SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup 
Language based models

Zi, Zhike

doi:10.1093/bioinformatics/btr038

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SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models

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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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Zi, Z. (2011). SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models. Bioinformatics, 27(7), 1028-1029. doi:10.1093/bioinformatics/btr038.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0027-A135-0

Abstract

Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors.