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Bioinformatics Advance Access originally published online on June 25, 2008
Bioinformatics 2008 24(17):1963-1965; doi:10.1093/bioinformatics/btn319
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparing simulation results of SBML capable simulators

Frank T. Bergmann 1,2,* and Herbert M. Sauro 1

1University of Washington, Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061 and 2Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being able to compare their simulation results.

Summary: We present an approach to compare simulation results between several SBML capable simulators and provide a website for the community to share simulation results.

Availability: The website with simulation results and additional material can be found under: http://sys-bio.org/sbwWiki/compare. The software used to generate the simulation results is available on the website for download.

Contact: fbergman@u.washington.edu

Associate Editor: Trey Ideker

Received on December 4, 2007; revised on June 2, 2008; accepted on June 19, 2008

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