SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

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TitleSBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
Publication TypeJournal Article
Year of Publication2009
AuthorsDräger, A, Planatscher, H, Wouamba, DMotsou, Schröder, A, Hucka, M, Endler, L, Golebiewski, M, Müller, W, Zell, A
JournalBioinformatics
Volume25
Issue11
Pagination1455-6
Date Published2009 Jun 1
ISSN1367-4811
KeywordsDatabase Management Systems, Humans, Programming Languages, Software, Systems Biology, User-Computer Interface
Abstract

<p><b>SUMMARY: </b>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(A)T(E)X, 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(A)T(E)X and PDF, and provides many settings for customization.</p><p><b>AVAILABILITY: </b>Source code, documentation and a web service are freely available at (http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX).</p>

DOI10.1093/bioinformatics/btp170
Alternate JournalBioinformatics
PubMed ID19307240
PubMed Central IDPMC2682517