PEtab-Interoperable specification of parameter estimation problems in systems biology
Autor: | Leonard Schmiester, Fabian Fröhlich, Alejandro F. Villaverde, Dilan Pathirana, Julio R. Banga, Polina Lakrisenko, Jens Timmer, Svenja Kemmer, Simon Merkt, Janine Egert, Carolin Loos, Philipp Städter, Clemens Kreutz, Dantong Wang, Lukas Refisch, Wolfgang Müller, Yannik Schälte, Sven Sahle, Erika Dudkin, Elba Raimúndez, Frank Bergmann, Tacio Camba, Franz-Georg Wieland, Adrian L. Hauber, Marcus Rosenblatt, Lara Fuhrmann, Jan Hasenauer, Daniel Weindl, Paul Stapor |
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Přispěvatelé: | European Commission |
Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
0301 basic medicine
Markup language Databases Factual Computer science Interoperability Social Sciences computer.software_genre Systems Science Quantitative Biology - Quantitative Methods 0302 clinical medicine Psychology Biology (General) Quantitative Methods (q-bio.QM) Language Data Management Reusability computer.programming_language Ecology Estimation theory Programming language Simulation and Modeling Systems Biology Applied Mathematics Software Engineering Computational Theory and Mathematics Modeling and Simulation Physical Sciences 1207.02 Sistemas de Control Engineering and Technology Algorithms Research Article Optimization Computer and Information Sciences QH301-705.5 Systems biology Research and Analysis Methods Models Biological 03 medical and health sciences Cellular and Molecular Neuroscience 3328 Procesos Tecnológicos Genetics SBML Molecular Biology Ecology Evolution Behavior and Systematics Models Statistical Software Tools System Stability Data Visualization Cognitive Psychology Biology and Life Sciences Reproducibility of Results Experimental data Python (programming language) 030104 developmental biology 3311.02 Ingeniería de Control FOS: Biological sciences Cognitive Science Programming Languages computer Mathematics 030217 neurology & neurosurgery Neuroscience |
Zdroj: | PLoS Computational Biology Digital.CSIC. Repositorio Institucional del CSIC instname PLoS Computational Biology, Vol 17, Iss 1, p e1008646 (2021) PLoS Comput. Biol. 17:e1008646 (2021) |
Popis: | 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.) |
Databáze: | OpenAIRE |
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