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Journal Article

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

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Zi,  Zhike
Cell Signaling Dynamics (Zhike Zi), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Klipp,  Edda
Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Zi, Z., & Klipp, E. (2006). SBML-PET: a Systems Biology Markup Language-based parameter estimation tool. Bioinformatics, 22(21), 2704-2705. doi:10.1093/bioinformatics/btl443.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-8361-8
Abstract
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.