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Bioinformatics Advance Access originally published online on November 29, 2005
Bioinformatics 2006 22(4):514-515; doi:10.1093/bioinformatics/bti799
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology

Henning Schmidt * and Mats Jirstrand

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

*To whom correspondence should be addressed.

Summary: We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

Availability: The Systems Biology Toolbox for MATLAB is open source and freely available from http://www.sbtoolbox.org. The website also contains a tutorial, extensive documentation and examples.

Contact: henning{at}fcc.chalmers.se

Received on November 7, 2005; revised on November 22, 2005; accepted on November 23, 2005

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