Difference between revisions of "Supplement: Biomolecular Feedback Systems"

From FBSwiki
Jump to: navigation, search
(News (archive))
(Contents)
Line 26: Line 26:
 
|- valign=top
 
|- valign=top
 
| width=50% |
 
| width=50% |
* {{BFS pdf|Preface and Contents|bfs-frontmatter|23Jan11}}
+
* {{BFS pdf|Preface and Contents|bfs-frontmatter|11Jul12}}
 
* Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|01Jan11}}
 
* Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|01Jan11}}
 
** Systems Biology: Modeling, Analysis and the Role of Feedback
 
** Systems Biology: Modeling, Analysis and the Role of Feedback
Line 38: Line 38:
 
** Post-Transcriptional Regulation
 
** Post-Transcriptional Regulation
 
** Cellular Subsystems
 
** Cellular Subsystems
* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|23Jan11}}
+
* Chapter 3: {{BFS pdf|Dynamic Behavior|bfs-dynamics|11Jul12}}
 
** Input/Output Modeling
 
** Input/Output Modeling
 
** Analysis Near Equilibria
 
** Analysis Near Equilibria
Line 46: Line 46:
 
** 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|11Jul12}}
 
** Stochastic Modeling of Biochemical Systems
 
** Stochastic Modeling of Biochemical Systems
 
** Simulation of Stochastic Systems
 
** Simulation of Stochastic Systems
 
** Linearized Modeling and Analysis
 
** Linearized Modeling and Analysis
* Chapter 5: Feedback Examples
+
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
 
** {{BFS pdf|The lac Operon|bfs-lacoperon|16Jan12}}
 
** {{BFS pdf|The lac Operon|bfs-lacoperon|16Jan12}}
 
** (Heat shock)
 
** (Heat shock)
Line 57: Line 57:
 
** (Signaling pathways in yeast)
 
** (Signaling pathways in yeast)
 
| width=50% |
 
| width=50% |
* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|30Mar10}}
+
* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|11Jul12}}
 
** Biological Circuit Design
 
** Biological Circuit Design
 
** Introduction
 
** Introduction
Line 64: Line 64:
 
** The Repressilator
 
** The Repressilator
 
** Activator-repressor Clock
 
** Activator-repressor Clock
* Chapter 7: {{BFS pdf|Interconnecting Components|bfs-modules|30Mar10}}
+
* Chapter 7: {{BFS pdf|Interconnecting Components|bfs-modules|11Jul12}}
 
** Input/Output Modeling and the Modularity Assumption
 
** Input/Output Modeling and the Modularity Assumption
 
** Introduction to Retroactivity
 
** Introduction to Retroactivity
Line 83: Line 83:
 
** PID control
 
** PID control
 
** Limits of performance, Robust performance
 
** Limits of performance, Robust performance
* Appendix C: {{BFS pdf|Random Processes|bfs-random|26Dec10}}
+
* Appendix C: {{BFS pdf|Random Processes|bfs-random|11Jul12}}
 
** Random Variables
 
** Random Variables
 
** Continuous-State Random Processes
 
** Continuous-State Random Processes

Revision as of 17:31, 12 July 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)
  • 12 Jul 2012: Updated outline; new PDFs posted.
  • 16 Jan 2012: Updated outline; new PDFs for all chapters and appendices (coming later today)
  • 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
    • Oscillatory Behavior
    • Bifurcations
    • Model Reduction Techniques
  • Chapter 4: Stochastic Behavior (PDF)
    • Stochastic Modeling of Biochemical Systems
    • Simulation of Stochastic Systems
    • Linearized Modeling and Analysis
  • Chapter 5: Feedback Examples (PDF)

Additional Information