A MATLAB application from the field of systems biology was chosen for experimental runs. The application was created using SimBiology® which extends MATLAB® with functionality for modeling, simulating, and analyzing biochemical pathways.
The application allows a user to model and simulate the dynamics of a simple gene regulation network, and understand the effect of stochasticity on the final state of the system. A ensemble of stochastic runs were performed on a gene-regulation model, and the distribution of state was studied at any given time point. Several hundred thousand simulations might need to be performed to obtain a smooth probability distribution function, requiring several days of computation on one MATLAB.
% The model used in this script was adpated from the following publication : % Kepler TB, Elston TC. Stochasticity in transcriptional regulation: % Origins, consequences and % mathematical representations. Biophys J. % 2001;81:3116–3136. clear all
job=batch('Exercise5_simBioScriptParfor','matlabpool',2, 'Configuration', defaultParallelConfig());
hist(dataParfor(:,1)) title('Histogram of protein state at t = 1000 s') xlabel('Protein State') ylabel('Frequency')