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JSBML 1.0: providing a smorgasbord of options to encode systems biology models.

  • Author(s): Rodriguez, Nicolas
  • Thomas, Alex
  • Watanabe, Leandro
  • Vazirabad, Ibrahim Y
  • Kofia, Victor
  • Gómez, Harold F
  • Mittag, Florian
  • Matthes, Jakob
  • Rudolph, Jan
  • Wrzodek, Finja
  • Netz, Eugen
  • Diamantikos, Alexander
  • Eichner, Johannes
  • Keller, Roland
  • Wrzodek, Clemens
  • Fröhlich, Sebastian
  • Lewis, Nathan E
  • Myers, Chris J
  • Le Novère, Nicolas
  • Palsson, Bernhard Ø
  • Hucka, Michael
  • Dräger, Andreas
  • et al.
Abstract

Unlabelled

JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users.

Availability and implementation

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. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/.

Contact

jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

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