Software

Software

Modellling and Simulation of IntraCellular Dynamics: Choosing an Appropriate Framework

This page contains material related to the paper:

Wolkenhauer O, Ullah M, Kolch W, Cho KH
Modellling and Simulation of IntraCellular Dynamics: Choosing an Appropriate Framework
IEEE Transactions on NanoBioScience, Vol. 3, No. 3, pp. 200-207, September 2004; PMID: 15473072

These files are fully commented!

reactiondata.m
Sets parameters for simulations
gillespie.m
Function to implement gillespie algorithm
gma.m
Function to implement law of mass action
stoch_gma.m
Function that implements Gillespie algorithm and GMA
illu_a.m
Script file to illustrate dependence of a_\mu on initial number of molecules
illu_std.m
Script file to illustrate variability as a function of the initial number of molecules
illu_sim.m
Script file to compare solutions of the GMA with stochastic simulations
preprint.m
Function to prepare the figures for nice printing
matfactorial.m
Matrix version of factorial
matnchoosek.m
Matrix version of nchoosek

Info: Matlab-files are developed in Matlab 7