| Literature DB >> 33497393 |
Leonard Schmiester1,2, Yannik Schälte1,2, Frank T Bergmann3, Tacio Camba4,5, Erika Dudkin6, Janine Egert7,8, Fabian Fröhlich9, Lara Fuhrmann6, Adrian L Hauber8,10, Svenja Kemmer8,10, Polina Lakrisenko1,2, Carolin Loos1,2,11,12, Simon Merkt6, Wolfgang Müller13, Dilan Pathirana6, Elba Raimúndez1,2,6, Lukas Refisch7,8, Marcus Rosenblatt8,10, Paul L Stapor1,2, Philipp Städter1,2, Dantong Wang1,2, Franz-Georg Wieland8,10, Julio R Banga5, Jens Timmer8,10,14, Alejandro F Villaverde5, Sven Sahle3, Clemens Kreutz7,8,14, Jan Hasenauer1,2,6, Daniel Weindl1.
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.Entities:
Mesh：
Year: 2021 PMID： 33497393 PMCID： PMC7864467 DOI： 10.1371/journal.pcbi.1008646
Source DB: PubMed Journal: PLoS Comput Biol ISSN： 1553-734X Impact factor: 4.475