PEtab -- interoperable specification of parameter estimation problems in systems biology
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. Specifications of PEtab, the PEtab Python library, as well as links to examples, and all supporting software tools are available at https://github.com/PEtab-dev/PEtab, a snapshot is available at https://doi.org/10.5281/zenodo.3732958. All original content is available under permissive licenses.
Keywords
Cite
@article{arxiv.2004.01154,
title = {PEtab -- interoperable specification of parameter estimation problems in systems biology},
author = {Leonard Schmiester and Yannik Schälte and Frank T. Bergmann and Tacio Camba and Erika Dudkin and Janine Egert and Fabian Fröhlich and Lara Fuhrmann and Adrian L. Hauber and Svenja Kemmer and Polina Lakrisenko and Carolin Loos and Simon Merkt and Wolfgang Müller and Dilan Pathirana and Elba Raimúndez and Lukas Refisch and Marcus Rosenblatt and Paul L. Stapor and Philipp Städter and Dantong Wang and Franz-Georg Wieland and Julio R. Banga and Jens Timmer and Alejandro F. Villaverde and Sven Sahle and Clemens Kreutz and Jan Hasenauer and Daniel Weindl},
journal= {arXiv preprint arXiv:2004.01154},
year = {2021}
}