JSBML: a flexible Java library for working with SBML
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.
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.Attached Files
Published - Draeger2011p15391Bioinformatics.pdf
Supplemental Material - Differences_between_JSBML_and_libSBML.pdf
Supplemental Material - User_Guide.pdf
Files
Additional details
- PMCID
- PMC3137227
- Eprint ID
- 24676
- Resolver ID
- CaltechAUTHORS:20110804-100157010
- R15GM60203
- NIH
- European Molecular Biology Laboratory (EMBL)
- 0315756
- Bundesministerium für Bildung und Forschung (BMBF)
- 0315384C
- Bundesministerium für Bildung und Forschung (BMBF)
- 2R01GM070923
- NIH
- Created
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2011-08-04Created from EPrint's datestamp field
- Updated
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2021-11-09Created from EPrint's last_modified field