{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:12Z","timestamp":1740185112943,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"10","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM070923"],"award-info":[{"award-number":["R01 GM070923"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Computational modeling is widely used for deepening the understanding of biological processes. Parameterizing models to experimental data needs computationally efficient techniques for parameter estimation. Challenges for parameter estimation include in general the high dimensionality of the parameter space with local minima and in specific for stochastic modeling the intrinsic stochasticity.<\/jats:p>\n               <jats:p>Results: We implemented the recently suggested multiple shooting for stochastic systems (MSS) objective function for parameter estimation in stochastic models into COPASI. This MSS objective function can be used for parameter estimation in stochastic models but also shows beneficial properties when used for ordinary differential equation models. The method can be applied with all of COPASI\u2019s optimization algorithms, and can be used for SBML models as well.<\/jats:p>\n               <jats:p>Availability and implementation: The methodology is available in COPASI as of version 4.15.95 and can be downloaded from http:\/\/www.copasi.org.<\/jats:p>\n               <jats:p>Contact: \u00a0frank.bergmann@bioquant.uni-heidelberg.de or fbergman@caltech.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv759","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T01:09:07Z","timestamp":1455498547000},"page":"1586-1588","source":"Crossref","is-referenced-by-count":9,"title":["Piecewise parameter estimation for stochastic models in COPASI"],"prefix":"10.1093","volume":"32","author":[{"given":"Frank T.","family":"Bergmann","sequence":"first","affiliation":[{"name":"1 COS Heidelberg\/BioQuant, Heidelberg 69120, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sven","family":"Sahle","sequence":"additional","affiliation":[{"name":"1 COS Heidelberg\/BioQuant, Heidelberg 69120, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph","family":"Zimmer","sequence":"additional","affiliation":[{"name":"2 BIOMS, University of Heidelberg, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,1,18]]},"reference":[{"key":"2023020112265758700_btv759-B1","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1002\/gamm.200790024","article-title":"Numerical methods for parameter estimation in nonlinear differential algebraic equations","volume":"30","author":"Bock","year":"2007","journal-title":"GAMM Mitteilungen"},{"key":"2023020112265758700_btv759-B2","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"Copasi\u2014a complex pathway simulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020112265758700_btv759-B3","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":"2023020112265758700_btv759-B4","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.mbs.2014.03.001","article-title":"Stochastic differential equations as a tool to regularize the parameter estimation problem for continuous time dynamical systems given discrete time measurements","volume":"251","author":"Leander","year":"2014","journal-title":"Math. 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Biol."},{"year":"2015","author":"Zimmer","key":"2023020112265758700_btv759-B9"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/10\/1586\/49019467\/bioinformatics_32_10_1586.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/10\/1586\/49019467\/bioinformatics_32_10_1586.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:30:48Z","timestamp":1675290648000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/10\/1586\/1742593"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,18]]},"references-count":9,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2016,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv759","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2016,5,15]]},"published":{"date-parts":[[2016,1,18]]}}}