An efficient Java™ solver implementation for SBML

Andreas Dräger1, Roland Keller1, Alexander Dörr1, Stephanie Tscherneck1, Ute Hofmann2, Clemens Wrzodek1, Akira Funahashi3, Akito Tabira3, Benjamin Kandel2, Marcus Klein2, Maria Thomas2, Nicolas Rodriguez4, Nicolas Le Novère4, Ulrich M. Zanger2, and Andreas Zell1

1Center for Bioinformatics Tübingen (ZBIT), Germany, 2Dr. Margarethe Fischer-Bosch-Institute for Clinical Pharmacology (IKP), Stuttgart, Germany, 3Keio University, Graduate School of Science and Technology, Yokohama, Japan, 4European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom

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). In order to ensure a high reliability of this software, it has been benchmarked against the entire SBML Test Suite and all models from the database. It includes a large collection of nature-inspired heuristic optimization procedures for efficient model calibration. SBMLsimulator 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 simulation core library of SBMLsimulator can be obtained as a separate application programming library.

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™ 1.6 or higher is required. program.  -   (draeger - 2012-03-01 15:32)

This project is promoted by:

BMBF ZBIT Virtual Liver