PEtab—Interoperable specification of parameter estimation problems in systems biology
Public Library of Science, 2021
Online
academicJournal
Zugriff:
10 pages, 3 figures, 2 tables.-- This is an open access article distributed under the terms of the Creative Commons Attribution License ; 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 ; This work was supported by the European Union’s Horizon 2020 research and innovation program (CanPathPro; Grant no. 686282; J.H., D.W., P.L.S., E.D., S.M., A.F.V., J.R.B.), the German Federal Ministry of Education and Research (Grant no. 01ZX1916A; D.W., P.L. & 01ZX1705A; J.H., P.L. & Grant. no. 031L0159C; J.H. & de.NBI ModSim1, 031L0104A; F.T.B. & EA:Sys, 031L0080; J.E, L.R & Grant no. 031L0048; S.K., F.G.W. & 01ZX1310B; E.R.), the German Federal Ministry of Economic Affairs and Energy (Grant no. 16KN074236; D.P.), the German Research Foundation (Grant no. HA7376/1-1; Y.S.; CIBSS-EXC-2189-2100249960-390939984; C.K., J.T.; project ID: 272983813 - TRR 179; M.R. & Clusters of Excellence EXC 2047 and EXC 2151; E.R., J.H.), the Deutsche Krebshilfe (Grant no. 70112355; A.L.H.), the Human Frontier Science Program (Grant no. LT000259/2019-L1; F.F.), the National Institute of Health (Grant no. U54-CA225088; F.F.) ; Peer reviewed
Titel: |
PEtab—Interoperable specification of parameter estimation problems in systems biology
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Autor/in / Beteiligte Person: | Schmiester, Leonard ; Schälte, Yannik ; Bergmann, Frank T. ; Camba, Tacio ; Dudkin, Erika ; Egert, Janine ; Frölich, Fabian ; Fuhrmann, Lara ; Hauber, Adrian L. ; Kemmer, Svenja ; Lakrisenko, Polina ; Loos, Carolin ; Merkt, Simon ; Müller, Wolfgang ; Pathirana, Dilan ; Raimúndez, Elba ; Refisch, Lukas ; Rosenblatt, Marcus ; Stapor, Paul L. ; Städter, Philipp ; Wang, Dantong ; Wieland, Franz-Georg ; Banga, Julio R. ; Timmer, Jens ; Villaverde, A. F. ; Sahle, Sven ; Kreutz, Clemens ; Hasenauer, Jan ; Weindl, Daniel ; Commission, European |
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Veröffentlichung: | Public Library of Science, 2021 |
Medientyp: | academicJournal |
ISSN: | 1553-734X (print) ; 1553-7358 (print) |
DOI: | 10.13039/501100000780 |
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