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Bioinformatics Advance Access originally published online on August 22, 2006
Bioinformatics 2006 22(21):2704-2705; doi:10.1093/bioinformatics/btl443
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Zhike Zi and Edda Klipp *

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

*To whom correspondence should be addressed.

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.

Availability: http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

Contact: klipp{at}molgen.mpg.de, zhike_zi{at}molgen.mpg.de

Received on June 15, 2006; revised on August 2, 2006; accepted on August 14, 2006

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