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JSBML: a flexible Java library for working with SBML

Dräger, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and Dörr, Alexander and Wrzodek, Clemens and Le Novère, Nicolas and Zell, Andreas and Hucka, Michael (2011) JSBML: a flexible Java library for working with SBML. Bioinformatics, 27 (15). pp. 2167-2168. ISSN 1367-4803. PMCID PMC3137227. http://resolver.caltech.edu/CaltechAUTHORS:20110804-100157010

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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1093/bioinformatics/btr361DOIArticle
http://bioinformatics.oxfordjournals.org/content/27/15/2167PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137227/PubMed CentralArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Additional Information:© The Author(s) 2011. Published by Oxford University Press. 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. Received on March 29, 2011; revised on May 23, 2011; accepted on June 12, 2011. Funding: National Institute of General Medical Sciences (NIGMS, USA); funds from EMBL-EBI (Germany, UK); Federal Ministry of Education and Research (BMBF, Germany) in the projects Virtual Liver and Spher4Sys (grant numbers 0315756 and 0315384C). The grant number for the NIH grant that was, among others, used for the JSBML article reads 2R01GM070923.
Funders:
Funding AgencyGrant Number
NIHR15GM60203
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Bundesministerium für Bildung und Forschung (BMBF)0315756
Bundesministerium für Bildung und Forschung (BMBF)0315384C
NIH2R01GM070923
PubMed Central ID:PMC3137227
Record Number:CaltechAUTHORS:20110804-100157010
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20110804-100157010
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24676
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:04 Aug 2011 17:48
Last Modified:21 Dec 2016 22:56

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