{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:19:55Z","timestamp":1764688795606},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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<\/jats:p>\n               <jats:p>Contact: \u00a0hsauro@u.washington.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq512","type":"journal-article","created":{"date-parts":[[2010,9,10]],"date-time":"2010-09-10T00:18:07Z","timestamp":1284077887000},"page":"2794-2795","source":"Crossref","is-referenced-by-count":6,"title":["SBML2TikZ: supporting the SBML render extension in LaTeX"],"prefix":"10.1093","volume":"26","author":[{"given":"Si Yuan","family":"Shen","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of Washington, Seattle, WA 98195, USA"}]},{"given":"Frank","family":"Bergmann","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of Washington, Seattle, WA 98195, USA"}]},{"given":"Herbert M.","family":"Sauro","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of Washington, Seattle, WA 98195, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,9,9]]},"reference":[{"key":"2023012507543987100_B1","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/nbt0606-667","article-title":"Tools for kinetic modeling of biochemical networks","volume":"24","author":"Alves","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023012507543987100_B2","first-page":"1637","article-title":"SBW - a modular framework for systems biology","volume-title":"Proceedings of the 38th Conference on Winter Simulation, Series WSC '06","author":"Bergmann","year":"2006"},{"key":"2023012507543987100_B3","first-page":"1707","article-title":"CellDesigner: a modeling tool for biochemical networks","volume-title":"Proceedings for the 38th Conference on Winter Simulation, Series WSC '06","author":"Funahashi","year":"2006"},{"key":"2023012507543987100_B4","volume-title":"Complementing layout information with render information in SBML files.","author":"Gauges","year":"2009"},{"key":"2023012507543987100_B5","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for presentation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507543987100_B6","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nbt.1558","article-title":"The systems biology graphical notation","volume":"19","author":"Nov\u00e8re","year":"2009","journal-title":"Nat. Biotechnol."},{"key":"2023012507543987100_B7","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1089\/153623103322637670","article-title":"Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration","volume":"7","author":"Sauro","year":"2003","journal-title":"OMICS"},{"key":"2023012507543987100_B8","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1093\/bioinformatics\/btq154","article-title":"Arcadia: a visualization tool for metabolic pathways","volume":"26","author":"Vill\u00e9ger","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/21\/2794\/48853450\/bioinformatics_26_21_2794.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/21\/2794\/48853450\/bioinformatics_26_21_2794.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:55:28Z","timestamp":1674633328000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/21\/2794\/213895"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,9,9]]},"references-count":8,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2010,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq512","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,11,1]]},"published":{"date-parts":[[2010,9,9]]}}}