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

SBML2LATEX: Conversion of SBML files into human-readable reports

Bioinformatics vol. 25 (2009), no. 11, pp. 1455-1456


Abstract

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 SBML2LATEX, 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, LATEX and PDF, and provides many settings for customization. AVAILABILITY: Source code, documentation and a web service are freely available at http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX.


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BibTeX

@article{Draeger2009b,
  author = {Dr\"ager, Andreas and Planatscher, Hannes and Wouamba, Dieudonn{\'e}
	Motsou and Schr\"oder, Adrian and Hucka, Michael and Endler, Lukas
	and Golebiewski, Martin and M\"uller, Wolfgang and Zell, Andreas},
  title = {{SBML2\LaTeX: Conversion of SBML files into human-readable reports}},
  journal = {Bioinformatics},
  year = {2009},
  volume = {25},
  pages = {1455--1456},
  number = {11},
  month = apr,
  abstract = {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 SBML2\LaTeX, 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, \LaTeX{}
	and PDF, and provides many settings for customization. AVAILABILITY:
	Source code, documentation and a web service are freely available
	at \url{http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX}.},
  doi = {10.1093/bioinformatics/btp170},
  pdf = {http://bioinformatics.oxfordjournals.org/cgi/reprint/25/11/1455.pdf},
  url = {http://dx.doi.org/10.1093/bioinformatics/btp170}
}