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Bioinformatics Advance Access originally published online on August 4, 2005
Bioinformatics 2005 21(18):3688-3690; doi:10.1093/bioinformatics/bti603
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Bifurcation discovery tool

Vijay Chickarmane 1,*, Sri R. Paladugu 1, Frank Bergmann 1 and Herbert M. Sauro 1,2

1Keck Graduate Institute 535 Watson Dr, Claremont, CA 91711, USA
2Control and Dynamical Systems, California Institute of Technology Pasadena, CA 91125

*To whom correspondence should be addressed.

Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation points in arbitrary ODE-based reaction networks by directing the user to regions in the parameter space, where such interesting dynamical behavior can be observed.

Results: We have implemented a genetic algorithm that searches for Hopf bifurcations, turning points and bistable switches. The software is implemented as a Systems Biology Workbench (SBW) enabled module and accepts the standard SBML model format. The interface permits a user to choose the parameters to be searched, admissible parameter ranges, and the nature of the bifurcation to be sought. The tool will return the parameter values for the model for which the particular behavior is observed.

Availability: The software, tutorial manual and test models are available for download at the following website: http:/www.sys-bio.org/ under the bifurcation link. The software is an open source and licensed under BSD.

Contact: vijay_chickarmane{at}kgi.edu

Received on April 8, 2005; revised on July 1, 2005; accepted on July 27, 2005

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