep14}}'''
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** Input/Output Modeling and the Modularity Assumption
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** Introduction to Retroactivity
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** Retroactivity in Gene Circuits
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** Retroactivity in Signaling Systems
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** Insulation Devices: Retroactivity Attentuation
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** A Case Study on the Use of Insulation Devices
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* '''Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|14Sep14}}'''
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** Competition for Shared Cellular Resources
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** Stochastic Effects: Design Tradeoffs in Systems with Large Gains
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* '''{{BFS pdf|Bibliography and Index|bfs-backmatter|14Sep14}}'''
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=== Resources ===
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* [[Errata|List of errata]]

Latest revision as of 04:57, 28 June 2015

Biomolecular Feedback Systems
Domitilla Del Vecchio and Richard M. Murray

Welcome to BFSwiki. This is the wiki for the text Biomolecular Feedback Systems by Domitilla Del Vecchio and Richard M. Murray. On this site you will find the complete text of the book as well as additional materials associated with the text.

Copyright in this book is held by Princeton University Press, who have kindly agreed to allow us to keep the book available on the web.

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.

News (archive)
  • 14 Sep 2014: PDFs posted for Version 1.1b
  • 10 Sep 2014: new web site set up

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
  • Bibliography and Index (PDF)

Resources