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wiki:chapter_2:biological_dynamics_and_reaction_kinetics [2013/04/03 11:09] emj |
wiki: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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| - | * These all depend on Mathematica (R) and xCellerator. | + | * These all depend on Mathematica(R) and xCellerator. See [[wiki:software_availability|Software availability]] |
| - | * Where to get xCellerator: http://www.xcellerator.info/ . | + | |
| * {{:wiki:chapter_2:intro_example.nb|Introductory example: {A->B, B->C}}} | * {{:wiki:chapter_2:intro_example.nb|Introductory example: {A->B, B->C}}} | ||
| * {{:wiki:chapter_2:massaction.nb|Mass action kinetics}} | * {{:wiki:chapter_2:massaction.nb|Mass action kinetics}} | ||
| * {{:wiki:chapter_2:ssa_example.nb|Stochastic simulation algorithm (SSA) example}} | * {{:wiki:chapter_2:ssa_example.nb|Stochastic simulation algorithm (SSA) example}} | ||
| - | * PIP3 metabolism | + | * {{: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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| * S-E-P deterministic simulation | * S-E-P deterministic simulation | ||
| * S-E-P stochastic simulation | * S-E-P stochastic simulation | ||
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