{"id":"https://openalex.org/W2973224855","doi":"https://doi.org/10.1371/journal.pcbi.1007342","title":"EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology","display_name":"EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology","publication_year":2019,"publication_date":"2019-09-13","ids":{"openalex":"https://openalex.org/W2973224855","doi":"https://doi.org/10.1371/journal.pcbi.1007342","mag":"2973224855","pmid":"https://pubmed.ncbi.nlm.nih.gov/31518349"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007342","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007342","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007342&type=printable","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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007342&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018448983","display_name":"S\u00e9bastien Picault","orcid":"https://orcid.org/0000-0001-9029-0555"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]},{"id":"https://openalex.org/I4210115519","display_name":"Centre de Recherche en Informatique","ror":"https://ror.org/020cdve92","country_code":"FR","type":"facility","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I4210091621","https://openalex.org/I4210115519","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I4210148006","display_name":"Laboratoire de G\u00e9nie des Proc\u00e9d\u00e9s \u2013 Environnement \u2013 Agro-alimentaire","ror":"https://ror.org/05ngxmx20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I4210095849","https://openalex.org/I4210127572","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I49451733","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210157468","display_name":"Oniris","ror":"https://ror.org/05q0ncs32","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210157468"]},{"id":"https://openalex.org/I4387155944","display_name":"Biologie, Epid\u00e9miologie et Analyse de Risque en Sant\u00e9 Animale","ror":"https://ror.org/059h64789","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210157468","https://openalex.org/I4387155944"]},{"id":"https://openalex.org/I7454413","display_name":"\u00c9cole Centrale de Lille","ror":"https://ror.org/01x441g73","country_code":"FR","type":"education","lineage":["https://openalex.org/I7454413"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"S\u00e9bastien Picault","raw_affiliation_strings":["BIOEPAR, INRA, Oniris, Nantes, France","Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Lille, France","BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (Universit\u00e9 de Lille - Campus scientifique - B\u00e2timent ESPRIT - Avenue Henri Poincar\u00e9 - 59655 Villeneuve d\u2019Ascq - France)"],"raw_orcid":"https://orcid.org/0000-0001-9029-0555","affiliations":[{"raw_affiliation_string":"BIOEPAR, INRA, Oniris, Nantes, France","institution_ids":["https://openalex.org/I4210157468"]},{"raw_affiliation_string":"Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Lille, France","institution_ids":["https://openalex.org/I7454413","https://openalex.org/I2279609970","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","institution_ids":["https://openalex.org/I4210148006","https://openalex.org/I4387155944"]},{"raw_affiliation_string":"CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (Universit\u00e9 de Lille - Campus scientifique - B\u00e2timent ESPRIT - Avenue Henri Poincar\u00e9 - 59655 Villeneuve d\u2019Ascq - France)","institution_ids":["https://openalex.org/I4210115519","https://openalex.org/I2279609970"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yu-Lin Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148006","display_name":"Laboratoire de G\u00e9nie des Proc\u00e9d\u00e9s \u2013 Environnement \u2013 Agro-alimentaire","ror":"https://ror.org/05ngxmx20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I4210095849","https://openalex.org/I4210127572","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I49451733","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210157468","display_name":"Oniris","ror":"https://ror.org/05q0ncs32","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210157468"]},{"id":"https://openalex.org/I4387155944","display_name":"Biologie, Epid\u00e9miologie et Analyse de Risque en Sant\u00e9 Animale","ror":"https://ror.org/059h64789","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210157468","https://openalex.org/I4387155944"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yu-Lin Huang","raw_affiliation_strings":["BIOEPAR, INRA, Oniris, Nantes, France","BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOEPAR, INRA, Oniris, Nantes, France","institution_ids":["https://openalex.org/I4210157468"]},{"raw_affiliation_string":"BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","institution_ids":["https://openalex.org/I4210148006","https://openalex.org/I4387155944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049680247","display_name":"Vianney Sicard","orcid":"https://orcid.org/0000-0002-4909-5544"},"institutions":[{"id":"https://openalex.org/I4210148006","display_name":"Laboratoire de G\u00e9nie des Proc\u00e9d\u00e9s \u2013 Environnement \u2013 Agro-alimentaire","ror":"https://ror.org/05ngxmx20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I4210095849","https://openalex.org/I4210127572","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I49451733","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210157468","display_name":"Oniris","ror":"https://ror.org/05q0ncs32","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210157468"]},{"id":"https://openalex.org/I4387155944","display_name":"Biologie, Epid\u00e9miologie et Analyse de Risque en Sant\u00e9 Animale","ror":"https://ror.org/059h64789","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210157468","https://openalex.org/I4387155944"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vianney