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PEtab-Interoperable specification of parameter estimation problems in systems biology

dc.contributor.authorSchmiester, Leonard
dc.contributor.authorSchälte, Yannik
dc.contributor.authorBergmann, Frank T.
dc.contributor.authorCamba, Tacio
dc.contributor.authorDudkin, Erika
dc.contributor.authorEgert, Janine
dc.contributor.authorFröhlich, Fabian
dc.contributor.authorFuhrmann, Lara
dc.contributor.authorHauber, Adrian L.
dc.contributor.authorKemmer, Svenja
dc.contributor.authorLakrisenko, Polina
dc.contributor.authorLoos, Carolin
dc.contributor.authorMerkt, Simon
dc.contributor.authorMüller, Wolfgang
dc.contributor.authorPathirana, Dilan
dc.contributor.authorRaimúndez, Elba
dc.contributor.authorRefisch, Lukas
dc.contributor.authorRosenblatt, Marcus
dc.contributor.authorStapor, Paul L.
dc.contributor.authorStädter, Philipp
dc.contributor.authorWang, Dantong
dc.contributor.authorWieland, Franz-Georg
dc.contributor.authorBanga, Julio R.
dc.contributor.authorTimmer, Jens
dc.contributor.authorFernandez Villaverde, Alejandro 
dc.contributor.authorSahle, Sven
dc.contributor.authorKreutz, Clemens
dc.contributor.authorHasenauer, Jan
dc.contributor.authorWeindl, Daniel
dc.date.accessioned2022-07-13T07:43:30Z
dc.date.available2022-07-13T07:43:30Z
dc.date.issued2021-01-26
dc.identifier.citationPLoS Computational Biology, 17(1): e1008646 (2021)spa
dc.identifier.issn15537358
dc.identifier.urihttp://hdl.handle.net/11093/3682
dc.description.abstractReproducibility 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.spa
dc.language.isoengspa
dc.publisherPLoS Computational Biologyspa
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titlePEtab-Interoperable specification of parameter estimation problems in systems biologyen
dc.typearticlespa
dc.rights.accessRightsopenAccessspa
dc.identifier.doi10.1371/journal.pcbi.1008646
dc.identifier.editorhttps://dx.plos.org/10.1371/journal.pcbi.1008646spa
dc.publisher.departamentoEnxeñaría de sistemas e automáticaspa
dc.publisher.grupoinvestigacionGrupo de Control non Liñalspa
dc.subject.unesco3328 Procesos Tecnológicosspa
dc.subject.unesco1207.02 Sistemas de Controlspa
dc.subject.unesco3311.02 Ingeniería de Controlspa
dc.date.updated2022-07-08T08:55:09Z
dc.computerCitationpub_title=PLoS Computational Biology|volume=17|journal_number=1|start_pag=e1008646|end_pag=spa


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    Attribution 4.0 International
    Except where otherwise noted, this item's license is described as Attribution 4.0 International