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Bioinformatics Advance Access originally published online on January 18, 2007
Bioinformatics 2007 23(5):646-647; doi:10.1093/bioinformatics/btl668
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB

Henning Schmidt

Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Chalmers Science Park, SE-41288 Göteborg


  Abstract

Summary: We present the SBaddon package as an extension to the Systems Biology Toolbox for MATLAB (SBtoolbox). The goal of this extension is to provide the users of the SBtoolbox with important functionality that is needed for parameter estimation applications. While simulation in the SBtoolbox relies on the MATLAB ODE solvers, the SBaddon package provides considerably increased simulation performance through automatic generation of compiled simulation functions. Furthermore, the package contains improved optimization algorithms, forward parameter sensitivity analysis and basic numeric parameter identifiability analysis.

Availability: The SBaddon package is open source and freely available for non-commercial use. Commercial use of SBaddon is only possible through a specific licensing agreement (contact sbaddon{at}sbtoolbox.org). SBaddon can be obtained from http://www.sbtoolbox.org/SBaddon. The website also contains extensive documentation, and examples.

Contact: henning{at}fcc.chalmers.se

Received on November 9, 2006; revised on December 8, 2006; accepted on December 29, 2006

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