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Bioinformatics. 2010 Nov 1;26(21):2794-5. doi: 10.1093/bioinformatics/btq512. Epub 2010 Sep 9.

SBML2TikZ: supporting the SBML render extension in LaTeX.

Author information

1
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.

Abstract

MOTIVATION:

The SBML Render Extension enables coloring and shape information of biochemical models to be stored in the Systems Biology Markup Language (SBML). Rendering of this stored graphical information in a portable and well supported system such as TeX would be useful for researchers preparing documentation and presentations. In addition, since the Render Extension is not yet supported by many applications, it is helpful for such rendering functionality be extended to the more popular CellDesigner annotation as well.

RESULTS:

SBML2TikZ supports automatic generation of graphics for biochemical models in the popular TeX typesetting system. The library generates a script of TeX macro commands for the vector graphics languages PGF/TikZ that can be compiled into scalable vector graphics described in a model.

AVAILABILITY:

Source code, documentation and compiled binaries for the SBML2TikZ library can be found at http://www.sbml2tikz.org. In addition, a web application is available at http://www.sys-bio.org/layout

PMID:
20829443
PMCID:
PMC2981496
DOI:
10.1093/bioinformatics/btq512
[Indexed for MEDLINE]
Free PMC Article
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