SBW - a modular framework for systems biology
Proceedings of the 38th conference on Winter simulation
Approaches to complexity reduction in a systems biology research environment (SYCAMORE)
Proceedings of the 38th conference on Winter simulation
Target driven biochemical network reconstruction based on petri nets and simulated annealing
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
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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@kgi.edu