Systems Biology: Computational and Mathematical Methods

by E. Mjolsness, P. Baldi, and B. Shapiro

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wiki:chapter_2:biological_dynamics_and_reaction_kinetics [2013/03/24 16:40] – [Text Outline] emjwiki:chapter_2:biological_dynamics_and_reaction_kinetics [2013/04/03 15:40] (current) – emj
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-====== Chapter 2: Biological Dynamics and Reaction Kinetics ======+====== Chapter 2: Reaction Kinetics and Biological Dynamics ======
  
  
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-    * Mass action kinetics +    * These all depend on Mathematica(R) and xCellerator. See [[wiki:software_availability|Software availability]] 
-    * Stochastic simulation algorithm +    * {{:wiki:chapter_2:intro_example.nb|Introductory example: {A->B, B->C}}} 
-    * PIP3 metabolism+    * {{:wiki:chapter_2:massaction.nb|Mass action kinetics}} 
 +    * {{:wiki:chapter_2:ssa_example.nb|Stochastic simulation algorithm (SSA) example}} 
 +    * {{:wiki:chapter_2:pip3metablismv2.nb|PIP3 metabolism}}
     * Analytic solution of 2×2 master equation for binding/unbinding     * Analytic solution of 2×2 master equation for binding/unbinding
     * Analytic solution of trivalent reaction A+B <–> C     * Analytic solution of trivalent reaction A+B <–> C
 +    * {{:wiki:chapter_2:huang_ferrell_1996_mapkv2.nb|MAPK cascade model}} of Huang and Ferrell 1996
  
  
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-==== Figures: sources ====+==== Figures - electronic sources ====
  
  
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     * S-E-P deterministic simulation     * S-E-P deterministic simulation
     * S-E-P stochastic simulation     * S-E-P stochastic simulation
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 +==== Bibliography - electronic access - chapter 2 ====
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 +    * [[:wiki:chapter_2:Chapter 2 electronic bibliography|Here]]
  
  
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     * 2.4 Causal network dynamics     * 2.4 Causal network dynamics
     * 2.5 Summary     * 2.5 Summary
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 ===== Missing Topics ===== ===== Missing Topics =====

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