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
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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