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

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

doi:10.1093/bioinformatics/btv341

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

Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.

Authors

Nicolas Rodriguez¹, Alex Thomas², Leandro Watanabe³, Ibrahim Y Vazirabad⁴, Victor Kofia⁵, Harold F Gómez⁶, Florian Mittag⁷, Jakob Matthes⁸, Jan Rudolph⁹, Finja Wrzodek⁷, Eugen Netz⁸, Alexander Diamantikos⁸, Johannes Eichner⁸, Roland Keller⁸, Clemens Wrzodek¹⁰, Sebastian Fröhlich¹¹, Nathan E Lewis², Chris J Myers³, Nicolas Le Novère¹, Bernhard Ø Palsson², Michael Hucka¹², Andreas Dräger¹³

Affiliations

¹ European Bioinformatics Institute (EBI), Hinxton, UK, Babraham Institute, Babraham Research Campus, Cambridge, UK.
² University of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
³ The University of Utah, Salt Lake City, UT, USA.
⁴ Marquette University, Milwaukee, WI, USA.
⁵ The University of Toronto, Toronto, ON, Canada.
⁶ Boston University, Boston, MA, USA.
⁷ European Bioinformatics Institute (EBI), Hinxton, UK, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
⁸ Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
⁹ Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, Tel Aviv University, Tel Aviv, Israel.
¹⁰ Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, Roche Pharmaceutical Research and Early Development, pRED Informatics, Roche Innovation Center, Penzberg, Germany.
¹¹ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany and.
¹² The California Institute of Technology, Pasadena, CA, USA.
¹³ University of California, San Diego, La Jolla, CA, USA, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.

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.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computer Simulation
Models, Biological*
Programming Languages
Software*
Systems Biology*

Abstract

Publication types

MeSH terms

Grants and funding