{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:11:07Z","timestamp":1780110667646,"version":"3.54.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors.<\/jats:p>\n               <jats:p>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\/.<\/jats:p>\n               <jats:p>Contact: \u00a0zhike.zi@bioss.uni-freiburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr038","type":"journal-article","created":{"date-parts":[[2011,2,9]],"date-time":"2011-02-09T01:56:03Z","timestamp":1297216563000},"page":"1028-1029","source":"Crossref","is-referenced-by-count":16,"title":["SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models"],"prefix":"10.1093","volume":"27","author":[{"given":"Zhike","family":"Zi","sequence":"first","affiliation":[{"name":"1 BIOSS Centre for Biological Signalling Studies, 2Center for Biological Systems Analysis (ZBSA) and 3Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Freiburg, Germany"},{"name":"1 BIOSS Centre for Biological Signalling Studies, 2Center for Biological Systems Analysis (ZBSA) and 3Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Freiburg, Germany"},{"name":"1 BIOSS Centre for Biological Signalling Studies, 2Center for Biological Systems Analysis (ZBSA) and 3Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,2,8]]},"reference":[{"key":"2023012512160665300_B1","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1126\/science.1184913","article-title":"Covering a broad dynamic range: information processing at the erythropoietin receptor","volume":"328","author":"Becker","year":"2010","journal-title":"Science"},{"key":"2023012512160665300_B2","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"LibSBML: an API library for SBML","volume":"24","author":"Bornstein","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512160665300_B3","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/0167-8191(96)00024-5","article-title":"A high-performance, portable implementation of the MPI message passing interface standard","volume":"22","author":"Gropp","year":"1996","journal-title":"Parallel Comput."},{"key":"2023012512160665300_B4","first-page":"55","article-title":"ODEPACK, a systematized collection of ODE solvers","volume-title":"Scientific Computing.","author":"Hindmarsh","year":"1983"},{"key":"2023012512160665300_B5","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/1471-2105-10-199","article-title":"DOTcvpSB, a software toolbox for dynamic optimization in systems biology","volume":"10","author":"Hirmajer","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012512160665300_B6","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI\u2013a COmplex PAthway Simulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512160665300_B7","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012512160665300_B8","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1093\/bioinformatics\/bti753","article-title":"libSRES: a C library for stochastic ranking evolution strategy for parameter estimation","volume":"22","author":"Ji","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512160665300_B9","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1093\/bioinformatics\/btq276","article-title":"DA 1.0: parameter estimation of biological pathways using data assimilation approach","volume":"26","author":"Koh","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512160665300_B10","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/bioinformatics\/btn350","article-title":"Dynamical modeling and multi-experiment fitting with PottersWheel","volume":"24","author":"Maiwald","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512160665300_B11","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1137\/0111030","article-title":"An algorithm for least-squares estimation of nonlinear parameters","volume":"11","author":"Marquardt","year":"1963","journal-title":"J. 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