Deterministic Modelling and Stochastic Simulation of Pathways using Matlab

This page contains material related to the paper:

Ullah M, Schmidt H, Cho KH, Wolkenhauer O
Deterministic Modelling and Stochastic Simulation of Pathways using Matlab
IEE Proc Systems Biology, Vol.153, No.2, pp. 53-60, March 2006; PMID: 16986253

Main Matlab M-files

enzymkin.m
Temporal evolution for enzyme kinetic example
gma.m
Function that implements the generalized law of mass action
MAPK.xls
Excel spreadsheet containg pathway information
mapk.mat
Data file needed for simulation
genmapk.m
Script file to generate the data file mapk.mat
timehistory.m
Temporal evolution for MAPK pathway
stimresp.m
Stimulus response curve for MAPK pathway
kholodenko.m
Illustrtates Michaelis-Menten Kinetics for MAPK pathway
reactiondata.m
Parameters for the enzymatic example
stoch.m
Function to implement Gillespie algorithm
enzkin_stoch.m
Stochastic simulation of enzymatic example using Gillespie algorithm
calcium.m
Stochastic simulation of calcium example using Markov process
importSBML.m
imports an SBML model and determines the data required for simulation
test.xml
test SBML model for importSBML.m

Additional example (Lotka-Voltera model)

lotka_voltera_data.m
parameters for the Lotka-Voltera example
lotka_voltera_sim.m
Stochastic simulation of Lotka-Voltera example

Info: Matlab-files are developed in Matlab 7