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Bioinformatics Advance Access originally published online on June 22, 2007
Bioinformatics 2007 23(14):1859-1861; doi:10.1093/bioinformatics/btm231
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Stochastic simulation GUI for biochemical networks

Ravishankar Rao Vallabhajosyula 1,* and Herbert M. Sauro 2

1Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA and 2Department of Bioengineering, University of Washington, Seattle, WA 98195, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: This article describes the development of a useful graphical user interface for stochastic simulation of biochemical networks which allows model builders to run stochastic simulations of their models and perform statistical analysis on the results. These include the construction of correlations, power-spectral densities and transfer functions between selected inputs and outputs.

Availability: The software is licensed under the BSD open source license and is available at http://sourceforge.net/projects/jdesigner. In addition, a more detailed account of the algorithms employed in the tool can be found at the Wiki at http://www.sys-bio.org/sbwWiki.

Contact: rrao{at}kgi.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Olga Troyanskaya

Received on December 16, 2006; revised on April 17, 2007; accepted on April 26, 2007

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[Abstract] [Full Text] [PDF]


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