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.
@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 = {http://www.mdpi.com/2079-3197/2/4/246/pdf},
url = {http://www.mdpi.com/2079-3197/2/4/246}
}