{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:54:09Z","timestamp":1775984049592,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T00:00:00Z","timestamp":1508716800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, for which the user can provide a deterministic objective function in MATLAB.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PESTO is a MATLAB toolbox, freely available under the BSD license. The source code, along with extensive documentation and example code, can be downloaded from https:\/\/github.com\/ICB-DCM\/PESTO\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx676","type":"journal-article","created":{"date-parts":[[2017,10,20]],"date-time":"2017-10-20T11:22:27Z","timestamp":1508498547000},"page":"705-707","source":"Crossref","is-referenced-by-count":94,"title":["PESTO: Parameter EStimation TOolbox"],"prefix":"10.1093","volume":"34","author":[{"given":"Paul","family":"Stapor","sequence":"first","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9963-6057","authenticated-orcid":false,"given":"Daniel","family":"Weindl","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}]},{"given":"Benjamin","family":"Ballnus","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"given":"Sabine","family":"Hug","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3680-0627","authenticated-orcid":false,"given":"Carolin","family":"Loos","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"given":"Anna","family":"Fiedler","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"given":"Sabrina","family":"Krause","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"given":"Sabrina","family":"Hro\u00df","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"given":"Fabian","family":"Fr\u00f6hlich","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-3312","authenticated-orcid":false,"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"},{"name":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,10,23]]},"reference":[{"key":"2023012712380835200_btx676-B1","doi-asserted-by":"crossref","first-page":"125009.","DOI":"10.1088\/0266-5611\/32\/12\/125009","article-title":"Integration based profile likelihood calculation for PDE constrained parameter estimation problems","volume":"32","author":"Boiger","year":"2016","journal-title":"Inverse Prob"},{"key":"2023012712380835200_btx676-B2","doi-asserted-by":"crossref","first-page":"136.","DOI":"10.1186\/1471-2105-15-136","article-title":"MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics","volume":"15","author":"Egea","year":"2014","journal-title":"BMC Bioinf"},{"key":"2023012712380835200_btx676-B3","doi-asserted-by":"crossref","first-page":"e1005331.","DOI":"10.1371\/journal.pcbi.1005331","article-title":"Scalable parameter estimation for genome-scale biochemical reaction networks","volume":"13","author":"Fr\u00f6hlich","year":"2017","journal-title":"PLoS Comput. 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