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 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 support for SBML Level 3 packages. JSBML does not currently reimplement some of the more complex functions of libSBML such as consistency-checking and SBML validation; instead, these can be accessed via web services.
JSBML release DOIs
We provide Zenodo DOIs for specific releases, so that you can cite the exact version of the software that you use:
- JSBML release 1.2 ⇒ 10.5281/zenodo.200544
- JSBML release 1.1 ⇒ 10.5281/zenodo.55323
- JSBML release 1.0 ⇒ 10.5281/zenodo.55635
- JSBML release 0.8 ⇒ 10.5281/zenodo.55636
Article citations are crucial to our ability to justify continued development of JSBML, as well as our academic careers. If you use JSBML, we ask that you please cite one of the following papers:
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, and Andreas Dräger. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics, 31(20): 3383–3386. (Freely available directly from Bioinformatics.)
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.)
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 is the result of hard work by many people, including numerous (Ph.D.) students. We thank the following contributors especially (in alphabetical order):
Meike Aichele 1, Piero Dalle Pezze 2 Alexander Diamantikos 1, Alexander Dörr 1, Andreas Dräger 1, Marine Dumousseau 2, Johannes Eichner 1, Sebastian Fröhlich 4, Harold F. Gómez 5 Thomas M. Hamm 1 Michael Hucka 6, Roland Keller 1, Victor Kofia 7, Jakob Matthes 1, Florian Mittag 1,2, Sarah Rachel Müller vom Hagen 1, Sebastian Nagel 1, Eugen Netz 1, Alexander Peltzer 1, Nicolas Rodriguez 2,8, Jan Rudolph 1, Simon Schäfer 1, Alex Thomas 3, Ibrahim Y. Vazirabad 9, Leandro Watanabe 10, Clemens Wrzodek 1, Finja Wrzodek 1,2 Thomas J. Zajac 1
JSBML principal investigators:
Michael Hucka 5
Nicolas Le Novère 2,7
Akira Funahashi 11
Chris J. Myers 10
Nathan E. Lewis 2
Bernhard Ø. Palsson 2
Andreas Zell 1
1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany,
2 European Bioinformatics Institute (EBI), Hinxton, UK,
3 University of California, San Diego, La Jolla, CA, USA
4 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
5 Boston University, Boston, MA, USA
6 The California Institute of Technology, Pasadena, CA, USA
7 The University of Toronto, Toronto, ON, Canada
8 Babraham Institute, Babraham Research Campus, Cambridge, UK
9 Marquette University, Milwaukee, WI, USA
10 The University of Utah, Salt Lake City, UT, USA
11 Keio University, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, Japan
The development of JSBML is funded in part by a grant from the National Institute of General Medical Sciences (NIGMS, USA, award number GM070923), as well as by funds from the Babraham Institute (UK), a Marie-Curie International Outgoing Fellowship (IOF) within the European Commision's 7th Framework Programme for Research and Technological Development (project AMBiCon grant number 332020). Google supports this work as part of the Google Summer of Code 2014 initiative.
Further support comes from 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).