## 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.

## Submitting Parallel Version Using Jobs and Task

numberOfRuns = 20; noWorkers = 2;

## Creating Job and associated Tasks

% Number of tasks per worker runsPerWorkers = ones(noWorkers,1).*floor(numberOfRuns/noWorkers) ; runsPerWorkers(end) = numberOfRuns - sum(runsPerWorkers(1:end-1)); % Create job job = createJob(); % uses defaultParallelConfig % Create tasks for job2 distributing runs across workers for i = 1 : noWorkers createTask(job, @sbiosimulate_wrapper, 1, {runsPerWorkers}); end

## Submitting Job

disp('Submitting job ...'); submit(job) disp('Waiting for job ...'); waitForState(job,'finished') disp('Job Finished');

Submitting job ... Waiting for job ... Job Finished

## Collect Results from Job

output = getAllOutputArguments(job); % Get output arguments histData = cell2mat(output); % Combine output to get data for histogram % Plot results hist(histData(:,1)) title('Histogram of protein state at t = 1000 s') xlabel('Protein State') ylabel('Frequency')

## Destroy job

```
destroy(job);
disp('Job destroyed...');
```

Job destroyed...