{"id":"https://openalex.org/W3014365047","doi":"https://doi.org/10.1371/journal.pcbi.1008646","title":"PEtab\u2014Interoperable specification of parameter estimation problems in systems biology","display_name":"PEtab\u2014Interoperable specification of parameter estimation problems in systems biology","publication_year":2021,"publication_date":"2021-01-26","ids":{"openalex":"https://openalex.org/W3014365047","doi":"https://doi.org/10.1371/journal.pcbi.1008646","mag":"3014365047","pmid":"https://pubmed.ncbi.nlm.nih.gov/33497393"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008646","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008646","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1008646","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085002161","display_name":"Leonard Schmiester","orcid":"https://orcid.org/0000-0001-7946-3232"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leonard Schmiester","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7946-3232","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082656548","display_name":"Yannik Sch\u00e4lte","orcid":"https://orcid.org/0000-0003-1293-820X"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yannik Sch\u00e4lte","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1293-820X","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076617999","display_name":"Frank Bergmann","orcid":"https://orcid.org/0000-0001-5553-4702"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frank T. Bergmann","raw_affiliation_strings":["BioQUANT/COS, Heidelberg University, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-5553-4702","affiliations":[{"raw_affiliation_string":"BioQUANT/COS, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078049763","display_name":"Tacio Camba","orcid":null},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Tacio Camba","raw_affiliation_strings":["BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain","Department of Applied Mathematics II, University of Vigo, Vigo, Galicia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain","institution_ids":[]},{"raw_affiliation_string":"Department of Applied Mathematics II, University of Vigo, Vigo, Galicia, Spain","institution_ids":["https://openalex.org/I6289922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026146978","display_name":"Erika Dudkin","orcid":"https://orcid.org/0000-0002-9649-0029"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erika Dudkin","raw_affiliation_strings":["Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9649-0029","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026419564","display_name":"Janine Egert","orcid":"https://orcid.org/0000-0002-2032-7081"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Janine Egert","raw_affiliation_strings":["Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany","Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003197068","display_name":"Fabian Fr\u00f6hlich","orcid":"https://orcid.org/0000-0002-5360-4292"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fabian Fr\u00f6hlich","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210155419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070873003","display_name":"Lara Fuhrmann","orcid":"https://orcid.org/0000-0001-6405-0654"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lara Fuhrmann","raw_affiliation_strings":["Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6405-0654","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053049078","display_name":"Adrian L. Hauber","orcid":"https://orcid.org/0000-0002-3053-5124"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Adrian L. Hauber","raw_affiliation_strings":["Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","Institute of Physics, University of Freiburg, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-3053-5124","affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Physics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011456534","display_name":"Svenja Kemmer","orcid":"https://orcid.org/0000-0001-7708-0545"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Svenja Kemmer","raw_affiliation_strings":["Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","Institute of Physics, University of Freiburg, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7708-0545","affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Physics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001044691","display_name":"Polina Lakrisenko","orcid":"https://orcid.org/0000-0002-7626-8420"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Polina Lakrisenko","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7626-8420","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048802653","display_name":"Carolin Loos","orcid":"https://orcid.org/0000-0003-3680-0627"},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Carolin Loos","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3680-0627","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021665404","display_name":"Simon Merkt","orcid":"https://orcid.org/0000-0002-8017-4494"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Simon Merkt","raw_affiliation_strings":["Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0002-8017-4494","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060937863","display_name":"Wolfgang G. M\u00fcller","orcid":"https://orcid.org/0000-0002-4980-3512"},"institutions":[{"id":"https://openalex.org/I71030271","display_name":"Heidelberg Institute for Theoretical Studies","ror":"https://ror.org/01f7bcy98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I71030271"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wolfgang M\u00fcller","raw_affiliation_strings":["Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4980-3512","affiliations":[{"raw_affiliation_string":"Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany","institution_ids":["https://openalex.org/I71030271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029598458","display_name":"Dilan Pathirana","orcid":"https://orcid.org/0000-0001-7000-2659"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dilan