{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T23:15:02Z","timestamp":1775776502090,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T00:00:00Z","timestamp":1700697600000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/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"}]},{"name":"Germany\u2019s Excellence Strategy","award":["EXC 2047\/1 390685813"],"award-info":[{"award-number":["EXC 2047\/1 390685813"]}]},{"name":"Germany\u2019s Excellence Strategy","award":["EXC 2151 390873048"],"award-info":[{"award-number":["EXC 2151 390873048"]}]},{"DOI":"10.13039\/501100000854","name":"Human Frontier Science Program","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000854","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Federal Ministry of Education and Research"},{"DOI":"10.13039\/100008662","name":"Joachim Herz Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008662","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. pyPESTO is a modular framework for systematic parameter estimation, with scalable algorithms for optimization and uncertainty quantification. While tailored to ordinary differential equation problems, pyPESTO is broadly applicable to black-box parameter estimation problems. Besides own implementations, it provides a unified interface to various popular simulation and inference methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>pyPESTO is implemented in Python, open-source under a 3-Clause BSD license. Code and documentation are available on GitHub (https:\/\/github.com\/icb-dcm\/pypesto).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad711","type":"journal-article","created":{"date-parts":[[2023,11,22]],"date-time":"2023-11-22T17:53:55Z","timestamp":1700675635000},"source":"Crossref","is-referenced-by-count":50,"title":["pyPESTO: a modular and scalable tool for parameter estimation for dynamic models"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1293-820X","authenticated-orcid":false,"given":"Yannik","family":"Sch\u00e4lte","sequence":"first","affiliation":[{"name":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"},{"name":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany"},{"name":"Department of Mathematics, Technical University of Munich , 85748 Garching, 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