PEtab—Interoperable specification of parameter estimation problems in systems biology

@article{Schmiester2021PEtabInteroperableSO,
  title={PEtab—Interoperable specification of parameter estimation problems in systems biology},
  author={Leonard Schmiester and Yannik Schalte and Frank T. Bergmann and Tacio Camba and Erika Dudkin and Janine Egert and Fabian Frohlich and Lara Fuhrmann and Adrian L Hauber and Svenja Kemmer and Polina Lakrisenko and Carolin Loos and S. A. M. Merkt and Dilan Pathirana and Elba Raim'undez and Lukas Refisch and Marcus Rosenblatt and Paul Stapor and Philip A. Stadter and Dantong Wang and Franz-Georg Wieland and Julio R. Banga and Jens Timmer and Alejandro Fern{\'a}ndez Villaverde and Sven Sahle and Clemens Kreutz and Jan Hasenauer and Daniel Weindl Institute of Computational Biology and Helmholtz Zentrum Munchen -- German Research Center for Envi Health and Center for Mathematics and Technische Universitat Munchen and BioQUANTCOS and Heidelberg Northwestern University and Department of Applied Mathematics and University of Vigo and BioProcess Engineering Group and IIM-CSIC and Faculty of Mathematics and Natural Sciences and University of Bonn and Faculty of Veterinary Medicine and Medical Center and Institute of Medical Biometry and Statistics and Fdm - Freiburg Center for Data Analysis and Modeling and University of Freiburg and Department of Biology and Harvard Medical School and Institute of Metal Physics and Ragon Institute of Mgh and Mit and Harvard and Cambridge and Department of Mechanical Engineering and Massachusetts Institute of Technology and Signalling Research Centres Bioss and Cibss},
  journal={PLoS Computational Biology},
  year={2021},
  volume={17}
}
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… 

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