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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; [...]

PEtab—Interoperable specification of parameter estimation problems in systems biology

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  • Medientyp: E-Artikel
  • Titel: PEtab—Interoperable specification of parameter estimation problems in systems biology
  • Beteiligte: 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; [...]
  • Erschienen: Public Library of Science (PLoS), 2021
  • Erschienen in: PLOS Computational Biology
  • Sprache: Englisch
  • DOI: 10.1371/journal.pcbi.1008646
  • ISSN: 1553-7358
  • Entstehung:
  • Anmerkungen:
  • Beschreibung: <jats:p>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.</jats:p>
  • Zugangsstatus: Freier Zugang