{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T18:53:13Z","timestamp":1791226393347,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1014774","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000}}],"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["390685813 - EXC 2047"],"award-info":[{"award-number":["390685813 - EXC 2047"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["390873048 - EXC 2151"],"award-info":[{"award-number":["390873048 - EXC 2151"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["432325352 \u2013 SFB 1454"],"award-info":[{"award-number":["432325352 \u2013 SFB 1454"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01ZX1916A"],"award-info":[{"award-number":["01ZX1916A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019180","name":"HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["101126146"],"award-info":[{"award-number":["101126146"]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031L0293C"],"award-info":[{"award-number":["031L0293C"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Network for Bioinformatics Infrastructure \u2013 de.NBI","award":["W-de.NBI-016"],"award-info":[{"award-number":["W-de.NBI-016"]}],"id":[{"id":"https:\/\/ror.org\/01vmpm840","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["VR2017-05117"],"award-info":[{"award-number":["VR2017-05117"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["VR2023-04319"],"award-info":[{"award-number":["VR2023-04319"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001729","name":"Stiftelsen f\u00f6r Strategisk Forskning","doi-asserted-by":"publisher","award":["FFL15-0238"],"award-info":[{"award-number":["FFL15-0238"]}],"id":[{"id":"10.13039\/501100001729","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["499552394 \u2013 SFB 1597"],"award-info":[{"award-number":["499552394 \u2013 SFB 1597"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>A central question in mathematical modeling of biological systems is determining which processes are most relevant and how they can be described. There are often competing hypotheses, which yield different models. Model comparison requires parameter optimization and sampling methods. Yet, standards for the specification of model selection problems and the swift evaluation of a broad spectrum of approaches are not available. PEtab Select addresses this challenge by providing a concise, standardized specification of model selection and its associated calibration problems through a new file format standard and software package. The standard facilitates the compact representation of even very large model selection problems; in one example, billions of model alternatives. PEtab Select builds on the PEtab standard for the specification of parameter estimation problems, and enables the use of state-of-the-art modelling and calibration workflows utilizing COPASI, Data2Dynamics, PEtab.jl, and pyPESTO. PEtab Select supports common model selection criteria (e.g., Akaike and Bayesian information criteria) and can be easily extended to use others. To ensure flexibility, PEtab Select implements several model space exploration approaches, including basic brute-force, forward, and backward selection, and also advanced, flexible selection methods. PEtab Select introduces the first standardization of model selection tasks, filling a critical gap in existing computational pipelines. It constitutes an essential contribution to FAIR research software in systems biology by promoting interoperability and reusability in model selection.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1014774","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:01:28Z","timestamp":1790798488000},"page":"e1014774","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["PEtab Select: Specification standard and supporting software for automated model selection"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7000-2659","authenticated-orcid":true,"given":"Dilan","family":"Pathirana","sequence":"first","affiliation":[{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Bonn Center for Mathematical Life Sciences"]},{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Life and Medical Sciences (LIMES) Institute"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5553-4702","authenticated-orcid":true,"given":"Frank T.","family":"Bergmann","sequence":"additional","affiliation":[{"name":"Heidelberg University","place":["Heidelberg, Germany"],"department":["BioQUANT"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1820-7375","authenticated-orcid":true,"given":"Domagoj","family":"Doresic","sequence":"additional","affiliation":[{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Bonn Center for Mathematical Life Sciences"]},{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Life and Medical Sciences (LIMES) Institute"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Polina","family":"Lakrisenko","sequence":"additional","affiliation":[{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Bonn Center for Mathematical Life Sciences"]},{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Life and Medical Sciences (LIMES) Institute"]},{"name":"Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH)","place":["Neuherberg, Germany"],"department":["Computational Health Center"]},{"name":"Technische Universit\u00e4t M\u00fcnchen","place":["Munich, Germany"],"department":["School of Life Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-2304-4263","authenticated-orcid":true,"given":"Sebastian","family":"Persson","sequence":"additional","affiliation":[{"name":"Chalmers University of Technology, and