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.
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.)
There's also a JSBML group on LinkedIn. If you're on LinkedIn and interested in JSBML, feel free to join the group!
JSBML is the result of hard work by many people, including several (PhD) students. We especially thank the following contributors (in alphabetical order):
Sarah Rachel Müller vom Hagen1,
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
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).