{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T15:49:35Z","timestamp":1722872975088},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":1930,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"Abstract<\/jats:title>\n Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java\u2122 programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend.<\/jats:p>\n Availability: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http:\/\/sbml.org\/Software\/JSBML.<\/jats:p>\n Contact: \u00a0jsbml-team@sbml.org<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr361","type":"journal-article","created":{"date-parts":[[2011,6,23]],"date-time":"2011-06-23T00:58:29Z","timestamp":1308790709000},"page":"2167-2168","source":"Crossref","is-referenced-by-count":68,"title":["JSBML: a flexible Java library for working with SBML"],"prefix":"10.1093","volume":"27","author":[{"given":"Andreas","family":"Dr\u00e4ger","sequence":"first","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Nicolas","family":"Rodriguez","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Marine","family":"Dumousseau","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Alexander","family":"D\u00f6rr","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Clemens","family":"Wrzodek","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Nicolas","family":"Le Nov\u00e8re","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Andreas","family":"Zell","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Michael","family":"Hucka","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 3Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,22]]},"reference":[{"key":"2023012511550577000_B1","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"LibSBML: an API Library for SBML","volume":"24","author":"Bornstein","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012511550577000_B2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1752-0509-2-39","article-title":"SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks","volume":"2","author":"Dr\u00e4ger","year":"2008","journal-title":"BMC Syst. 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Biotechnol."},{"key":"2023012511550577000_B8","first-page":"137","article-title":"Adding semantics in kinetics models of biochemical pathways","volume-title":"2nd International ESCEC Workshop","author":"Le Nov\u00e8re","year":"2006"},{"key":"2023012511550577000_B9","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. 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