University of Gothenburg","place":["Gothenburg, Sweden"],"department":["Department of Mathematical Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4353-1181","authenticated-orcid":true,"given":"Niklas","family":"Neubrand","sequence":"additional","affiliation":[{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Institute of Medical Biometry and Statistics (IMBI), Medical Faculty and Medical Center"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Timmer","sequence":"additional","affiliation":[{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Institute of Physics"]},{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["CIBSS, Centre for Integrative Biological Signalling Studies"]},{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Freiburg Center for Data Analysis and Modelling"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clemens","family":"Kreutz","sequence":"additional","affiliation":[{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Institute of Medical Biometry and Statistics (IMBI), Medical Faculty and Medical Center"]},{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["CIBSS, Centre for Integrative Biological Signalling Studies"]},{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Freiburg Center for Data Analysis and Modelling"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harald","family":"Binder","sequence":"additional","affiliation":[{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Institute of Medical Biometry and Statistics (IMBI), Medical Faculty and Medical Center"]},{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["CIBSS, Centre for Integrative Biological Signalling Studies"]},{"name":"University of Freiburg","place":["Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"],"department":["Freiburg Center for Data Analysis and Modelling"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marija","family":"Cvijovic","sequence":"additional","affiliation":[{"name":"Chalmers University of Technology, and University of Gothenburg","place":["Gothenburg, Sweden"],"department":["Department of Mathematical Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9963-6057","authenticated-orcid":true,"given":"Daniel","family":"Weindl","sequence":"additional","affiliation":[{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Bonn Center for Mathematical Life Sciences"]},{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Life and Medical Sciences (LIMES) Institute"]},{"name":"Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH)","place":["Neuherberg, Germany"],"department":["Computational Health Center"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-3312","authenticated-orcid":true,"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Bonn Center for Mathematical Life Sciences"]},{"name":"University of Bonn","place":["Bonn, Germany"],"department":["Life and Medical Sciences (LIMES) Institute"]},{"name":"Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH)","place":["Neuherberg, Germany"],"department":["Computational Health Center"]},{"name":"Technische Universit\u00e4t M\u00fcnchen","place":["Munich, Germany"],"department":["School of Life Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"with the PEtab Select community","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"issue":"9","key":"pcbi.1014774.ref001","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0074335","article-title":"Lessons learned from quantitative dynamical modeling in systems biology","volume":"8","author":"A Raue","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"pcbi.1014774.ref002","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab387","article-title":"A protocol for dynamic model calibration","volume":"23","author":"AF Villaverde","year":"2022","journal-title":"Brief Bioinform"},{"key":"pcbi.1014774.ref003","doi-asserted-by":"crossref","DOI":"10.1007\/b97636","volume-title":"Model Selection and Multimodel Inference","author":"KP Burnham","year":"2004"},{"issue":"4","key":"pcbi.1014774.ref004","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":"M Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"pcbi.1014774.ref005","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/1752-0509-5-198","article-title":"Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language","volume":"5","author":"D Waltemath","year":"2011","journal-title":"BMC Syst Biol"},{"issue":"1","key":"pcbi.1014774.ref006","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1008646","article-title":"PEtab-Interoperable specification of parameter estimation problems in systems biology","volume":"17","author":"L Schmiester","year":"2021","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"pcbi.1014774.ref007","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification","volume":"19","author":"H Akaike","year":"1974","journal-title":"IEEE Trans Automat Contr"},{"issue":"1","key":"pcbi.1014774.ref008","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1080\/03610927808827599","article-title":"Further analysis of the data by Akaike\u2019s information criterion and the finite corrections","volume":"7","author":"N Sugiura","year":"1978","journal-title":"Communications in Statistics - Theory and Methods"},{"issue":"2","key":"pcbi.1014774.ref009","doi-asserted-by":"crossref","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating the Dimension of a Model","volume":"6","author":"G Schwarz","year":"1978","journal-title":"Ann Statist"},{"issue":"430","key":"pcbi.1014774.ref010","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1080\/01621459.1995.10476572","article-title":"Bayes