Introduction

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).

Publications

  1. SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
    Cite this
    Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A, 2009-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Andreas Dräger
    Developer

  2. Hannes Planatscher
    Developer

  3. Dieudonné Motsou Wouamba
    Developer

  4. Adrian Schröder
    Developer

  5. Michael Hucka
    Developer

  6. Lukas Endler
    Developer

  7. Martin Golebiewski
    Developer

  8. Wolfgang Müller
    Developer

  9. Andreas Zell
    Investigator

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Summary
AccessionBT006496
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndreas Zell