Pathirana","raw_affiliation_strings":["Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7000-2659","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025694782","display_name":"Elba Raim\u00fandez","orcid":"https://orcid.org/0000-0002-2790-6668"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Elba Raim\u00fandez","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-2790-6668","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047322826","display_name":"Lukas Refisch","orcid":"https://orcid.org/0000-0002-9049-1944"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lukas Refisch","raw_affiliation_strings":["Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany","Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9049-1944","affiliations":[{"raw_affiliation_string":"Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059299168","display_name":"Marcus Rosenblatt","orcid":"https://orcid.org/0000-0002-7234-1328"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marcus Rosenblatt","raw_affiliation_strings":["Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","Institute of Physics, University of Freiburg, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7234-1328","affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Physics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038659090","display_name":"Paul Stapor","orcid":"https://orcid.org/0000-0002-7567-3985"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Paul L. Stapor","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7567-3985","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016122054","display_name":"Philipp St\u00e4dter","orcid":"https://orcid.org/0000-0002-4586-6604"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philipp St\u00e4dter","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4586-6604","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101939585","display_name":"Dantong Wang","orcid":"https://orcid.org/0000-0002-3277-5033"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dantong Wang","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-3277-5033","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070456560","display_name":"Franz-Georg Wieland","orcid":"https://orcid.org/0000-0002-5629-8622"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Franz-Georg Wieland","raw_affiliation_strings":["Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","Institute of Physics, University of Freiburg, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5629-8622","affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Physics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090264675","display_name":"Julio R. Banga","orcid":"https://orcid.org/0000-0002-4245-0320"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Julio R. Banga","raw_affiliation_strings":["BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain"],"raw_orcid":"https://orcid.org/0000-0002-4245-0320","affiliations":[{"raw_affiliation_string":"BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052831097","display_name":"Jens Timmer","orcid":"https://orcid.org/0000-0003-4517-1383"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jens Timmer","raw_affiliation_strings":["Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","Institute of Physics, University of Freiburg, Freiburg, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute of Physics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032919554","display_name":"Alejandro F. Villaverde","orcid":"https://orcid.org/0000-0001-7401-7380"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alejandro F. Villaverde","raw_affiliation_strings":["BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain"],"raw_orcid":"https://orcid.org/0000-0001-7401-7380","affiliations":[{"raw_affiliation_string":"BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111964760","display_name":"Sven Sahle","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sven Sahle","raw_affiliation_strings":["BioQUANT/COS, Heidelberg University, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioQUANT/COS, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076933919","display_name":"Clemens Kreutz","orcid":"https://orcid.org/0000-0002-8796-5766"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Clemens Kreutz","raw_affiliation_strings":["Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany","Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-8796-5766","affiliations":[{"raw_affiliation_string":"Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063254041","display_name":"Jan Hasenauer","orcid":"https://orcid.org/0000-0002-4935-3312"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jan Hasenauer","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4935-3312","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014811978","display_name":"Daniel Weindl","orcid":"https://orcid.org/0000-0001-9963-6057"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Weindl","raw_affiliation_strings":["Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9963-6057","affiliations":[{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen-German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen\u2014German Research Center for Environmental Health, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5063254041"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I3018134672","https://openalex.org/I62916508"],"apc_list":{"value":2575,"currency":"USD","value_usd":2575},"apc_paid":{"value":2575,"currency":"USD","value_usd":2575},"fwci":5.7434,"has_fulltext":true,"cited_by_count":111,"citation_normalized_percentile":{"value":0.97443256,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"e1008646","last_page":"e1008646"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9676694869995117},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.752321720123291},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7257285714149475},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6981735229492188},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.6443665027618408},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.6396329402923584},{"id":"https://openalex.org/keywords/reusability","display_name":"Reusability","score":0.6005432605743408},