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:10.1371/journal.pcbi.1008646

PEtab-Interoperable specification of parameter estimation problems in systems biology

PLoS Comput Biol. 2021 Jan 26;17(1):e1008646. doi: 10.1371/journal.pcbi.1008646. eCollection 2021 Jan.

Authors

Leonard Schmiester^{1

2}, Yannik Schälte^{1

2}, Frank T Bergmann³, Tacio Camba^{4

5}, Erika Dudkin⁶, Janine Egert^{7

8}, Fabian Fröhlich⁹, Lara Fuhrmann⁶, Adrian L Hauber^{8

10}, Svenja Kemmer^{8

10}, Polina Lakrisenko^{1

2}, Carolin Loos^{1

2

11

12}, Simon Merkt⁶, Wolfgang Müller¹³, Dilan Pathirana⁶, Elba Raimúndez^{1

2

6}, Lukas Refisch^{7

8}, Marcus Rosenblatt^{8

10}, Paul L Stapor^{1

2}, Philipp Städter^{1

2}, Dantong Wang^{1

2}, Franz-Georg Wieland^{8

10}, Julio R Banga⁵, Jens Timmer^{8

10

14}, Alejandro F Villaverde⁵, Sven Sahle³, Clemens Kreutz^{7

8

14}, Jan Hasenauer^{1

2

6}, Daniel Weindl¹

Affiliations

¹ Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
² Center for Mathematics, Technische Universität München, Garching, Germany.
³ BioQUANT/COS, Heidelberg University, Heidelberg, Germany.
⁴ Department of Applied Mathematics II, University of Vigo, Vigo, Galicia, Spain.
⁵ BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain.
⁶ Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
⁷ Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany.
⁸ Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany.
⁹ Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.
¹⁰ Institute of Physics, University of Freiburg, Freiburg, Germany.
¹¹ Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.
¹² Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
¹³ Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany.
¹⁴ Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Databases, Factual
Models, Biological
Models, Statistical
Programming Languages*
Reproducibility of Results
Systems Biology / methods*

Grants and funding

U54 CA225088/CA/NCI NIH HHS/United States