An efficient Java™ solver implementation for SBML
Authors: Andreas Dräger, Roland Keller, Meike Aichele, Robin Fähnrich, Stephanie Hoffmann, Fabian Schwarzkopf, Alexander Dörr, Max Zwiessele, Marcel Kronfeld, Philip Stevens, Clemens Wrzodek, Fabian Becker, Stefan Fischer
Contributors to predecessor projects: Sandra Saliger, Simon Schäfer, Dieudonné Motsou Wouamba, Hannes Borch
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.
For mor information, see the Users' Guide at http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator/
- Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur Sigurjónsson, Óttar Rolfsson, Julian Heinrich, and Andreas Dräger. Visualizing metabolic network dynamics through time-series metabolomic data [ DOI | PubMed | PDF | BibTeX ]
- Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computation, 2(4):246-257, December 2014. [ DOI | link ]
- 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 ]