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Enhancing e-Infrastructures with Advanced Technical Computing: Parallel MATLAB® on the Grid

Enhancing e-Infrastructures with Advanced Technical Computing: Parallel MATLAB® on the Grid

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12 Sep 2008 (Updated )

code exercises for M11 tutorial at SC08

Exercise5_batch_parfor

Contents

Information about model application

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

Submitting a Script that Uses Parfor

job=batch('Exercise5_simBioScriptParfor','matlabpool',2, 'Configuration', defaultParallelConfig());

Wait for results and load back into the client workspace

wait(job);
load(job);

Plotting histogram of the results

hist(dataParfor(:,1))
title('Histogram of protein state at t = 1000 s')
xlabel('Protein State')
ylabel('Frequency')

Destroy job when finished

destroy(job);

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