A protocol for dynamic model calibration

19 pages, 6 figures, 2 tables.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License

Detalles Bibliográficos
Autores: Villaverde, A. F., Pathirana, Dilan, Fröhlich, Fabian, Hasenauer, Jan, Banga, Julio R.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/261052
Acceso en línea:http://hdl.handle.net/10261/261052
Access Level:acceso abierto
Palabra clave:Systems biology
Dynamic modelling
Parameter estimation
Identification
Identifiability
Optimization
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spelling A protocol for dynamic model calibrationVillaverde, A. F.Pathirana, DilanFröhlich, FabianHasenauer, JanBanga, Julio R.Systems biologyDynamic modellingParameter estimationIdentificationIdentifiabilityOptimization19 pages, 6 figures, 2 tables.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial LicenseOrdinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and nonmeasurable parameters, which have to be determined by fitting the model to experimental data. In order to perform this task, known as parameter estimation or model calibration, the modeller faces challenges such as poor parameter identifiability, lack of sufficiently informative experimental data and the existence of local minima in the objective function landscape. These issues tend to worsen with larger model sizes, increasing the computational complexity and the number of unknown parameters. An incorrectly calibrated model is problematic because it may result in inaccurate predictions and misleading conclusions. For nonexpert users, there are a large number of potential pitfalls. Here, we provide a protocol that guides the user through all the steps involved in the calibration of dynamic models. We illustrate the methodology with two models and provide all the code required to reproduce the results and perform the same analysis on new models. Our protocol provides practitioners and researchers in biological modelling with a one-stop guide that is at the same time compact and sufficiently comprehensive to cover all aspects of the problemEuropean Union’s Horizon 2020 Research and Innovation Programme (grant no. 686282) (‘CANPATHPRO’); Spanish MINECO/FEDER Project SYNBIOCONTROL (DPI2017-82896-C2-2-R to J.R.B.); Ramón y Cajal Fellowship (RYC-2019-027537-I to A.F.V.) from the Ministerio de Ciencia e innovación, Spain; Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (ED431F 2021/003 to A.F.V.); Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC 2151 - 390873048 to J.H.), (EXC-2047/1 - 390685813 to D.P.); German Federal Ministry of Economic Affairs and Energy (grant no. 16KN074236 to D.P.). Ministerio de Ciencia e Innovación, Spain (grant PID2020-117271RB-C22, ‘BIODYNAMICS’, to J.R.B.; Funding for open access charge: Universidade de Vigo/CISUG)Peer reviewedOxford University PressEuropean CommissionMinisterio de Economía y Competitividad (España)Ministerio de Ciencia, Innovación y Universidades (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/261052reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/686282info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/DPI2017-82896-C2-2-Rinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117271RB-C22https://doi.org/10.1093/bib/bbab387Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2610522026-05-22T06:33:51Z
dc.title.none.fl_str_mv A protocol for dynamic model calibration
title A protocol for dynamic model calibration
spellingShingle A protocol for dynamic model calibration
Villaverde, A. F.
Systems biology
Dynamic modelling
Parameter estimation
Identification
Identifiability
Optimization
title_short A protocol for dynamic model calibration
title_full A protocol for dynamic model calibration
title_fullStr A protocol for dynamic model calibration
title_full_unstemmed A protocol for dynamic model calibration
title_sort A protocol for dynamic model calibration
dc.creator.none.fl_str_mv Villaverde, A. F.
Pathirana, Dilan
Fröhlich, Fabian
Hasenauer, Jan
Banga, Julio R.
author Villaverde, A. F.
author_facet Villaverde, A. F.
Pathirana, Dilan
Fröhlich, Fabian
Hasenauer, Jan
Banga, Julio R.
author_role author
author2 Pathirana, Dilan
Fröhlich, Fabian
Hasenauer, Jan
Banga, Julio R.
author2_role author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Ministerio de Economía y Competitividad (España)
Ministerio de Ciencia, Innovación y Universidades (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Systems biology
Dynamic modelling
Parameter estimation
Identification
Identifiability
Optimization
topic Systems biology
Dynamic modelling
Parameter estimation
Identification
Identifiability
Optimization
description 19 pages, 6 figures, 2 tables.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/261052
url http://hdl.handle.net/10261/261052
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/686282
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/DPI2017-82896-C2-2-R
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117271RB-C22
https://doi.org/10.1093/bib/bbab387
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
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