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SBML-PET-MPI is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets. SBML-PET-MPI can run on Windows, Linux and Mac OS systems.

Features

  • SBML-PET-MPI supports model import and export in SBML format.
  • SBML-PET-MPI estimates parameter values by fitting multiple experimental data sets. Experimental data can be produced under different conditions.
  • SBML-PET-MPI can implement uncertainty and identifiability analysis of the estimated parameters with profile likelihood exploit algorithm or bootstrap method with synthetic data sets.
  • SBML-PET-MPI is parallelized using MPI protocol and has good speed up scalability with the number of processors.
  • SBML-PET-MPI supports events that describe the discontinuous state changes in the model.
  • SBML-PET-MPI supports normalized data, the standard deviation of the data and the noise or measurement error existed in the experiments.
  • SBML-PET-MPI supports constraints of the model.

Messages

  • SBML-PET-MPI published in Bioinformatics. Auguest 11, 2011. Memory leaking bug found in updating the BestFitnessSBML.xml files.  It is fixed in the future release of SBML-PET-MPI v1.2. March 29, 2011, SBML ...
    Posted Aug 11, 2011, 5:20 AM by Zhike Zi
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Free for Noncommercial usage

Copyright © 2010, Zhike Zi