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Bioinformatics Advance Access originally published online on May 18, 2006
Bioinformatics 2006 22(15):1879-1885; doi:10.1093/bioinformatics/btl195
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A model diagram layout extension for SBML

Ralph Gauges *, Ursula Rost , Sven Sahle and Katja Wegner

Bioinformatics and Computational Biochemistry, EML Research Schloss-Wolfsbrunnen Weg 33, D-69118 Heidelberg, Germany

*To whom correspondence should be addressed.

Motivation: Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model.

Results: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation.

Availability: The complete specification can be found on (http://projects.villa-bosch.de/bcb/sbml/ (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, http://www.sbml.org/software/libsbml/).

Contact: Ralph.Gauges{at}eml-r.villa-bosch.de

Supplementary information: Supplementary data are available on Bioinformatics online.

Received on March 29, 2006; revised on May 10, 2006; accepted on May 15, 2006

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