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PEtab—Interoperable specification of parameter estimation problems in systems biology

Author

Listed:
  • 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

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.Author summary: Parameter estimation is a common and crucial task in modeling, as many models depend on unknown parameters which need to be inferred from data. There exist various tools for tasks like model development, model simulation, optimization, or uncertainty analysis, each with different capabilities and strengths. In order to be able to easily combine tools in an interoperable manner, but also to make results accessible and reusable for other researchers, it is valuable to define parameter estimation problems in a standardized form. Here, we introduce PEtab, a parameter estimation problem definition format which integrates with established systems biology standards for model and data specification. As the novel format is already supported by eight software tools with hundreds of users in total, we expect it to be of great use and impact in the community, both for modeling and algorithm development.

Suggested Citation

  • 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 Loo, 2021. "PEtab—Interoperable specification of parameter estimation problems in systems biology," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-10, January.
    • Handle: RePEc:plo:pcbi00:1008646
    DOI: 10.1371/journal.pcbi.1008646
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    References listed on IDEAS

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    1. Hiroaki Kitano, 2002. "Computational systems biology," Nature, Nature, vol. 420(6912), pages 206-210, November.
    2. Fabian Fröhlich & Barbara Kaltenbacher & Fabian J Theis & Jan Hasenauer, 2017. "Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-18, January.
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