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4775310754776001},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.44997745752334595},{"id":"https://openalex.org/keywords/estimation","display_name":"Estimation","score":0.4335038661956787},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4245026111602783},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.38163381814956665},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3535084128379822},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.20151430368423462},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18918877840042114},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.1666986048221588},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1554742455482483},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.14817294478416443},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13183042407035828},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12061107158660889}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9676694869995117},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.752321720123291},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7257285714149475},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6981735229492188},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.6443665027618408},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.6396329402923584},{"id":"https://openalex.org/C137981799","wikidata":"https://www.wikidata.org/wiki/Q1369184","display_name":"Reusability","level":3,"score":0.6005432605743408},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4775310754776001},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.44997745752334595},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.4335038661956787},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4245026111602783},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.38163381814956665},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3535084128379822},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.20151430368423462},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18918877840042114},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.1666986048221588},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1554742455482483},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.14817294478416443},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13183042407035828},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12061107158660889},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":12,"locations":[{"id":"doi:10.1371/journal.pcbi.1008646","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008646","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:33497393","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33497393","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:2004.01154","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2004.01154","pdf_url":"https://arxiv.org/pdf/2004.01154","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:figshare.com:article/13049522","is_oa":true,"landing_page_url":"https://figshare.com/articles/presentation/PEtab_Interoperable_Specification_of_Parameter_Estimation_Problems_in_Systems_Biology/13049522","pdf_url":"https://figshare.com/articles/presentation/PEtab_Interoperable_Specification_of_Parameter_Estimation_Problems_in_Systems_Biology/13049522","source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7864467","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7864467","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1008646","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008646","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:c3dd6d0bbd004deaba2fc5b1d5df8992","is_oa":true,"landing_page_url":"https://doaj.org/article/c3dd6d0bbd004deaba2fc5b1d5df8992","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 1, p e1008646 (2021)","raw_type":"article"},{"id":"pmh:oai:mediatum.ub.tum.de:node/1730611","is_oa":true,"landing_page_url":"https://mediatum.ub.tum.de/1730611","pdf_url":null,"source":{"id":"https://openalex.org/S4377196330","display_name":"mediaTUM  (Technical University of Munich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I62916508","host_organization_name":"Technical University of Munich","host_organization_lineage":["https://openalex.org/I62916508"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:opus-zb.helmholtz-muenchen.de:61210","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=61210","pdf_url":null,"source":{"id":"https://openalex.org/S4377196115","display_name":"Site cant be reached","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput. Biol. 17:e1008646 (2021)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:push-zb.helmholtz-munich.de:61210","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=61210","pdf_url":null,"source":{"id":"https://openalex.org/S7407055352","display_name":"PuSH - Publication Server of Helmholtz Zentrum M\u00fcnchen","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput. Biol. 17:e1008646 (2021)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.investigo.biblioteca.uvigo.es:11093/3682","is_oa":true,"landing_page_url":"https://dx.plos.org/10.1371/journal.pcbi.1008646","pdf_url":null,"source":{"id":"https://openalex.org/S4377196408","display_name":"Investigo Institutional repository of UVigo (Universidade de Vigo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I6289922","host_organization_name":"Universidade de Vigo","host_organization_lineage":["https://openalex.org/I6289922"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"doi:10.6084/m9.figshare.13049522.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.13049522.