PEtab—Interoperable specification of parameter estimation problems in systems biology |
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| Authors: | Leonard Schmiester,Yannik Schä lte,Frank T. Bergmann,Tacio Camba,Erika Dudkin,Janine Egert,Fabian Frö hlich,Lara Fuhrmann,Adrian L. Hauber,Svenja Kemmer,Polina Lakrisenko,Carolin Loos,Simon Merkt,Wolfgang Mü ller,Dilan Pathirana,Elba Raimú ndez,Lukas Refisch,Marcus Rosenblatt,Paul L. Stapor,Philipp Stä dter,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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| Abstract: | 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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