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SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

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.

10.3390/computation2040246

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Computation
Computation 2(4) : 246
1st Dec 2014

Alexander Dörr, Roland Keller, Andreas Zell, Andreas Dräger

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[Roland Keller] [Andreas Zell] [Andreas Dräger]

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None

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Cell and Intercellular
Views: 1586
  • Created: 14th Jan 2015 at 15:05
  • Last updated: 10th Jun 2015 at 18:36

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