title: JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
abstract: 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.
  
  
  METHODS
  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/.
  
  
  BACKGROUND
  jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: European Bioinformatics Institute (EBI), Hinxton, UK, Babraham Institute, Babraham Research Campus, Cambridge, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rodriguez
authors.affiliation: University of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Thomas
authors.affiliation: The University of Utah, Salt Lake City, UT, USA.
authors.forename: Leandro
authors.initials: L
authors.lastname: Watanabe
authors.affiliation: Marquette University, Milwaukee, WI, USA.
authors.forename: Ibrahim Y
authors.initials: IY
authors.lastname: Vazirabad
authors.affiliation: The University of Toronto, Toronto, ON, Canada.
authors.forename: Victor
authors.initials: V
authors.lastname: Kofia
authors.affiliation: Boston University, Boston, MA, USA.
authors.forename: Harold F
authors.initials: HF
authors.lastname: Gómez
authors.affiliation: European Bioinformatics Institute (EBI), Hinxton, UK, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Mittag
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Jakob
authors.initials: J
authors.lastname: Matthes
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Jan
authors.initials: J
authors.lastname: Rudolph
authors.affiliation: European Bioinformatics Institute (EBI), Hinxton, UK, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Finja
authors.initials: F
authors.lastname: Wrzodek
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Eugen
authors.initials: E
authors.lastname: Netz
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Diamantikos
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Eichner
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Keller
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, Roche Pharmaceutical Research and Early Development, pRED Informatics, Roche Innovation Center, Penzberg, Germany.
authors.forename: Clemens
authors.initials: C
authors.lastname: Wrzodek
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany and.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Fröhlich
authors.affiliation: University of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Nathan E
authors.initials: NE
authors.lastname: Lewis
authors.affiliation: The University of Utah, Salt Lake City, UT, USA.
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Myers
authors.affiliation: European Bioinformatics Institute (EBI), Hinxton, UK, Babraham Institute, Babraham Research Campus, Cambridge, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
authors.affiliation: University of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Bernhard Ø
authors.initials: BØ
authors.lastname: Palsson
authors.affiliation: The California Institute of Technology, Pasadena, CA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hucka
authors.affiliation: University of California, San Diego, La Jolla, CA, USA, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Dräger
mesh_terms: D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D012984:Software; D049490:Systems Biology