SBML-PET: A systems biology markup language-based parameter estimation tool. Summary: The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system.

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  1. Afraites, Lekbir; Atlas, Abdelghafour: Parameters identification in the mathematical model of immune competition cells (2015)
  2. Zi, Zhike; Klipp, Edda: Sbml-pet: A systems biology markup language-based parameter estimation tool (2006) ioport