Numerical simulation of SBML models
- Several solvers from the Apache Commons Math Library included
- Rosenbrock solver for integration of stiff differential equation systems
- Clear separation of SBML interpretation and integration routines
- Fast SBML interpretation by using a transformed syntax graph
- Full support of SBML events, algebraic rules and fast reactions
- Support of all all models from the SBML Test Suite (v. 2.2) for all levels and versions: Simulation results
Support for SED-ML
- Several quality functions for computation of the distance from simulated data to some given data
Documentation of the application programing interfacesTo get startet with this library, please see the API documentation (JavaDoc) for the most recent Version 1.4. See the introduction, use-cases, and coding examples here: Description.
In case you like to use older versions, you can find the documentation here: Release Notes for user-visible changes.
DownloadYou can obtain all versions of this library by going to the sourceforge download area of the project.
Mailing list and tracker
Please don't hesitate to contact the developer's mailing list email@example.com.
If you encounter any bugs, or like to ask for a feature request, please use the tracker.
Authors and license
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this each version of software distribution and also available online as LGPL 3.0.
Copyright © 2007-2014 jointly by the following organizations:
- University of Tuebingen, Germany
- Keio University, Japan
- Harvard University, USA
- The University of Edinburgh, UK
- EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- The University of California, San Diego, La Jolla, CA, USA
- The Babraham Institute, Cambridge, UK
The main developers of this library are:
- Richard Adams
- Akira Funahashi
- Noriko Hiroi
- Nicolas Le Novère
- Hannes Planatscher
- Nicolas Rodriguez
- Akito Tabira
- Andreas Zell
- Michael J. Ziller
Many thanks to B. Kotcon, S. Mesuro, D. Rozenfeld, A. Yodpinyanee, A. Perez, E. Doi, R. Mehlinger, S. Ehrlich, M. Hunt, G. Tucker, P. Scherpelz, A. Becker, E. Harley, and C. Moore, Harvey Mudd College, USA, for providing a Java implementation of Rosenbrock's method as part of the ODEToolkit.
We like to thank Michael T. Cooling, University of Auckland, New Zealand, for fruitful discussion.