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


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


Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, HepatoSys

Bioinformatics 25(11): 1455-6
23rd Mar 2009

Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell

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[Andreas Dräger] [Adrian Schröder] [Martin Golebiewski] [Wolfgang Müller] [Andreas Zell]

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Views: 2200
  • Created: 11th Jan 2011 at 11:11
  • Last updated: 24th Oct 2013 at 16:21

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