Bifurcation discovery tool.
BACKGROUND
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.


BACKGROUND
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.
Chickarmane
Vijay
V
Keck Graduate Institute, Claremont, CA 91711, USA. vijay_chickarmane@kgi.edu
Paladugu
Sri R
SR
Bergmann
Frank
F
Sauro
Herbert M
HM
D000465:Algorithms; D001671:Biochemistry / Q000379:methods*; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D003198:Computer Simulation; D020407:Internet; D017711:Nonlinear Dynamics; D009991:Oscillometry; D012984:Software; D049490:Systems Biology / Q000379:methods; D013995:Time; D013997:Time Factors