JSBML: a flexible Java library for working with SBML.

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TitleJSBML: a flexible Java library for working with SBML.
Publication TypeJournal Article
Year of Publication2011
AuthorsDräger, A, Rodriguez, N, Dumousseau, M, Dörr, A, Wrzodek, C, Le Novère, N, Zell, A, Hucka, M
JournalBioinformatics
Volume27
Issue15
Pagination2167-8
Date Published2011 Aug 1
ISSN1367-4811
KeywordsComputer Simulation, Database Management Systems, Information Storage and Retrieval, Models, Biological, Programming Languages, Software, Systems Biology
Abstract

<p><b>SUMMARY: </b>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 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.</p><p><b>AVAILABILITY: </b>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.</p>

DOI10.1093/bioinformatics/btr361
Alternate JournalBioinformatics
PubMed ID21697129
PubMed Central IDPMC3137227
Grant List2R01GM070923 / GM / NIGMS NIH HHS / United States
BB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
R01 GM070923 / GM / NIGMS NIH HHS / United States