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Published October 15, 2015 | Published + Supplemental Material
Journal Article Open

JSBML 1.0: providing a smorgasbord of options to encode systems biology models


JSBML, the official pure Java programming library for the SBML format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users.

Additional Information

The Author(s) 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received December 17, 2014. Revision received March 27, 2015. Accepted May 29, 2015. First published online: June 16, 2015. The authors are grateful to Meike Aichele, Alexander Dörr, Marine Dumousseau, Akira Funahshi, Stephanie Hoffmann, Sarah R. Müller vom Hagen, Sebastian Nagel, Alexander Peltzer, Simon Schäfer, and Andreas Zell. Funding: A National Institute of Health grant for the continued development of essential SBML software support (NIH, United States, award number GM070923), European Union projects Syn-Sys (FP7 242167) and BBSRC Signalling Institute Strategic Programme (BBS/E/B/000C0419), a National Science Foundation grant (CCF-1218095), a Marie Curie International Outgoing Fellowship within the EU 7th Framework Program for Research and Technological Development (project AMBiCon, 332020), Google Inc. (Summer of Code 2014), the Federal Ministry of Education and Research (BMBF, Germany) as part of the Virtual Liver Network (grant number 0315756). We acknowledge support by the German Research Foundation (DFG) and the Open Access Publishing Fund of the University of Tuebingen. AT, NEL, and BØP acknowledge generous support from the Novo Nordisk Foundation that has been provided to the Center for Biosustainability at the Technical University of Denmark. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of our funding agencies.

Attached Files

Published - Bioinformatics-2015-Rodriguez-3383-6.pdf

Supplemental Material - sbml_lvl3_extensions.pdf


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