JSBML: a flexible Java library for working with SBML

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 o...

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Main Authors:	Dräger, Andreas, Rodriguez, Nicolas, Dumousseau, Marine, Dörr, Alexander, Wrzodek, Clemens, Le Novère, Nicolas, Zell, Andreas, Hucka, Michael
Format:	Online
Language:	English
Published:	Oxford University Press 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137227/

id	pubmed-3137227
recordtype	oai_dc
spelling	pubmed-31372272011-07-15 JSBML: a flexible Java library for working with SBML Dräger, Andreas Rodriguez, Nicolas Dumousseau, Marine Dörr, Alexander Wrzodek, Clemens Le Novère, Nicolas Zell, Andreas Hucka, Michael Applications Note 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™ 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. Oxford University Press 2011-08-01 2011-06-22 /pmc/articles/PMC3137227/ /pubmed/21697129 http://dx.doi.org/10.1093/bioinformatics/btr361 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Dräger, Andreas Rodriguez, Nicolas Dumousseau, Marine Dörr, Alexander Wrzodek, Clemens Le Novère, Nicolas Zell, Andreas Hucka, Michael
spellingShingle	Dräger, Andreas Rodriguez, Nicolas Dumousseau, Marine Dörr, Alexander Wrzodek, Clemens Le Novère, Nicolas Zell, Andreas Hucka, Michael JSBML: a flexible Java library for working with SBML
author_facet	Dräger, Andreas Rodriguez, Nicolas Dumousseau, Marine Dörr, Alexander Wrzodek, Clemens Le Novère, Nicolas Zell, Andreas Hucka, Michael
author_sort	Dräger, Andreas
title	JSBML: a flexible Java library for working with SBML
title_short	JSBML: a flexible Java library for working with SBML
title_full	JSBML: a flexible Java library for working with SBML
title_fullStr	JSBML: a flexible Java library for working with SBML
title_full_unstemmed	JSBML: a flexible Java library for working with SBML
title_sort	jsbml: a flexible java library for working with sbml
description	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™ 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.
publisher	Oxford University Press
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137227/
_version_	1611465754511671296

JSBML: a flexible Java library for working with SBML

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