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Bioinformatics. 2006 Nov 1;22(21):2704-5. Epub 2006 Aug 22.

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

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  • 1Max Planck Institute for Molecular Genetics, Ihnestr. 73 14195 Berlin, Germany.


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.

AVAILABILITY: The website also contains detailed documentation for SBML-PET.

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