Systems Biology Simulation Core Library

Welcome to the Systems Biology Simulation Core Library!

The Systems Biology Simulation Core Library provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project and can be used on every operating system, for which a Java Virtual Machine is available.

Please note that this project does not contain any user interface, neither a command-line interface, nor a graphical user interface. This project has been developed as a pure programming library. To support the Minimum Information About a Simulation Experiment (MIASE) effort, it understands Simulation Experiment Description Markup Language (SED-ML) files.

Its abstract type and interface hierarchy facilitates the implementation of further community standards, such as CellML.

When using the Simulation Core Library, please cite:
Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger. The systems biology simulation core algorithm. BMC Systems Biology, 7:55, July 2013. [ DOI | link | pdf ]


Numerical simulation of SBML models

Support for SED-ML

Documentation of the application programing interfaces

To 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: Here you can find Release Notes for user-visible changes.


You 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

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:

  1. University of Tuebingen, Germany
  2. Keio University, Japan
  3. Harvard University, USA
  4. The University of Edinburgh, UK
  5. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
  6. The University of California, San Diego, La Jolla, CA, USA
  7. The Babraham Institute, Cambridge, UK

The main developers of this library are:

Contributors (in alphabetic order): Your contribution is welcome. If you like to participate in this effort, please contact the developers' mailing list and join the team!


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.

Special thanks to D. M. Wouamba, P. Stevens, M. Zwießele, M. Kronfeld, and A. Schröder for source code contribution and fruitful discussion.

This work was funded by the Federal Ministry of Education and Research (BMBF, Germany) as part of the Virtual Liver Network.