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Bioinformatics Advance Access published online on August 4, 2005
Bioinformatics, 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@oupjournals.org
Received April 8, 2005
Revised July 1, 2005
Accepted July 27, 2005

Applications note

Bifurcation discovery tool

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

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

* To whom correspondence should be addressed.
Vijay Chickarmane, E-mail: vijay_chickarmane{at}kgi.edu


  Abstract

Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation, and chaotic dynamics. This article describes a tool which 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 open source and licensed under BSD.


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