Dräger, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and Dörr, Alexander and Wrzodek, Clemens and Le Novère, Nicolas and Zell, Andreas and Hucka, Michael

JSBML: a flexible Java library for working with SBML

Bioinformatics vol. 27 (2011), no. 15, pp. 2167-2168


Abstract

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. 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.


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BibTeX

@article{Draeger2011b,
  author = {Dr\"ager, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and
	D\"orr, Alexander and Wrzodek, Clemens and {Le Nov\`{e}re}, Nicolas
	and Zell, Andreas and Hucka, Michael},
  title = {{JSBML: a flexible Java library for working with SBML}},
  journal = {Bioinformatics},
  year = {2011},
  volume = {27},
  pages = {2167--2168},
  number = {15},
  month = jun,
  abstract = {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\texttrademark{}
	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. Availability: Source code, binaries, and
	documentation for JSBML can be freely obtained under the terms of
	the LGPL 2.1 from the website \url{http://sbml.org/Software/JSBML}.},
  doi = {10.1093/bioinformatics/btr361},
  pdf = {http://bioinformatics.oxfordjournals.org/content/27/15/2167.full.pdf},
  url = {http://bioinformatics.oxfordjournals.org/content/27/15/2167}
}