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Bioinformatics Advance Access published online on June 22, 2007
Bioinformatics, 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 a,* and Herbert M. Sauro b

aKeck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA
bDepartment of Bioengineering, University of Washington, Seattle, WA 98195, USA

*to whom correspondence should be addressed. Dr. Ravishankar Vallabhajosyula, E-mail: rrao{at}kgi.edu


  Abstract

Motivation: This paper 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.

Associate Editor: Dr. Olga Troyanskaya

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

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