{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T20:54:57Z","timestamp":1793134497057,"version":"4.5.0"},"reference-count":0,"publisher":"Walter de Gruyter GmbH","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Parameter estimation is a central task in data-driven computational modeling, and a clear, unambiguous, and commonly understood specification of parameter estimation problems is essential for reproducibility and interoperability. PEtab provides a standardized framework for defining such problems in systems biology and systems medicine, particularly for ordinary differential equation models. This document describes the second version of the PEtab format, PEtab 2.0. PEtab 2.0 simplifies and clarifies how estimation problems are defined, while also extending the standard to support more complex and realistic experimental setups. Key improvements include support for additional model formats beyond SBML, expanded and improved specification of parameter priors for Bayesian parameter estimation, and a more flexible description of experiments that allows multiple conditions, time periods, and pre-equilibration steps within a single simulation. Additional updates refine the definition of model parameters, measurement noise, and observation models, and remove ambiguous or confusing features from earlier versions. Version 2 also includes a general extension mechanism, to add functionality for specialized applications not covered by the core standard.<\/jats:p>","DOI":"10.1515\/jib-2026-0004","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T04:55:33Z","timestamp":1786596933000},"source":"Crossref","is-referenced-by-count":2,"title":["The parameter estimation tables (PEtab) format version 2"],"prefix":"10.1515","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7000-2659","authenticated-orcid":false,"given":"Dilan","family":"Pathirana","sequence":"first","affiliation":[{"name":"Bonn Center for Mathematical Life Sciences , University of Bonn , Bonn , Germany"},{"name":"Life and Medical Sciences (LIMES) Institute , University of Bonn , Bonn , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5360-4292","authenticated-orcid":false,"given":"Fabian","family":"Fr\u00f6hlich","sequence":"additional","affiliation":[{"name":"Dynamics of Living Systems Laboratory , The Francis Crick Institute , 1 Midland Rd , London NW1 1AT , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-2304-4263","authenticated-orcid":false,"given":"Sebastian","family":"Persson","sequence":"additional","affiliation":[{"name":"Dynamics of Living Systems Laboratory , The Francis Crick Institute , 1 Midland Rd , London NW1 1AT , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5553-4702","authenticated-orcid":false,"given":"Frank T.","family":"Bergmann","sequence":"additional","affiliation":[{"name":"BioQUANT \u2013 Heidelberg University , INF 267, 69120 Heidelberg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1725-179X","authenticated-orcid":false,"given":"Matthias","family":"K\u00f6nig","sequence":"additional","affiliation":[{"name":"Humboldt-Universit\u00e4t zu Berlin, Faculty of Life Sciences, Department of Biology , Systems Medicine of the Liver , Unter den Linden 6, 10099 Berlin , Germany"},{"name":"Institute of Structural Mechanics and Dynamics in Aerospace Engineering , University of Stuttgart , Pfaffenwaldring 27, 70569 Stuttgart , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6388-2405","authenticated-orcid":false,"given":"Paul F.","family":"Lang","sequence":"additional","affiliation":[{"name":"Deep Origin , South San Francisco , CA , USA"},{"name":"JuliaHub , Cambridge , MA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Severin","family":"Bang","sequence":"additional","affiliation":[{"name":"Institute of Physics , University of Freiburg , Freiburg im Breisgau , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7708-0545","authenticated-orcid":false,"given":"Svenja","family":"Kemmer","sequence":"additional","affiliation":[{"name":"Institute of Physics , University of Freiburg , Freiburg im Breisgau , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-3312","authenticated-orcid":false,"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[{"name":"Bonn Center for Mathematical Life Sciences , University of Bonn , Bonn , Germany"},{"name":"Life and Medical Sciences (LIMES) Institute , University of Bonn , Bonn , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9963-6057","authenticated-orcid":false,"given":"Daniel","family":"Weindl","sequence":"additional","affiliation":[{"name":"Bonn Center for Mathematical Life Sciences , University of Bonn , Bonn , Germany"},{"name":"Life and Medical Sciences (LIMES) Institute , University of Bonn , Bonn , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"374","published-online":{"date-parts":[[2026,8,13]]},"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.1515\/jib-2026-0004\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.1515\/jib-2026-0004\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:55:57Z","timestamp":1787032557000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.1515\/jib-2026-0004\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":0,"alternative-id":["10.1515\/jib-2026-0004"],"URL":"https:\/\/doi.org\/10.1515\/jib-2026-0004","relation":{},"ISSN":["1613-4516"],"issn-type":[{"value":"1613-4516","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]},"article-number":"20260004"}}