%0 Journal Article %1 Zi2011SBMLPETMPI %A Zi, Zhike %D 2011 %J Bioinformatics %K high-performance-computing parallel-algorithms parameter-estimation %R 10.1093/bioinformatics/btr038 %T SBML-PET-MPI: A parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models %U http://dx.doi.org/10.1093/bioinformatics/btr038 %X Summary: 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 data sets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors.Availability: 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/Contact: zhike.zi@bioss.uni-freiburg.de

@article{Zi2011SBMLPETMPI, abstract = {Summary: 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 data sets. The tool is developed and parallelized using the message passing interface ({MPI}) protocol, which provides good scalability with the number of {processors.Availability}: {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/Contact}: zhike.zi@bioss.uni-freiburg.de}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Zi, Zhike}, biburl = {https://www.bibsonomy.org/bibtex/21fe3e90d1ee3286cbd1b2644be9ba132/karthikraman}, citeulike-article-id = {8790358}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btr038}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/early/2011/02/08/bioinformatics.btr038.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/early/2011/02/08/bioinformatics.btr038.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/21303862}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=21303862}, day = 8, doi = {10.1093/bioinformatics/btr038}, interhash = {94745b89f180780aabdf57072c865d8b}, intrahash = {1fe3e90d1ee3286cbd1b2644be9ba132}, issn = {1367-4811}, journal = {Bioinformatics}, keywords = {high-performance-computing parallel-algorithms parameter-estimation}, month = feb, pmid = {21303862}, posted-at = {2011-02-10 11:05:21}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {{SBML}-{PET}-{MPI}: A parallel parameter estimation tool for Systems Biology Markup Language ({SBML}) based models}, url = {http://dx.doi.org/10.1093/bioinformatics/btr038}, year = 2011 }