PLoS Computational Biology (Jan 2021)

PEtab-Interoperable specification of parameter estimation problems in systems biology.

  • 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

DOI
https://doi.org/10.1371/journal.pcbi.1008646
Journal volume & issue
Vol. 17, no. 1
p. e1008646

Abstract

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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.