Model Fitting Tools for BioSPICE and the Systems
Biology Workbench
Vijay S. Chickarmane, Cameron Wellock, Herbert M. Sauro
ABSTRACT
As a contribution to the BioSPICE project, we have developed an optimization module, for the task of fitting kinetic rate constants to time series concentration data. The algorithms use, both local searches, such as the Levenberg-Marquardt, and simplex, as well
as global search methods such as simulated annealing and real coded genetic algorithms. We provide a description of the modules in terms of the algorithms used, and the software components. We describe a few test cases which serve the purpose of demonstrating the software. We comment on determination of confidence limits, and issues related to observability of the fitted parameters.
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Bifurcation discovery tool
Vijay Chickarmane, Sri R. Paladugu, Frank Bergmann, and Herbert M. Sauro
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 BiologyWorkbench (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 here. The software is an open source and licensed under BSD.
Contact: vijay_chickarmane@kgi.edu
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