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

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.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8361-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-9E59-A
Genre: Journal Article

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 Creators:
Zi, Zhike1, Author              
Klipp, Edda2, Author              
Affiliations:
1Cell Signaling Dynamics (Zhike Zi), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2117284              
2Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433554              

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 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.

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Language(s): eng - English
 Dates: 2006-11
 Publication Status: Published in print
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 Identifiers: eDoc: 313076
DOI: 10.1093/bioinformatics/btl443
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Title: Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 22 (21) Sequence Number: - Start / End Page: 2704 - 2705 Identifier: ISSN: 1367-4803