LibSBML: an API library for SBML

Creators: Bornstein, Benjamin J.; Keating, Sarah M.; Jouraku, Akiya; Hucka, Michael

Abstract

LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software.

Additional Information

© 2008 The Author. Published by Oxford University Press. Received and revised on January 13, 2008; accepted on January 31, 2008. Advance Access publication February 5, 2008. Associate Editor: Olga Troyanskaya. We warmly thank the following individuals for code contributions and bug fixes: Frank Bergmann, Bill Denney (Octave language bindings), Andrew Finney, Christoph Flamm (Perl language bindings), Ralph Gauges (SBML Layout extension support), Martin Ginkel (Lisp bindings), Damon Hachmeister, Johan Hattne, Stefan Hoops (first interface to the Expat XML parser), Ben Kovitz, Konstantin Kozlov, Michael Lawrence, Rainer Machné, and Jacek Puchalka. We also thank all other people who used, tested, reported, and otherwise contributed to the development of libSBML over the years. The development of libSBML has been supported by the following organizations: the National Institutes of Health (USA) under grants R01 GM070923 and R01 GM077671; the International Joint Research Program of NEDO (Japan); the JST ERATOSORST Program (Japan); the Japanese Ministry of Agriculture; the Japanese Ministry of Education, Culture, Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the Army Research Office's Institute for Collaborative Biotechnologies (USA); the Air Force Office of Scientific Research (USA); the California Institute of Technology (USA); the University of Hertfordshire (UK); the Molecular Sciences Institute (USA); the Systems Biology Institute (Japan); and Keio University (Japan).

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