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SBMLsimulator

An efficient Java™ solver implementation for SBML

Publications on SBMLsimulator

When using SBMLsimulator in your work, 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. Computation, 2(4):246--257, December 2014. [ DOI | 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 ]

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Main program features

SBMLsimulator 1.2

  • Accurate: 100 % of the SBML Test Suite version 2.3.2 (5,339 models in 68.6 s)
  • Fast: 500 integration steps of the glycolysis (Biomodel 42) computed in 0.319 s (with Rosenbrock's solver).
  • JSBML-based (Java library for SBML)
  • Platform independent: Tested on Windows, Linux, and Mac OS
  • Bilingual user interface (English and German)
  • All program features also available through the command-line interface
  • Nine numerical integration methods, including the Rosenbrock Solver for stiff systems
  • Heuristic optimization framework EvA2 included

Availability of SBMLsimulator

SBMLsimulator is available in two different forms:
  1. As a stand-alone application that simulates models stored in SBML files and calibrates these with respect to given data.
  2. As a Java™ Web Start version, which allows users to directly launch this application from your browser.

User guide and API documentation of SBMLsimulator

The user guide of SBMLsimulator can be found here.

A toy data set for playing with SBMLsimulator is available here. It was created from biomodel #324, which was used for demonstrating the capabilities of SBMLsimulator in the user guide.

An API documentation can be found for the following versions:

which allows users to costumize SBMLsimulator or to access its methods from their own programs.

Documentation of Systems Biology Simulation Core Library

The API documentation of Systems Biology Simulation Core Library, which is integrated in SBMLsimulator, can be found here.