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PEtab: interoperable specification of parameter estimation problems in systems biology

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 par...

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Main Authors: Schmiester, Leonard (Author) , Schälte, Yannik (Author) , Bergmann, Frank T. (Author) , Camba, Tacio (Author) , Dudkin, Erika (Author) , Egert, Janine (Author) , Fröhlich, Fabian (Author) , Fuhrmann, Lara (Author) , Hauber, Adrian L. (Author) , Kemmer, Svenja (Author) , Lakrisenko, Polina (Author) , Loos, Carolin (Author) , Merkt, Simon (Author) , Müller, Wolfgang (Author) , Pathirana, Dilan (Author) , Raimúndez, Elba (Author) , Refisch, Lukas (Author) , Rosenblatt, Marcus (Author) , Stapor, Paul L. (Author) , Städter, Philipp (Author) , Wang, Dantong (Author) , Wieland, Franz-Georg (Author) , Banga, Julio R. (Author) , Timmer, Jens (Author) , Villaverde, Alejandro F. (Author) , Sahle, Sven (Author) , Kreutz, Clemens (Author) , Hasenauer, Jan (Author) , Weindl, Daniel (Author)
Format: Article (Journal)
Language:English
Published: January 26, 2021
In: PLoS Computational Biology
Year: 2021, Volume: 17, Issue: 1, Pages: 1-10
ISSN:1553-7358
DOI:10.1371/journal.pcbi.1008646
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1371/journal.pcbi.1008646
Verlag, lizenzpflichtig, Volltext: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008646
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Author Notes:Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl

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520 |a 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. 
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