Difference between revisions of "Supplement: Biomolecular Feedback Systems"
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{{supheaderBiological Systems}}  {{supheaderBiological Systems}}  
−  <font size="+1">Domitilla Del Vecchio (  +  <font size="+1">Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)</font> 
−  {{  +  {{warningThis page is out of date. See http://www.cds.caltech.edu/~murray/BFSwiki for the latest version}} 
−  This  +  
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−  +  __NOTOC__  
+  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 [[http:www.mit.edu/~ddv/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.  
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−  +  
−  +  
−  ===  +  <! {{BFS quick links}} > 
−  The  +  ===== News ([[BFS:Archived newsarchive]]) ===== 
+  * 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 57) + bibliography. A {{BFS pdfcomplete manuscriptbfspublic19Jan14}} 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 {{BFS pdfcomplete manuscriptbfspublic11Jul12}} is also available.  
+  <p>  
−  {  +  === Contents === 
+  { width=100% border=1  
 valign=top   valign=top  
 width=50%    width=50%   
−  +  * {{BFS pdfPreface and Contentsbfsfrontmatter05Dec13}}  
−  +  * Chapter 1: {{BFS pdfIntroductory Conceptsbfsintro05Dec13}}  
−  *  +  ** 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: {{BFS pdfCore Processesbfscoreproc07Dec13}} 
−  **  +  ** Modeling Techniques 
−  *  +  ** Transcription and Translation 
−  *  +  ** Transcriptional Regulation 
−  *  +  ** PostTranscriptional Regulation 
−  *  +  ** Cellular Subsystems 
−  +  * Chapter 3: {{BFS pdfDynamic Behaviorbfsdynamics11Dec13}}  
−  +  ** Analysis Near Equilibria  
−  *  +  ** Robustness 
−  *  +  ** Oscillatory Behavior 
−  *  +  ** Bifurcations 
−  *  +  ** Model Reduction Techniques 
−  +  * Chapter 4: {{BFS pdfStochastic Modeling and Analysisbfsstochastic06Jan14}}  
−  +  ** Stochastic Modeling of Biochemical Systems  
−  *  +  ** Simulation of Stochastic Systems 
−  *  +  ** Input/Output Linear Stochastic Systems 
−  *  +  <! 
−  +  * Chapter 5: {{BFS pdfFeedback Examplesbfsfbkexamps11Jul12}}  
−  +  ** The ''lac'' Operon  
−    +  ** Bacterial chemotaxisbfschemotaxis 
−  +  >  
−  +  
−  *  +  
−  *  +  
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−  }  +  
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−  The  +  
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 width=50%    width=50%   
−  *  +  * Chapter 5: {{BFS pdfBiological Circuit Componentsbfscircuits19Jan14}} 
−  *  +  ** Introduction to Biological Circuit Design 
−  *  +  ** Negative Autoregulation 
−  *  +  ** The Toggle Switch 
−  * Activatorrepressor  +  ** The Repressilator 
−  * Chemotaxis:  +  ** Activatorrepressor Clock 
−  * Input  +  ** An Incoherent Feedforward Loop (IFFL) 
−    +  ** Bacterial Chemotaxis 
−  *  +  * Chapter 6: {{BFS pdfInterconnecting Componentsbfsmodules19Jan14}} 
−  *  +  ** 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: {{BFS pdfDesign Tradeoffsbfstradeoffs19Jan14}} 
−  *  +  ** Competition for Shared Cellular Resources 
−  *  +  ** Stochastic Effects: Design Tradeoffs in Systems with Large Gains 
−  *  +  * Appendix A: A Primer on Control Theory 
+  <!  
+  * 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_genome.html What is a Genome]  
+  ** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_molecular.html Molecular Genetics: Piecing It Together]  
+  ** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]  
+  * Appendix C: {{BFS pdfRandom Processesbfsrandom11Jul12}}  
+  ** Random Variables  
+  ** ContinuousState Random Processes  
+  ** DiscreteState Random Processes  
+  >  
+  * {{BFS pdfBibliography and Indexbfsbackmatter19Jan14}}  
}  }  
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Latest revision as of 22:01, 14 September 2014
Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)

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 57) + 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

