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

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

Bioinformatics (2015)


Abstract

Summary: JSBML, the official pure Java programming library for the 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: 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.

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

Contact: mailto:jsbml-development@googlegroups.com


Downloads and Links

[doi] [pdf] [pdf]


BibTeX

@article{Rodriguez2015,
  author = {Rodriguez, Nicolas and Thomas, Alex and Watanabe, Leandro and
    Vazirabad, Ibrahim Y. and Kofia, Victor and G\'{o}mez, Harold F. and Mittag,
    Florian and Matthes, Jakob and Rudolph, Jan D. and Wrzodek, Finja and Netz,
    Eugen and Diamantikos, Alexander and Eichner, Johannes and Keller, Roland
    and Wrzodek, Clemens and Fr\"ohlich, Sebastian and Lewis, Nathan E. and
    Myers, Chris J. and {Le Nov\`{e}re}, Nicolas and Palsson, Bernhard {\O}. and
    Hucka, Michael and Dr\"ager, Andreas},
  title = {{JSBML 1.0: providing a smorgasbord of options to encode systems biology models}},
  journal = {Bioinformatics},
  year = {2015},
  month = jun,
  doi = {10.1093/bioinformatics/btv341},
  abstract = {Summary: JSBML, the official pure Java programming library for the
    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
    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: 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}.

    Supplementary Information: More information about JSBML can be found in the
    user guide at \url{http://sbml.org/Software/JSBML/docs/}.

    Contact: \url{mailto:jsbml-development@googlegroups.com}},
  url = {http://bioinformatics.oxfordjournals.org/content/31/20/3383},
  eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.full.pdf+html},
  pdf = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.full.pdf},
}