Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
5. Matlab Interface
6. Optimization
6. Bifurcation
maintained by Frank Bergmann

Algorithm Development

In silico Evolution

Conservation Analysis

Optimization Methods

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.

Full Paper

Bifurcation Discovery

Bifurcation discovery tool

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

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.


Full Paper

sysbio/algorithmdevelopment.txt · Last modified: 2009/01/11 17:27 (external edit)

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