title: SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.
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.
  
  
  BACKGROUND
  SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.
authors.affiliation: BIOSS Centre for Biological Signalling Studies, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany. zhike.zi@bioss.uni-freiburg.de
authors.forename: Zhike
authors.initials: Z
authors.lastname: Zi
mesh_terms: D000465:Algorithms; D008954:Models, Biological; D011381:Programming Languages; D012984:Software; D049490:Systems Biology / Q000379:methods*