PEtab-Interoperable specification of parameter estimation problems in systems biology.

Algorithms Databases, Factual Models, Biological Models, Statistical Programming Languages Reproducibility of Results Systems Biology / methods

Journal

PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922

Informations de publication

Date de publication:
01 2021
Historique:
received: 07 08 2020
accepted: 18 12 2020
revised: 05 02 2021
pubmed: 27 1 2021
medline: 15 5 2021
entrez: 26 1 2021
Statut: epublish

Résumé

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

Identifiants

DOI: 10.1371/journal.pcbi.1008646 PMID: 33497393 PMC: PMC7864467
pubmed: 33497393
doi: 10.1371/journal.pcbi.1008646
pii: PCOMPBIOL-D-20-01416
pmc: PMC7864467
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

e1008646

Subventions

Organisme : NCI NIH HHS
ID : U54 CA225088
Pays : United States

Déclaration de conflit d'intérêts

The authors have declared that no competing interests exist.

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Auteurs

Leonard Schmiester (L)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
ORCID: 0000-0001-7946-3232

Yannik Schälte (Y)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
ORCID: 0000-0003-1293-820X

Frank T Bergmann (FT)

BioQUANT/COS, Heidelberg University, Heidelberg, Germany.
ORCID: 0000-0001-5553-4702

Tacio Camba (T)

Department of Applied Mathematics II, University of Vigo, Vigo, Galicia, Spain.
BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain.

Erika Dudkin (E)

Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
ORCID: 0000-0002-9649-0029

Janine Egert (J)

Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany.
Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.

Fabian Fröhlich (F)

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

Lara Fuhrmann (L)

Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
ORCID: 0000-0001-6405-0654

Adrian L Hauber (AL)

Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
Institute of Physics, University of Freiburg, Freiburg, Germany.
ORCID: 0000-0002-3053-5124

Svenja Kemmer (S)

Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
Institute of Physics, University of Freiburg, Freiburg, Germany.
ORCID: 0000-0001-7708-0545

Polina Lakrisenko (P)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
ORCID: 0000-0002-7626-8420

Carolin Loos (C)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
ORCID: 0000-0003-3680-0627

Simon Merkt (S)

Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
ORCID: 0000-0002-8017-4494

Wolfgang Müller (W)

Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany.
ORCID: 0000-0002-4980-3512

Dilan Pathirana (D)

Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
ORCID: 0000-0001-7000-2659

Elba Raimúndez (E)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
ORCID: 0000-0002-2790-6668

Lukas Refisch (L)

Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany.
Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
ORCID: 0000-0002-9049-1944

Marcus Rosenblatt (M)

Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
Institute of Physics, University of Freiburg, Freiburg, Germany.
ORCID: 0000-0002-7234-1328

Paul L Stapor (PL)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
ORCID: 0000-0002-7567-3985

Philipp Städter (P)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
ORCID: 0000-0002-4586-6604

Dantong Wang (D)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
ORCID: 0000-0002-3277-5033

Franz-Georg Wieland (FG)

Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
Institute of Physics, University of Freiburg, Freiburg, Germany.
ORCID: 0000-0002-5629-8622

Julio R Banga (JR)

BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain.
ORCID: 0000-0002-4245-0320

Jens Timmer (J)

Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
Institute of Physics, University of Freiburg, Freiburg, Germany.
Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.

Alejandro F Villaverde (AF)

BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain.
ORCID: 0000-0001-7401-7380

Sven Sahle (S)

BioQUANT/COS, Heidelberg University, Heidelberg, Germany.

Clemens Kreutz (C)

Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany.
Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
ORCID: 0000-0002-8796-5766

Jan Hasenauer (J)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Center for Mathematics, Technische Universität München, Garching, Germany.
Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
ORCID: 0000-0002-4935-3312

Daniel Weindl (D)

Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
ORCID: 0000-0001-9963-6057

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › PEtab-Interoperable specification of parameter...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › PEtab-Interoperable specification of parameter...
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles biologiques › PEtab-Interoperable specification of parameter...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Modèles statistiques › PEtab-Interoperable specification of parameter...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Langages de programmation › PEtab-Interoperable specification of parameter...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › PEtab-Interoperable specification of parameter...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Biologie des systèmes › PEtab-Interoperable specification of parameter...