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Bifurcation discovery tool

Chickarmane, Vijay and Paladugu, Sri R. and Bergmann, Frank and Sauro, Herbert M. (2005) Bifurcation discovery tool. Bioinformatics, 21 (18). pp. 3688-3690. ISSN 1367-4803. http://resolver.caltech.edu/CaltechAUTHORS:CHIoupbioinfo05

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Abstract

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.


Item Type:Article
Additional Information:© The Author 2005. Published by Oxford University Press. All rights reserved. Received on April 8, 2005; revised on July 1, 2005; accepted on July 27, 2005. V.C. would like to acknowledge Professor John Tyson for fruitful discussions and encouragement. The authors thank Anastasia Deckard for a critical review of the manuscript. H.M.S., V.C. and F.B. are grateful to generous support from the DARPA/IPTO BioCOMP program, contract number MIPR 03-M296-01. SRP is supported by a grant from the DOE GTL Program. Conflict of Interest: none declared.
Record Number:CaltechAUTHORS:CHIoupbioinfo05
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:CHIoupbioinfo05
Alternative URL:http://dx.doi.org/10.1093/bioinformatics/bti603
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4374
Collection:CaltechAUTHORS
Deposited By: Lindsay Cleary
Deposited On:18 Aug 2006
Last Modified:26 Dec 2012 08:59

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