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

Zhike Zi | Zendy

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

Author(s) -

Zhike Zi

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr038

Subject(s) - sbml , markup language , computer science , scalability , interface (matter) , programming language , systems biology , computational science , parallel computing , theoretical computer science , bioinformatics , database , operating system , xml , biology , bubble , maximum bubble pressure method

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.

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