PEtab swMATH ID: 36544 Software Authors: 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 Description: PEtab - interoperable specification of parameter estimation problems in systems biology. 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. Specifications of PEtab, the PEtab Python library, as well as links to examples, and all supporting software tools are available at this https URL, a snapshot is available at this https URL. All original content is available under permissive licenses. Homepage: https://petab.readthedocs.io/en/stable/ Source Code: https://github.com/PEtab-dev/PEtab Dependencies: Python Keywords: Quantitative Methods; arXiv_q-bio.QM; Python; Parameter estimation; SBML; Systems Biology Related Software: Data2Dynamics; COPASI; AMIGO; pyPESTO; Antimony; Python; PyBioNetFit; PESTO; AMICI; ScrumPy; MOCCASIN; SimpleSBML; libSBML; yaml2sbml; phraSED-ML; tellurium; CellML; MEIGO; BioNetGen; R Cited in: 1 Document Standard Articles 1 Publication describing the Software Year PEtab - interoperable specification of parameter estimation problems in systems biology arXiv 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 2020 Cited by 3 Authors 1 Hasenauer, Jan 1 Schmiester, Leonard 1 Weindl, Daniel Cited in 1 Serial 1 Journal of Mathematical Biology Cited in 2 Fields 1 Dynamical systems and ergodic theory (37-XX) 1 Numerical analysis (65-XX) Citations by Year