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Audiovisual"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008646","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008646","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1014860659","display_name":null,"funder_award_id":"CIBSS-EXC 2189","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1773647165","display_name":null,"funder_award_id":"031L0048","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2303140048","display_name":null,"funder_award_id":"031L0104A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G259924242","display_name":null,"funder_award_id":"EXC\u20102189","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2677494621","display_name":null,"funder_award_id":"HA7376/1-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G292661107","display_name":null,"funder_award_id":"70112355","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2984623031","display_name":null,"funder_award_id":"de.NBI ModSim1","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4549622993","display_name":null,"funder_award_id":"EXC 2151","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4606494704","display_name":null,"funder_award_id":"01ZX1705A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4787627496","display_name":null,"funder_award_id":"01ZX1916A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4850509644","display_name":null,"funder_award_id":"U54\u2010CA225088","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4866485077","display_name":null,"funder_award_id":"EXC-2189","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4935269520","display_name":"EXC 2189: CIBSS  Centre for Integrative Biological Signalling Studies","funder_award_id":"390939984","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5601183438","display_name":null,"funder_award_id":"EXC 2151","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5601541323","display_name":"TRR 179: Determinanten und Dynamik der Elimination versus Persistenz bei HepatitisVirusInfektionen","funder_award_id":"272983813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G591746060","display_name":null,"funder_award_id":"EXC-2047","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5976804734","display_name":null,"funder_award_id":"390939984","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6040084496","display_name":null,"funder_award_id":"390939984","funder_id":"https://openalex.org/F4320323556","funder_display_name":"Deutsche Krebshilfe"},{"id":"https://openalex.org/G6069382169","display_name":null,"funder_award_id":"01ZX1310B","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6238101420","display_name":null,"funder_award_id":"686282","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G64039306","display_name":null,"funder_award_id":"TRR179\u00a0","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G648832721","display_name":null,"funder_award_id":"031L0048","funder_id":"https://openalex.org/F4320323556","funder_display_name":"Deutsche Krebshilfe"},{"id":"https://openalex.org/G6687862170","display_name":null,"funder_award_id":"70112355","funder_id":"https://openalex.org/F4320323556","funder_display_name":"Deutsche Krebshilfe"},{"id":"https://openalex.org/G7152315737","display_name":null,"funder_award_id":"01ZX1310B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7180852343","display_name":null,"funder_award_id":"EXC-2189","funder_id":"https://openalex.org/F4320323556","funder_display_name":"Deutsche Krebshilfe"},{"id":"https://openalex.org/G7515004340","display_name":"Generation of the CanPath prototype - a platform for predictive cancer pathway modeling","funder_award_id":"686282","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7604816726","display_name":null,"funder_award_id":"031L0080","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G79716705","display_name":null,"funder_award_id":"031L0048","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8254834712","display_name":null,"funder_award_id":"031L0159C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8669258325","display_name":null,"funder_award_id":"70112355","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323556","display_name":"Deutsche Krebshilfe","ror":"https://ror.org/01wxdd722"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W2023106695","https://openalex.org/W2096951208","https://openalex.org/W2102653059","https://openalex.org/W2123783513","https://openalex.org/W2125615370","https://openalex.org/W2143784594","https://openalex.org/W2145267275","https://openalex.org/W2150908245","https://openalex.org/W2156730317","https://openalex.org/W2170122529","https://openalex.org/W2179083909","https://openalex.org/W2303100661","https://openalex.org/W2324218546","https://openalex.org/W2525009482","https://openalex.org/W2765845615","https://openalex.org/W2884300959","https://openalex.org/W2889674659","https://openalex.org/W2949499968","https://openalex.org/W2949631852","https://openalex.org/W2950665010","https://openalex.org/W2953380254","https://openalex.org/W2964392985","https://openalex.org/W2970732621","https://openalex.org/W3044040797","https://openalex.org/W3095434667","https://openalex.org/W6931018114"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573"],"abstract_inverted_index":{"Reproducibility":[0],"and":[1,51,62,82,99,105],"reusability":[2],"of":[3,6,23,40,54,88,101],"the":[4,21,38,59],"results":[5],"data-based":[7],"modeling":[8],"studies":[9],"are":[10],"essential.":[11],"Yet,":[12],"there":[13],"has":[14],"been-so":[15],"far-no":[16],"broadly":[17],"supported":[18],"format":[19,35],"for":[20,97],"specification":[22,39],"parameter":[24,41,83,109],"estimation":[25,42,84,110],"problems":[26,43,111],"in":[27,90],"systems":[28],"biology.":[29],"Here,":[30],"we":[31],"introduce":[32],"PEtab,":[33],"a":[34,52,94,102],"which":[36],"facilitates":[37],"using":[44],"Systems":[45],"Biology":[46],"Markup":[47],"Language":[48],"(SBML)":[49],"models":[50],"set":[53],"tab-separated":[55],"value":[56],"files":[57],"describing":[58],"observation":[60],"model":[61,80],"experimental":[63],"data":[64],"as":[65,67],"well":[66],"parameters":[68],"to":[69],"be":[70],"estimated.":[71],"We":[72,92],"already":[73],"implemented":[74],"PEtab":[75,103],"support":[76],"into":[77],"eight":[78],"well-established":[79],"simulation":[81],"toolboxes":[85],"with":[86],"hundreds":[87],"users":[89],"total.":[91],"provide":[93],"Python":[95],"library":[96],"validation":[98],"modification":[100],"problem":[104],"currently":[106],"20":[107],"example":[108],"based":[112],"on":[113],"recent":[114],"studies.":[115]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":4}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}