@article{Doerr2014a,
  author   = {D\"orr, Alexander and Keller, Roland and Zell, Andreas and Dr\"ager, Andreas},
  title    = {{SBMLsimulator: a Java tool for model simulation and parameter estimation in systems
    biology}},
  journal  = {Computation},
  year     = {2014},
  volume   = {2},
  pages    = {246--257},
  number   = {4},
  month    = dec,
  abstract = {The identification of suitable model parameters for biochemical reactions has been
    recognized as a quite difficult endeavor. Parameter values from literature or experiments can
    often not directly be combined in complex reaction systems. Nature-inspired optimization
    techniques can find appropriate sets of parameters that calibrate a model to experimentally
    obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology
    Simulation Core Library for dynamic simulation of biochemical models with the heuristic
    optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with
    various options as well as a fully-featured command-line interface for large-scale and
    script-based model simulation and calibration. In a parameter estimation study based on a
    published model and artificial data we demonstrate the capability of SBMLsimulator to identify
    parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the
    parameter space and for the large-scale model calibration and estimation of uncertain parameter
    values.},
  doi      = {10.3390/computation2040246},
  issn     = {2079-3197},
  keywords = {SBML; ODE modeling; Simulation; Parameter estimation},
  pdf      = {https://www.mdpi.com/2079-3197/2/4/246/pdf},
  url      = {https://www.mdpi.com/2079-3197/2/4/246}
}