SBMLsimulator

An efficient Java™ solver implementation for SBML

Alexander Dörr1, Roland Keller1, Andreas Zell1, and Andreas Dräger1,2


1Center for Bioinformatics Tübingen (ZBIT), Germany, 2Systems Biology Research Group, University of California, San Diego, La Jolla, CA, USA


Short description: SBMLsimulator is a fast, accurate, and easily usable program for dynamic model simulation and heuristic parameter optimization of models encoded in the Systems Biology Markup Language (SBML). For simulation it contains the Systems Biology Simulation Core Library, which has been benchmarked against the entire SBML Test Suite and all models from the Biomodels.net database. SBMLsimulator includes a large collection of nature-inspired heuristic optimization procedures for efficient model calibration. It provides an intuitive Graphical User Interface (GUI) and several command-line options to be suitable for large-scale batch processing and model calibration. SBMLsimulator runs on all platforms that provide a standard Java Virtual Machine and is based on the open-source library JSBML. The integrated Systems Biology Simulation Core Library can be obtained as a separate application programming library.

Please cite:
[1] Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computational Biology, December 2014. [ details | link | link ]
[2] 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 | details | link | pdf ]

info
Fourth Release: You can now download the new version 1.2.1 of SBMLsimulator. See the Release Notes for details..  -   (keller - 2014-07-17 14:30). Note that the Web Start version does not provide the optimization routines. If you want to conduct a parameter estimation, please use the stand-alone version. This version requires Java™ 1.6 or higher for its execution.
Third Release: You can now download the new version 1.2 of SBMLsimulator. See the Release Notes for details..  -   (keller - 2014-04-24 15:20). Note that the Web Start version does not provide the optimization routines. If you want to conduct a parameter estimation, please use the stand-alone version. This version requires Java™ 1.6 or higher for its execution.
Second Release: You can now download the new version 1.1 of SBMLsimulator. See the Release Notes for details..  -   (draeger - 2013-04-25 15:11). Note that the Web Start version does not provide the optimization routines. If you want to conduct a parameter estimation, please use the stand-alone version.
First Release: Click here to download SBMLsimulator. Note that an installation of Java™ 1.5 or higher is required. program.  -   (draeger - 2012-03-01 15:32)

This project is promoted by:

BMBF European Commission ZBIT Virtual Liver