Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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(Contents)
(Contents)
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** Input/Output Modeling
 
** Input/Output Modeling
 
** Analysis Near Equilibria
 
** Analysis Near Equilibria
 +
** Robustness
 
** Analysis of Reaction Rate Equations
 
** Analysis of Reaction Rate Equations
 
** Limit Cycle Behavior
 
** Limit Cycle Behavior
** Analysis Using Describing Functions
 
 
** Bifurcations
 
** Bifurcations
 
** Model Reduction Techniques
 
** Model Reduction Techniques
 
* Chapter 4: {{BFS pdf|Stochastic Behavior|bfs-stochastic|16Jan11}}
 
* Chapter 4: {{BFS pdf|Stochastic Behavior|bfs-stochastic|16Jan11}}
 
** Stochastic Modeling of Biochemical Systems
 
** Stochastic Modeling of Biochemical Systems
** (Simulation of Stochastic Systems)
+
** Simulation of Stochastic Systems
** Analysis of Stochastic Systems
+
** Linearized Modeling and Analysis
** (Linearized Modeling and Analysis)
+
** (Markov Chain Modeling and Analysis)
+
** (System Identification Techniques)
+
** (Model Reduction)
+
 
| width=50% |
 
| width=50% |
 
* Chapter 5: Feedback Examples
 
* Chapter 5: Feedback Examples
** Lac Operon
+
** {{BFS pdf|The lac Operon|bfs-lacoperon|16Jan12}}
** Phage <math>\lambda</math>
+
** (Heat shock)
** Signaling pathways in yeast
+
** (Phage <math>\lambda</math>)
 
** {{BFS pdf|Bacterial chemotaxis|bfs-chemotaxis|11Mar10}}
 
** {{BFS pdf|Bacterial chemotaxis|bfs-chemotaxis|11Mar10}}
 +
** (Signaling pathways in yeast)
 
* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|30Mar10}}
 
* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|30Mar10}}
 
** Biological Circuit Design
 
** Biological Circuit Design
 +
** Introduction
 
** Self-repressed Gene
 
** Self-repressed Gene
 
** The Toggle Switch
 
** The Toggle Switch
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* Chapter 7: {{BFS pdf|Interconnecting Components|bfs-modules|30Mar10}}
 
* Chapter 7: {{BFS pdf|Interconnecting Components|bfs-modules|30Mar10}}
 
** Input/Output Modeling and the Modularity Assumption
 
** Input/Output Modeling and the Modularity Assumption
** Beyond the Modularity Assumption: Retroactivity
+
** Introduction to Retroactivity
 +
** Retroactivity in Gene Transcriptional Circuits
 +
** Retroactivity in Signaling Systems
 
** Insulation Devices to Enforce Modularity  
 
** Insulation Devices to Enforce Modularity  
** Design of Genetic Circuits under the Modularity Assumption
+
** Retroactivity and noise
** Biological Realizations of an Insulation Component
+
* Chapter 8: Design Tradeoffs and Examples
* Chapter 8: Design Tradeoffs
+
* Chapter 9: Design Examples
+
 
* Appendix A: Cell Biology Primer (from NCBI)
 
* 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_cell.html What is a Cell]
Line 77: Line 75:
 
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_molecular.html Molecular Genetics: Piecing It Together]
 
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_molecular.html Molecular Genetics: Piecing It Together]
 
** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]
 
** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]
* Appendix B: A Primer on Control Theory
+
* Appendix B: {{BFS pdf|A Primer on Control Theory|bfs-control|16Jan12}}
 
* Appendix C: {{BFS pdf|Random Processes|bfs-random|26Dec10}}
 
* Appendix C: {{BFS pdf|Random Processes|bfs-random|26Dec10}}
 
* {{BFS pdf|Bibliography and Index|bfs-backmatter|23Jan11}}
 
* {{BFS pdf|Bibliography and Index|bfs-backmatter|23Jan11}}

Revision as of 18:36, 16 January 2012

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


This supplement 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 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)
  • 23 Jan 2011: Updated Ch 3: split out robustness analysis section and added intro material for oscillations section
  • 16 Jan 2011: Posted updated copy of Ch 3 and fixed link to Ch 4
    • Ch 3: notation changed to match Ch 2 + lots of little fixes
  • 27 Dec 2010: Updated outline, with updated links to Ch 1, 2 and 4
    • Ch 1: previous cell biology tutorial has been moved to Appendix A; replaced with general intro
    • Ch 2: moved cell dynamics and control to Ch 1; added new examples
    • Ch 4: moved overview of random processes to Appendix C; chapter still very incomplete
  • 30 Mar 2010: Posted circuits and modularity chapters

Contents

  • Preface and Contents (PDF)
  • Chapter 1: Introductory Concepts (PDF)
    • Systems Biology: Modeling, Analysis and the Role of Feedback
    • Dynamics and Control in the Cell
    • Control and Dynamical Systems Tools
    • 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)
    • Input/Output Modeling
    • Analysis Near Equilibria
    • Robustness
    • Analysis of Reaction Rate Equations
    • Limit Cycle Behavior
    • Bifurcations
    • Model Reduction Techniques
  • Chapter 4: Stochastic Behavior (PDF)
    • Stochastic Modeling of Biochemical Systems
    • Simulation of Stochastic Systems
    • Linearized Modeling and Analysis

Additional Information