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JSBML

Latest stable release: 0.8
Latest development release: 1.0-beta1
Main authors: Andreas Dräger and Nicolas Rodriguez

JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

JSBML development goals and plans

JSBML is participating in the 2014 Google Summer of Code!
Contact us for more details.

The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other. Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 Release 1 specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML such as consistency-checking and SBML validation; instead, these will be accessed via web services.

JSBML publications

Article citations are crucial to our academic careers. If you use JSBML, we ask that you please cite the following paper:

Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, and Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics (2011), 27(15):2167–2168. (Freely available directly from Bioinformatics.)

JSBML community

There is a mailing list and web forum, jsbml-development, devoted to discussions about JSBML. There's also a JSBML group on LinkedIn. If you're on LinkedIn and interested in JSBML, feel free to join the group!

JSBML contributors

JSBML is the result of hard work by many people, including several (Ph.D.) students. We thank the following contributors especially (in alphabetical order):

Meike Aichele1, Alexander Diamantikos1, Alexander Dörr1, Andreas Dräger1,2, Marine Dumousseau3, Johannes Eichner1, Sebastian Fröhlich4, Michael Hucka5, Roland Keller1,
Jakob Matthes1, Florian Mittag1,3, Sarah Rachel Müller vom Hagen1, Sebastian Nagel1, Eugen Netz1, Alexander Peltzer1, Nicolas Rodriguez3,6, Jan Rudolph1, Simon Schäfer1, Alex Thomas2,
Clemens Wrzodek1, Finja Wrzodek1,3

JSBML principal investigators:

Michael Hucka5
Nicolas Le Novère3,6
Bernhard Ø. Palsson2
Andreas Zell1

Institutes:

1Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany,
2University of California, San Diego, La Jolla, CA, USA
3European Bioinformatics Institute (EBI), Hinxton, UK,
4Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
5The California Institute of Technology, Pasadena, CA, USA
6Babraham Institute, Babraham Research Campus, Cambridge, UK

Funding acknowledgements

Currently, the main developers come from the Babraham Institute and the University of California, San Diego. The development of JSBML is funded in part by a grant from the National Institute of General Medical Sciences (NIGMS, USA), as well as by funds from the Babraham Institute (UK), the Federal Ministry of Education and Research (BMBF, Germany) in the Virtual Liver Network and the MedSys project Spher4Sys as well as the University of Tübingen (Germany).


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This page was last modified 17:30, 11 April 2014.



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