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Bioinformatics Advance Access published online on March 23, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm105
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SBML Export Interface for the Systems Biology Toolbox for MATLAB

Henning Schmidt 1, Gunnar Drews 2, Julio Vera 2 and Olaf Wolkenhauer 2

1Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden
2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany

*To whom correspondence should be addressed. Henning Schmidt, E-mail: henning{at}fcc.chalmers.se, henning.schmidt{at}fcc.chalmers.se


  Abstract

Summary: In this application note we present an SBML export interface for the Systems Biology Toolbox for MATLAB. This interface allows modelers to automatically convert models, represented in the oolbox's own format (SBmodels) to SBML files. Since SBmodels do not explicitly contain all the information that is required to generate SBML, the necessary information is gathered by parsing SBmodels. The export can be done in two different ways. Firstly, it is possible to call the export from the command line, thereby directly converting a model to an SBML file. The second option is to inspect and edit the conversion results with the help of a graphical user interface, and to subsequently export the model to SBML.

Availability: The SBML export interface has been integrated into the Systems Biology Toolbox for MATLAB, which is open source and freely available from http://www.sbtoolbox.org. The website also contains a tutorial, extensive documentation, and examples.

Associate Editor: Prof. Martin Bishop

Received on January 29, 2007; revised on March 9, 2007; accepted on March 9, 2007

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