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SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
Andreas Dräger1, Hannes Planatscher, Dieudonné Motsou Wouamba
1Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany. andreas.draeger@uni-tuebingen.de
Bioinformatics (Oxford, England)
|March 25, 2009
Summary
Systems Biology Markup Language (SBML) models are hard to read. SBML2LaTeX converts SBML to human-readable formats like LaTeX, aiding understanding and error detection.
Area of Science:
- Systems Biology
- Computational Biology
- Bioinformatics
Background:
- Systems Biology Markup Language (SBML) is a standard for computational models.
- SBML's XML format is difficult for human interpretation.
- Existing visualization tools often omit crucial model details.
Purpose of the Study:
- To develop a tool for generating human-readable reports from SBML models.
- To facilitate broader understanding and error detection in systems biology models.
- To support scientific writing with comprehensive model documentation.
Main Methods:
- Developed SBML2LaTeX, a Java-based standalone program.
- Implemented a web service for direct SBML conversion.
- Enabled conversion to LaTeX, PDF, and DVI formats with customization options.
Main Results:
- SBML2LaTeX generates human-readable reports from SBML files.
- The tool makes complex components like unit declarations and kinetic equations visible.
- A web service offers convenient online conversion capabilities.
Conclusions:
- SBML2LaTeX addresses the need for human-readable SBML model reports.
- The tool enhances model comprehension, scientific writing, and error checking.
- Freely available source code, documentation, and a web service support adoption.
