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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.
 
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.
  
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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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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.
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control theory.  This book is being written by [[Domitilla Del Vecchio]] and [[Richard M. Murray]] based on a variety of presentations, lectures and notes.
 
  
 
===== News ([[Archived news|archive]]) =====
 
===== News ([[Archived news|archive]]) =====
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* 14 Sep 2014: PDFs posted
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* 14 Sep 2014: PDFs posted for [[Version 1.1b]]
 
* 10 Sep 2014: new web site set up
 
* 10 Sep 2014: new web site set up
  
 
=== Contents ===
 
=== Contents ===
 
{| width=100% border=1  
 
{| width=100% border=1  
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|- valign=top
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| width=50% |
 
| width=50% |
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* {{BFS pdf|Preface and Contents|bfs-frontmatter|14Sep14}}
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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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* '''Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|14Sep14}}'''
 
** Systems Biology: Modeling, Analysis and the Role of Feedback
 
** Systems Biology: Modeling, Analysis and the Role of Feedback
 
** The Cell as a System
 
** The Cell as a System
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** Input/Output Modeling
 
** Input/Output Modeling
 
** From Systems to Synthetic Biology
 
** From Systems to Synthetic Biology
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* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|14Sep14}}
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* '''Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|14Sep14}}'''
 
** Modeling Techniques
 
** Modeling Techniques
 
** Transcription and Translation
 
** Transcription and Translation
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** Post-Transcriptional Regulation
 
** Post-Transcriptional Regulation
 
** Cellular Subsystems
 
** Cellular Subsystems
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* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|14Sep14}}
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* '''Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|14Sep14}}'''
 
** Analysis Near Equilibria
 
** Analysis Near Equilibria
 
** Robustness
 
** Robustness
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** Bifurcations
 
** Bifurcations
 
** Model Reduction Techniques
 
** Model Reduction Techniques
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* Chapter 4: {{BFS pdf|Stochastic Modeling and Analysis|bfs-stochastic|14Sep14}}
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* '''Chapter 4: {{BFS pdf|Stochastic Modeling and Analysis|bfs-stochastic|14Sep14}}'''
 
** Stochastic Modeling of Biochemical Systems
 
** Stochastic Modeling of Biochemical Systems
 
** Simulation of Stochastic Systems
 
** Simulation of Stochastic Systems
 
** Input/Output Linear Stochastic Systems
 
** Input/Output Linear Stochastic Systems
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* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|14Sep14}}
 
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** The ''lac'' Operon
 
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** Bacterial chemotaxis|bfs-chemotaxis
 
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-->
 
 
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| width=50% |
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* Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|14Sep14}}
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* '''Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|14Sep14}}'''
 
** Introduction to Biological Circuit Design
 
** Introduction to Biological Circuit Design
 
** Negative Autoregulation
 
** Negative Autoregulation
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** An Incoherent Feedforward Loop (IFFL)
 
** An Incoherent Feedforward Loop (IFFL)
 
** Bacterial Chemotaxis
 
** Bacterial Chemotaxis
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* Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|14Sep14}}
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* '''Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|14Sep14}}'''
 
** Input/Output Modeling and the Modularity Assumption
 
** Input/Output Modeling and the Modularity Assumption
 
** Introduction to Retroactivity
 
** Introduction to Retroactivity
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** Insulation Devices: Retroactivity Attentuation  
 
** Insulation Devices: Retroactivity Attentuation  
 
** A Case Study on the Use of Insulation Devices
 
** 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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* '''Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|14Sep14}}'''
 
** Competition for Shared Cellular Resources
 
** Competition for Shared Cellular Resources
 
** Stochastic Effects: Design Tradeoffs in Systems with Large Gains
 
** Stochastic Effects: Design Tradeoffs in Systems with Large Gains
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<!--
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* '''{{BFS pdf|Bibliography and Index|bfs-backmatter|14Sep14}}'''
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* Appendix A: A Primer on Control Theory
 
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* Appendix A: Cell Biology Primer (from NCBI)
 
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** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_cell.html What is a Cell]
 
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** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_genome.html What is a Genome]
 
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** [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|14Sep14}}
 
 
|}
 
|}
  
 
=== Resources ===
 
=== Resources ===
 
* [[Errata|List of errata]]
 
* [[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

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