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Bioinformatics Advance Access published online on November 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm566
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The SBML Discrete Stochastic Models Test Suite

Thomas W. Evans 1, Colin S. Gillespie 2,3 and Darren J. Wilkinson 2,3,*

1Department of Mathematical Sciences, University of Liverpool, Liverpool, L69 7ZL.
2School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
3Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN), Newcastle University.

*To whom correspondence should be addressed. Darren J. Wilkinson, E-mail: d.j.wilkinson{at}ncl.ac.uk


  Abstract

Motivation: Stochastic simulation is a very important tool for mathematical modelling. However it is difficult to check the correctness of a stochastic simulator, since any two realisations from a single model will typically be different.

Results: We have developed a test suite of stochastic models which have been solved either analytically or using numerical methods. This allows the accuracy of stochastic simulators to be tested against known results. The test suite is already being used by a number of stochastic simulator developers.

Availability: The latest version of the test suite can be obtained from http://www.calibayes.ncl.ac.uk/Resources/dsmts/ and is licensed under GNU Lesser General Public License.

Contact: d.j.wilkinson{at}ncl.ac.uk

Associate Editor: Prof. Thomas Lengauer

Received on September 17, 2007; revised on October 18, 2007; accepted on November 7, 2007

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