JSBML

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Latest stable release: 0.8
Latest development release: 1.0-a1
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

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 for those who desire it. 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, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.

JSBML publications

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. (Copy available under open-access terms directly from Bioinformatics.)

JSBML community

There is a mailing list and web forum, jsbml-development, devoted to discussions about JSBML. Please visit the subscription page to subscribe to the mailing list.

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 (PhD) students. We especially thank the following contributors (in alphabetical order):

Meike Aichele¹, Finja Büchel^1,2, Alexander Diamantikos¹, Alexander Dörr¹, Andreas Dräger¹, Marine Dumousseau², Johannes Eichner¹, Sebastian Fröhlich³, Roland Keller¹, Jakob Matthes¹, Florian Mittag^1,2, Sarah Rachel Müller vom Hagen¹, Sebastian Nagel¹, Eugen Netz¹, Alexander Peltzer¹, Nicolas Rodriguez², Jan Rudolph¹, Simon Schäfer¹, Clemens Wrzodek¹

Institutes:
¹Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany,
²European Bioinformatics Institute (EBI), Hinxton, UK,
³Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

JSBML principal investigators

• Michael Hucka
• Nicolas Le Novère
• Andreas Zell

Funding acknowledgements

Currently, the main developers come from the European Bioinformatics Institute (EBI) and the University of Tübingen. 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 EMBL-EBI (Germany & 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).