{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T07:28:25Z","timestamp":1790407705697,"version":"4.1.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted format.<\/jats:p>\n               <jats:p>Summary: Two modules, SBMLSupportLayout and SBWAutoLayout, support reading, creating, manipulating and writing layout information for biochemical models. SBMLSupportLayout can read, update, add and render model layout information. SBWAutoLayout can automatically layout models, graphically manipulate model layout and generate layout information for models without layout information.<\/jats:p>\n               <jats:p>Availability: SBMLSupportLayout and SBWAutoLayout are distributed with the Systems Biology Workbench (SBW), which can be downloaded from . Additionally, their visualization and layout capabilities are available online at . Both modules run on Win32, Linux and the Mac OS X version is forthcoming.<\/jats:p>\n               <jats:p>Contact: \u00a0fbergman@kgi.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl520","type":"journal-article","created":{"date-parts":[[2006,10,13]],"date-time":"2006-10-13T07:47:15Z","timestamp":1160725635000},"page":"2966-2967","source":"Crossref","is-referenced-by-count":22,"title":["Supporting the SBML layout extension"],"prefix":"10.1093","volume":"22","author":[{"given":"Anastasia","family":"Deckard","sequence":"first","affiliation":[{"name":"Keck Graduate Institute, 535 Watson Dr Claremont \u00a0 CA 91711, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank T.","family":"Bergmann","sequence":"additional","affiliation":[{"name":"Keck Graduate Institute, 535 Watson Dr Claremont \u00a0 CA 91711, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herbert M.","family":"Sauro","sequence":"additional","affiliation":[{"name":"Keck Graduate Institute, 535 Watson Dr Claremont \u00a0 CA 91711, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,10,11]]},"reference":[{"key":"2023012409392241100_b1","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/35002125","article-title":"A synthetic oscillatory network of transcriptional regulators","volume":"403","author":"Elowitz","year":"2000","journal-title":"Nature"},{"key":"2023012409392241100_b2","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1002\/spe.4380211102","article-title":"Graph drawing by force-directed placement","volume":"21","author":"Fruchterman","year":"1991","journal-title":"Software, Practice and Experience"},{"key":"2023012409392241100_b3","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1093\/bioinformatics\/btl195","article-title":"A model diagram layout extension for SBML","volume":"22","author":"Gauges","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012409392241100_b4","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409392241100_b5","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1046\/j.1432-1327.2000.01197.x","article-title":"Negative feedback and ultrasensitivity can bring about oscillations, in the mitogen-activted protein kinase cascades","volume":"267","author":"Kholodenko","year":"2000","journal-title":"Eur. 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Biotechnol."},{"key":"2023012409392241100_b7","first-page":"221","article-title":"JARNAC: a system for interactive metabolic analysis","volume-title":"Animating the Cellular Map","author":"Sauro","year":"2000"},{"key":"2023012409392241100_b8","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":"2023012409392241100_b9","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1046\/j.1432-1327.2000.01527.x","article-title":"Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.","volume":"267","author":"Teusink","year":"2000","journal-title":"Eur. J. Biochem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/23\/2966\/48842699\/bioinformatics_22_23_2966.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/23\/2966\/48842699\/bioinformatics_22_23_2966.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:40:26Z","timestamp":1674553226000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/23\/2966\/279802"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,10,11]]},"references-count":9,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2006,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl520","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,12,1]]},"published":{"date-parts":[[2006,10,11]]}}}