{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T08:46:07Z","timestamp":1762505167937},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system.<\/jats:p>\n               <jats:p>Availability: \u00a0. The website also contains detailed documentation for SBML-PET.<\/jats:p>\n               <jats:p>Contact: \u00a0klipp@molgen.mpg.de, zhike_zi@molgen.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl443","type":"journal-article","created":{"date-parts":[[2006,8,23]],"date-time":"2006-08-23T03:33:41Z","timestamp":1156304021000},"page":"2704-2705","source":"Crossref","is-referenced-by-count":55,"title":["SBML-PET: a Systems Biology Markup Language-based parameter estimation tool"],"prefix":"10.1093","volume":"22","author":[{"given":"Zhike","family":"Zi","sequence":"first","affiliation":[{"name":"Max Planck Institute for Molecular Genetics, Ihnestr. 73 \u00a0 14195 Berlin, Germany"}]},{"given":"Edda","family":"Klipp","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Molecular Genetics, Ihnestr. 73 \u00a0 14195 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2006,8,22]]},"reference":[{"key":"2023012408420862800_b1","first-page":"55","article-title":"ODEPACK, a systematized collection of ODE solvers","volume-title":"Scientific Computing","author":"Hindmarsh","year":"1983"},{"key":"2023012408420862800_b2","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1093\/bioinformatics\/bti143","article-title":"Grid cellware: the first grid-enabled tool for modelling and simulating cellular processes","volume":"21","author":"Dhar","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408420862800_b3","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1471-2105-6-155","article-title":"Iterative approach to model identification of biological networks","volume":"6","author":"Gadkar","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012408420862800_b4","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":"2023012408420862800_b5","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1093\/bioinformatics\/bth122","article-title":"OBIYagns: a grid-based biochemical simulator with a parameter estimator","volume":"20","author":"Kimura","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408420862800_b6","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1006\/jtbi.1994.1234","article-title":"Evolutionary optimization of enzyme kinetic parameters; effect of constraints","volume":"171","author":"Klipp","year":"1994","journal-title":"J. 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