RT Journal Article
T1 PEtab-Interoperable specification of parameter estimation problems in systems biology
A1 Schmiester, Leonard
A1 Schälte, Yannik
A1 Bergmann, Frank T.
A1 Camba, Tacio
A1 Dudkin, Erika
A1 Egert, Janine
A1 Fröhlich, Fabian
A1 Fuhrmann, Lara
A1 Hauber, Adrian L.
A1 Kemmer, Svenja
A1 Lakrisenko, Polina
A1 Loos, Carolin
A1 Merkt, Simon
A1 Müller, Wolfgang
A1 Pathirana, Dilan
A1 Raimúndez, Elba
A1 Refisch, Lukas
A1 Rosenblatt, Marcus
A1 Stapor, Paul L.
A1 Städter, Philipp
A1 Wang, Dantong
A1 Wieland, Franz-Georg
A1 Banga, Julio R.
A1 Timmer, Jens
A1 Fernandez Villaverde, Alejandro
A1 Sahle, Sven
A1 Kreutz, Clemens
A1 Hasenauer, Jan
A1 Weindl, Daniel
K1 3328 Procesos Tecnológicos
K1 1207.02 Sistemas de Control
K1 3311.02 Ingeniería de Control
AB 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.
PB PLoS Computational Biology
SN 15537358
YR 2021
FD 2021-01-26
LK http://hdl.handle.net/11093/3682
UL http://hdl.handle.net/11093/3682
LA eng
NO PLoS Computational Biology, 17(1): e1008646 (2021)
DS Investigo
RD 12-sep-2024