{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T02:28:09Z","timestamp":1772159289478,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: CySBML is a plugin designed to work with Systems Biology Markup Language (SBML) in Cytoscape having the following features: SBML import, support of the SBML layout and qualitative model packages, navigation in network layouts based on SBML structure, access to MIRIAM and SBO-based annotations and SBML validation. CySBML includes an importer for BioModels to load SBML from standard repositories.<\/jats:p>\n               <jats:p>Availability and implementation: Freely available for non-commercial purposes through the Cytoscape plugin manager or for download at http:\/\/sourceforge.net\/projects\/cysbml\/.<\/jats:p>\n               <jats:p>Contact: \u00a0cysbml-team@lists.sourceforge.net<\/jats:p>\n               <jats:p>Supplementary Information: Tutorial, usage guide, installation instructions and additional figures are available for download at http:\/\/www.charite.de\/sysbio\/people\/koenig\/software\/cysbml\/.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts432","type":"journal-article","created":{"date-parts":[[2012,7,7]],"date-time":"2012-07-07T02:06:56Z","timestamp":1341626816000},"page":"2402-2403","source":"Crossref","is-referenced-by-count":52,"title":["CySBML: a Cytoscape plugin for SBML"],"prefix":"10.1093","volume":"28","author":[{"given":"Matthias","family":"K\u00f6nig","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hermann-Georg","family":"Holzh\u00fctter","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,7,5]]},"reference":[{"key":"2023012513025813800_bts432-B1","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/bioinformatics\/btm554","article-title":"Computing topological parameters of biological networks","volume":"24","author":"Assenov","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012513025813800_bts432-B2","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/msb.2011.77","article-title":"Controlled vocabularies and semantics in systems biology","volume":"7","author":"Courtot","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2023012513025813800_bts432-B3","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1093\/bioinformatics\/btr361","article-title":"JSBML: a flexible Java library for working with SBML","volume":"27","author":"Dr\u00e4ger","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012513025813800_bts432-B4","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1093\/bioinformatics\/btm032","article-title":"NetMatch: a Cytoscape plugin for searching biological networks","volume":"23","author":"Ferro","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012513025813800_bts432-B5","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":"2023012513025813800_bts432-B6","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":"2023012513025813800_bts432-B7","first-page":"96","article-title":"Fluxviz\u2014cytoscape plug-in for visualization of flux distributions in networks","volume":"24","author":"K\u00f6nig","year":"2010","journal-title":"Genome Inform."},{"key":"2023012513025813800_bts432-B8","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/1752-0509-1-58","article-title":"MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology","volume":"1","author":"Laibe","year":"2007","journal-title":"BMC Syst. Biol."},{"key":"2023012513025813800_bts432-B9","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2202-7-S1-S11","article-title":"Model storage, exchange and integration","volume":"7","author":"Le Nov\u00e8re","year":"2006","journal-title":"BMC Neurosci."},{"key":"2023012513025813800_bts432-B10","first-page":"137","article-title":"Adding semantics in kinetics models of biochemical pathways","volume-title":"2nd International ESCEC Workshop, ESEC","author":"Le Nov\u00e8re","year":"2006"},{"key":"2023012513025813800_bts432-B11","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/1752-0509-4-92","article-title":"BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models","volume":"4","author":"Li","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"2023012513025813800_bts432-B12","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/18\/2402\/48883805\/bioinformatics_28_18_2402.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/18\/2402\/48883805\/bioinformatics_28_18_2402.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:52:29Z","timestamp":1674672749000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/18\/2402\/251682"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,7,5]]},"references-count":12,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2012,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts432","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,9,15]]},"published":{"date-parts":[[2012,7,5]]}}}