PEtab-Interoperable specification of parameter estimation problems in systems biology.
Leonard SchmiesterYannik SchälteFrank T BergmannTacio CambaErika DudkinJanine EgertFabian FröhlichLara FuhrmannAdrian L HauberSvenja KemmerPolina LakrisenkoCarolin LoosSimon MerktWolfgang MüllerDilan PathiranaElba RaimúndezLukas RefischMarcus RosenblattPaul L StaporPhilipp StädterDantong WangFranz-Georg WielandJulio R BangaJens TimmerAlejandro F VillaverdeSven SahleClemens KreutzJan HasenauerDaniel WeindlPublished in: PLoS computational biology (2021)
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.