JSBML

JSBML is a community-driven project to create a free, open-source (under LGPL), 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.

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.

Please cite the papers if you use JSBML

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:

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, and Andreas Dräger. Bioinformatics, 31(20): 3383–3386, 2015.BibTeX EndNote
JSBML: a flexible Java library for working with SBML Andreas Dräger, Nicholas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicholas Le Novère, Andreas Zell, and Michael Hucka. Bioinformatics, 27(15):2167–2168, 2011.BibTeX EndNote

Software releases

We provide Zenodo DOIs for specific releases, so that you can cite the exact version of the software that you use:

License

JSBML is licensed under the LGPL v. 2.1 and Copyright (C) 2009-2020 jointly by the following organizations:

  1. The University of Tuebingen, Germany
  2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
  3. The California Institute of Technology, Pasadena, CA, USA
  4. The University of California, San Diego, La Jolla, CA, USA
  5. The Babraham Institute, Cambridge, UK

JSBML also uses third-party software libraries; these software libraries have their own copyright statements and distribution terms. Please see the files COPYING.txt and LICENSE in the JSBML software distributions for more information.

Community and help

There is a mailing list and web forum, jsbml-development@googlegroups.com, devoted to discussions about JSBML. If you’re using JSBML or interested in learning more, feel free to join the group! You can also reach the main developers directly via email at jsbml-team@googlegroups.com.

The separate documentation pages for JSBML include sections aimed at developers.

JSBML contributors

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

Developers

Meike Aichele 1, Piero Dalle Pezze 2 Alexander Diamantikos 1, Alexander Dörr 1, Andreas Dräger 1, Marine Dumousseau 2, Johannes Eichner 1, Lisa Falk, 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, Tramy Nguyen 8, Alexander Peltzer 1, Nicolas Rodriguez 2,9, Jan Rudolph 1, Simon Schäfer 1, Alex Thomas 3, Ibrahim Y. Vazirabad 10, Leandro Watanabe 8, 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.

Institutes

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 The University of Utah, Salt Lake City, UT, USA
9 Babraham Institute, Babraham Research Campus, Cambridge, UK
10 Marquette University, Milwaukee, WI, USA
11 Keio University, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, Japan

Funding acknowledgments

Currently, the main developers come from the Babraham Institute and the University of Tuebingen, Germany.

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 has also supported this work as part of the Google Summer of Code program.

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).