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Published March 23, 2009 | public
Journal Article

SBML2LATEX: Conversion of SBML files into human-readable reports


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 SBML2L^AT_EX, 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, L^AT_EX and PDF, and provides many settings for customization.

Additional Information

Short description: SBML2LaTeX is a tool to convert files in the System Biology Markup Language SBML) format into LaTeX files. A convenient online version (http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX/) is available, which allows the user to directly generate various file types from SBML including PDF, TeX, DVI, PS, EPS, GIF, JPG or PNG. SBML2LaTeX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose of SBML2LaTeX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication. © 2009 The Author(s). Received on January 21, 2009; revised on February 27, 2009; accepted on March 17, 2009. The authors are grateful to Henning Schmidt, Detlev Bannasch and Jochen Supper. Funding: German Federal Ministry of Education and Research (BMBF) [National Genome Research Network (NGFN+) under grant number 01GS08134; HepatoSys under grant number 0313080 L]; Federal state Baden-Württemberg in the Tübinger Bioinformatik-Grid under grant number 23-7532.24-4-18/1.

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