PEtab-Interoperable specification of parameter estimation problems in systems biology
Schmiester, Leonard; Schälte, Yannik; Bergmann, Frank T.; Camba, Tacio; Dudkin, Erika; Egert, Janine; Fröhlich, Fabian; Fuhrmann, Lara; Hauber, Adrian L.; Kemmer, Svenja; Lakrisenko, Polina; Loos, Carolin; Merkt, Simon; Müller, Wolfgang; Pathirana, Dilan; Raimúndez, Elba; Refisch, Lukas; Rosenblatt, Marcus; Stapor, Paul L.; Städter, Philipp; Wang, Dantong; Wieland, Franz-Georg; Banga, Julio R.; Timmer, Jens; Fernandez Villaverde, Alejandro; Sahle, Sven; Kreutz, Clemens; Hasenauer, Jan; Weindl, Daniel
DATE:
2021-01-26
UNIVERSAL IDENTIFIER: http://hdl.handle.net/11093/3682
EDITED VERSION: https://dx.plos.org/10.1371/journal.pcbi.1008646
UNESCO SUBJECT: 3328 Procesos Tecnológicos ; 1207.02 Sistemas de Control ; 3311.02 Ingeniería de Control
DOCUMENT TYPE: article
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.