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Bioinformatics Advance Access originally published online on March 23, 2009
Bioinformatics 2009 25(11):1455-1456; doi:10.1093/bioinformatics/btp170
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SBML2LATEX: Conversion of SBML files into human-readable reports

Andreas Dräger 1,*, Hannes Planatscher 1, Dieudonné Motsou Wouamba 1, Adrian Schröder 1, Michael Hucka 2, Lukas Endler 3, Martin Golebiewski 4, Wolfgang Müller 4 and Andreas Zell 1

1Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany, 2Beckman Institute BNMC, California Institute of Technology, Pasadena, CA, USA, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK and 4Scientific Databases and Visualization Group, EML Research gGmbH, Heidelberg, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LATEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LATEX and PDF, and provides many settings for customization.

Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX.

Contact:andreas.draeger{at}uni-tuebingen.de

Supplementary information:Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

Received on January 21, 2009; revised on February 27, 2009; accepted on March 17, 2009

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