%0 Journal Article %1 Shen2010SBML2TikZ %A Shen, Si Yuan Y. %A Bergmann, Frank %A Sauro, Herbert M. %D 2010 %J Bioinformatics (Oxford, England) %K sbml software tikz tool %R 10.1093/bioinformatics/btq512 %T SBML2TikZ: Supporting the SBML Render Extension in LATEX. %U http://dx.doi.org/10.1093/bioinformatics/btq512 %X 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 T(E)X 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 T(E)X typesetting system. The library generates a script of T(E)X 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. CONTACT: hsauro@u.washington.edu.

@article{Shen2010SBML2TikZ, 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 {T(E})X 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 {T(E})X typesetting system. The library generates a script of {T(E})X 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. {CONTACT}: hsauro@u.washington.edu.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Shen, Si Yuan Y. and Bergmann, Frank and Sauro, Herbert M.}, biburl = {https://www.bibsonomy.org/bibtex/28f71991b6105b1ff7c9ddfb35eb7b970/karthikraman}, citeulike-article-id = {7844846}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btq512}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20829443}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20829443}, day = 9, doi = {10.1093/bioinformatics/btq512}, interhash = {250766151b37d56ab1daf403fa8893a6}, intrahash = {8f71991b6105b1ff7c9ddfb35eb7b970}, issn = {1367-4811}, journal = {Bioinformatics (Oxford, England)}, keywords = {sbml software tikz tool}, month = sep, pmid = {20829443}, posted-at = {2010-09-16 15:11:28}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {{SBML2TikZ}: Supporting the {SBML} Render Extension in {LATEX}.}, url = {http://dx.doi.org/10.1093/bioinformatics/btq512}, year = 2010 }