This is the API reference manual for the Java language bindings of libSBML.

Authors: Ben Bornstein and Sarah Keating designed and wrote most of the software, with contributions from Frank Bergmann, Bill Denney, Christoph Flamm, Akira Funahashi, Michael Hucka, Ralph Gauges, Martin Ginkel, Alex Gutteridge, Stefan Hoops, Akiya Jouraku, Ben Kovitz, Rainer Machné, Nicolas Rodriguez, and many others in the SBML community.

Michael Hucka wrote most of this libSBML user and API documentation.

This manual describes the Java application programming interface (API) of libSBML, an open-source (LGPL) library for writing and manipulating the Systems Biology Markup Language (SBML). This version of libSBML supports all releases of SBML up through Level 2 Version 4. For more information about SBML, please visit http://sbml.org on the Internet. Please report bugs and other issues with libSBML using the tracker at http://sbml.org/Software/libSBML/issue-tracker.

Note to readers: Most of this manual is generated automatically from the C++ source code of libSBML. Owing to imperfections in the conversion software, it is not as complete as the C++ API manual. If you encounter undocumented members (such as constants), you may wish to check the corresponding text in the C++ API manual.

General information

• Building and installing libSBML
• Making libSBML accessible to software
• LibSBML features
• Bug reports, mailing lists, and related topics

Programming with libSBML in Java

• Reading and writing SBML content
• Mathematical Expressions and their Manipulation
• Known issues and pitfalls

Other topics

• Uninstalling LibSBML
• LibSBML license
• Summary of changes between libSBML versions

Please note: article citations are crucial to our academic careers. If you use libSBML and you publish papers about your software, we ask that you please cite the libSBML paper:

Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008) LibSBML: An API Library for SBML. Bioinformatics, 24(6):880-881.

This and other projects of the SBML Team have 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 ERATO-SORST 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).