Factors","volume":"90","author":"RE Kass","year":"1995","journal-title":"Journal of the American Statistical Association"},{"issue":"9","key":"pcbi.1014774.ref011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1011417","article-title":"Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models","volume":"19","author":"C T\u00f6nsing","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014774.ref012","doi-asserted-by":"crossref","DOI":"10.1214\/09-SS054","article-title":"A survey of cross-validation procedures for model selection","volume":"4","author":"S Arlot","year":"2010","journal-title":"Statist Surv"},{"issue":"1","key":"pcbi.1014774.ref013","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.cels.2016.01.002","article-title":"Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions","volume":"2","author":"T Blasi","year":"2016","journal-title":"Cell Syst"},{"issue":"3","key":"pcbi.1014774.ref014","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004784","article-title":"Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection","volume":"12","author":"A Milias-Argeitis","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014774.ref015","doi-asserted-by":"crossref","first-page":"88","DOI":"10.3389\/fmicb.2018.00088","article-title":"Saccharomyces cerevisiae and S. kudriavzevii Synthetic Wine Fermentation Performance Dissected by Predictive Modeling","volume":"9","author":"D Henriques","year":"2018","journal-title":"Front Microbiol"},{"issue":"1","key":"pcbi.1014774.ref016","doi-asserted-by":"crossref","first-page":"2477","DOI":"10.1038\/s41467-023-37430-y","article-title":"Positive feedback induces switch between distributive and processive phosphorylation of Hog1","volume":"14","author":"M Mosbacher","year":"2023","journal-title":"Nat Commun"},{"issue":"3","key":"pcbi.1014774.ref017","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007669","article-title":"Parallel Tempering with Lasso for model reduction in systems biology","volume":"16","author":"S Gupta","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"9","key":"pcbi.1014774.ref018","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0162366","article-title":"Driving the Model to Its Limit: Profile Likelihood Based Model Reduction","volume":"11","author":"T Maiwald","year":"2016","journal-title":"PLoS One"},{"issue":"1","key":"pcbi.1014774.ref019","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1093\/bioinformatics\/btz500","article-title":"Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis","volume":"36","author":"A Theorell","year":"2020","journal-title":"Bioinformatics"},{"issue":"21","key":"pcbi.1014774.ref020","doi-asserted-by":"crossref","first-page":"3558","DOI":"10.1093\/bioinformatics\/btv405","article-title":"Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems","volume":"31","author":"A Raue","year":"2015","journal-title":"Bioinformatics"},{"key":"pcbi.1014774.ref021","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v088.i10","article-title":"Dynamic modeling, parameter estimation, and uncertainty analysis in R","volume":"88","author":"D Kaschek","year":"2019","journal-title":"Journal of Statistical Software"},{"issue":"11","key":"pcbi.1014774.ref022","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad711","article-title":"pyPESTO: a modular and scalable tool for parameter estimation for dynamic models","volume":"39","author":"Y Sch\u00e4lte","year":"2023","journal-title":"Bioinformatics"},{"key":"pcbi.1014774.ref023","article-title":"PEtab.jl: Advancing the Efficiency and Utility of Dynamic Modelling","author":"S Persson","year":"2025","journal-title":"bioRxiv"},{"issue":"24","key":"pcbi.1014774.ref024","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI--a COmplex PAthway SImulator","volume":"22","author":"S Hoops","year":"2006","journal-title":"Bioinformatics"},{"issue":"90","key":"pcbi.1014774.ref025","doi-asserted-by":"crossref","first-page":"5553","DOI":"10.21105\/joss.05553","article-title":"BASICO: A simplified Python interface to COPASI","volume":"8","author":"FT Bergmann","year":"2023","journal-title":"JOSS"},{"issue":"8","key":"pcbi.1014774.ref026","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007230","article-title":"FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics","volume":"15","author":"M Gabel","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014774.ref027","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"MD Wilkinson","year":"2016","journal-title":"Sci Data"},{"issue":"1","key":"pcbi.1014774.ref028","doi-asserted-by":"crossref","first-page":"15","DOI":"10.5334\/jors.151","article-title":"DifferentialEquations.jl \u2013 A performant and feature-rich ecosystem for solving differential equations in Julia","volume":"5","author":"C Rackauckas","year":"2017","journal-title":"Journal of Open Research Software"},{"key":"pcbi.1014774.ref029","article-title":"Forward-Mode Automatic Differentiation in Julia","author":"J Revels","year":"2016","journal-title":"arXiv"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1014774","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014774","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T18:02:12Z","timestamp":1791223332000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014774"}},"subtitle":[],"editor":[{"given":"Christopher E","family":"Miles","sequence":"first","affiliation":[{"name":"University of Utah","place":["UNITED STATES OF AMERICA"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":29,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1014774","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]}}}