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Gillespie's Direct Method Stochastic Simulation Algorithm

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09 Dec 2011 (Updated )

Code to stochastically simulate coupled chemical reactions.

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Description

This code implements the Stochastic Simulation Algorithm (direct method) published by D.T. Gillespie in 1977 in the Journal of Physical Chemistry.

Default reactions and analytical solutions correspond to a simple model of gene expression for a single cell (Kaern et al.,Nat.Rev.Genet.,2005): Pro-->M-->P, with mRNA (M-->0) and protein (P-->0) decay, when the gene is assumed to be constantly expressed (Pro denotes the promoter of the gene) and cell volume is constant and set to unity. The mRNA and protein time series and probability histograms are plotted.

MATLAB release MATLAB 7.11 (R2010b)
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Comments and Ratings (3)
27 Mar 2013 ceci

ceci (view profile)

 
02 May 2012 Jody

Jody (view profile)

I found a typo, please contact me.
Regards,

JAM Lugger j.a.m.lugger@student.tue.nl

17 Feb 2012 Erdal Bizkevelci  
Updates
06 Jan 2012 1.3

Corrected minor typo in code.

21 Dec 2012 1.8

Minor change to code to allow user to limit access to waitbar function (to reduce runtime).

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