Sicard","raw_affiliation_strings":["BIOEPAR, INRA, Oniris, Nantes, France","BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)"],"raw_orcid":"https://orcid.org/0000-0002-4909-5544","affiliations":[{"raw_affiliation_string":"BIOEPAR, INRA, Oniris, Nantes, France","institution_ids":["https://openalex.org/I4210157468"]},{"raw_affiliation_string":"BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","institution_ids":["https://openalex.org/I4210148006","https://openalex.org/I4387155944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014924641","display_name":"Sandie Arnoux","orcid":"https://orcid.org/0000-0002-7577-2940"},"institutions":[{"id":"https://openalex.org/I4210148006","display_name":"Laboratoire de G\u00e9nie des Proc\u00e9d\u00e9s \u2013 Environnement \u2013 Agro-alimentaire","ror":"https://ror.org/05ngxmx20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I4210095849","https://openalex.org/I4210127572","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I49451733","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210157468","display_name":"Oniris","ror":"https://ror.org/05q0ncs32","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210157468"]},{"id":"https://openalex.org/I4387155944","display_name":"Biologie, Epid\u00e9miologie et Analyse de Risque en Sant\u00e9 Animale","ror":"https://ror.org/059h64789","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210157468","https://openalex.org/I4387155944"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sandie Arnoux","raw_affiliation_strings":["BIOEPAR, INRA, Oniris, Nantes, France","BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)"],"raw_orcid":"https://orcid.org/0000-0002-7577-2940","affiliations":[{"raw_affiliation_string":"BIOEPAR, INRA, Oniris, Nantes, France","institution_ids":["https://openalex.org/I4210157468"]},{"raw_affiliation_string":"BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","institution_ids":["https://openalex.org/I4210148006","https://openalex.org/I4387155944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050891408","display_name":"Ga\u00ebl Beaun\u00e9e","orcid":"https://orcid.org/0000-0002-0002-2627"},"institutions":[{"id":"https://openalex.org/I4210148006","display_name":"Laboratoire de G\u00e9nie des Proc\u00e9d\u00e9s \u2013 Environnement \u2013 Agro-alimentaire","ror":"https://ror.org/05ngxmx20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I4210095849","https://openalex.org/I4210127572","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I49451733","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210157468","display_name":"Oniris","ror":"https://ror.org/05q0ncs32","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210157468"]},{"id":"https://openalex.org/I4387155944","display_name":"Biologie, Epid\u00e9miologie et Analyse de Risque en Sant\u00e9 Animale","ror":"https://ror.org/059h64789","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210157468","https://openalex.org/I4387155944"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ga\u00ebl Beaun\u00e9e","raw_affiliation_strings":["BIOEPAR, INRA, Oniris, Nantes, France","BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)"],"raw_orcid":"https://orcid.org/0000-0002-0002-2627","affiliations":[{"raw_affiliation_string":"BIOEPAR, INRA, Oniris, Nantes, France","institution_ids":["https://openalex.org/I4210157468"]},{"raw_affiliation_string":"BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","institution_ids":["https://openalex.org/I4210148006","https://openalex.org/I4387155944"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084118579","display_name":"Pauline Ezanno","orcid":"https://orcid.org/0000-0002-0034-8950"},"institutions":[{"id":"https://openalex.org/I4210148006","display_name":"Laboratoire de G\u00e9nie des Proc\u00e9d\u00e9s \u2013 Environnement \u2013 Agro-alimentaire","ror":"https://ror.org/05ngxmx20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I4210095849","https://openalex.org/I4210127572","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I49451733","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210157468","display_name":"Oniris","ror":"https://ror.org/05q0ncs32","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210157468"]},{"id":"https://openalex.org/I4387155944","display_name":"Biologie, Epid\u00e9miologie et Analyse de Risque en Sant\u00e9 Animale","ror":"https://ror.org/059h64789","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210157468","https://openalex.org/I4387155944"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pauline Ezanno","raw_affiliation_strings":["BIOEPAR, INRA, Oniris, Nantes, France","BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)"],"raw_orcid":"https://orcid.org/0000-0002-0034-8950","affiliations":[{"raw_affiliation_string":"BIOEPAR, INRA, Oniris, Nantes, France","institution_ids":["https://openalex.org/I4210157468"]},{"raw_affiliation_string":"BIOEPAR - Biologie, Epid\u00e9miologie et analyse de risque en Sant\u00e9 Animale (ONIRIS : Site de la Chantrerie CS 40706 44307 Nantes cedex 3 Site de la G\u00e9raudi\u00e8re CS 82225 44322 Nantes cedex 3 - France)","institution_ids":["https://openalex.org/I4210148006","https://openalex.org/I4387155944"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5018448983"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2279609970","https://openalex.org/I4210115519","https://openalex.org/I4210148006","https://openalex.org/I4210157468","https://openalex.org/I4387155944","https://openalex.org/I7454413"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2130,"currency":"EUR","value_usd":2297},"fwci":2.6998,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.90346022,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"15","issue":"9","first_page":"e1007342","last_page":"e1007342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.9735000133514404,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.9664000272750854,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7146262526512146},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4834197759628296},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.4208701252937317},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35994091629981995},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32170093059539795},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24086371064186096}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7146262526512146},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4834197759628296},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.4208701252937317},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35994091629981995},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32170093059539795},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24086371064186096}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004813","descriptor_name":"Epidemiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004813","descriptor_name":"Epidemiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004813","descriptor_name":"Epidemiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1007342","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007342","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007342&type=printable","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:31518349","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31518349","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":null},{"id":"pmh:oai:HAL:hal-02288201v1","is_oa":true,"landing_page_url":"https://hal.science/hal-02288201","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"https://journals.plos.org/ploscompbiol/","raw_type":"Journal articles"},{"id":"pmh:oai:RePEc:plo:pcbi00:1007342","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007342","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:1313e1d7b5e84c4b9c7242fa3e17f5c6","is_oa":true,"landing_page_url":"https://doaj.org/article/1313e1d7b5e84c4b9c7242fa3e17f5c6","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 15, Iss 9, p e1007342 (2019)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/9827921","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/EMULSION_Transparent_and_flexible_multiscale_stochastic_models_in_human_animal_and_plant_epidemiology/9827921","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:lilloa.univ-lille.fr:20.500.12210/21745","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.12210/21745","pdf_url":null,"source":{"id":"https://openalex.org/S4306402203","display_name":"LillOA (Universit\u00e9 de Lille (University Of Lille))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210123514","host_organization_name":"Centre d'Etudes en Civilisations, Langues et Litt\u00e9ratures Etrang\u00e8res","host_organization_lineage":["https://openalex.org/I4210123514"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:prodinra.inra.fr:486936","is_oa":true,"landing_page_url":"http://prodinra.inra.fr/ft/BA4E181B-6FF6-4B16-8AD6-95141BF81361","pdf_url":null,"source":{"id":"https://openalex.org/S4306400794","display_name":"Prodinra (INRA Bordeaux-Aquitaine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210088668","host_organization_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","host_organization_lineage":["https://openalex.org/I4210088668"],"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 Computational Biology 9 (15), e1007342. (2019)","raw_type":"ARTICLE"},{"id":"pmh:oai:pubmedcentral.nih.gov:6760811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6760811","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007342","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007342","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007342&type=printable","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":[{"score":0.6600000262260437,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1420654861","display_name":null,"funder_award_id":"ANR-10-BINF-07","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G2165128509","display_name":null,"funder_award_id":"ANR-16-CE32-0007-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7526737271","display_name":null,"funder_award_id":"ANR-16-CE32-0007","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320323910","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/01x3gbx83"},{"id":"https://openalex.org/F4320338463","display_name":"CHIST-ERA","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2973224855.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W95380067","https://openalex.org/W117994012","https://openalex.org/W238475734","https://openalex.org/W321384525","https://openalex.org/W643404104","https://openalex.org/W1530103821","https://openalex.org/W1533652402","https://openalex.org/W1565963867","https://openalex.org/W1622128722","https://openalex.org/W1808258554","https://openalex.org/W1968192761","https://openalex.org/W1997851819","https://openalex.org/W2008985174","https://openalex.org/W2017198737","https://openalex.org/W2021921902","https://openalex.org/W2024749530","https://openalex.org/W2026609204","https://openalex.org/W2030400104","https://openalex.org/W2036318837","https://openalex.org/W2036495910","https://openalex.org/W2037972391","https://openalex.org/W2064374909","https://openalex.org/W2081272455","https://openalex.org/W2086822165","https://openalex.org/W2107324390","https://openalex.org/W2126393394","https://openalex.org/W2145408484","https://openalex.org/W2156537900","https://openalex.org/W2161728228","https://openalex.org/W2166022262","https://openalex.org/W2170588867","https://openalex.org/W2171795575","https://openalex.org/W2201498095","https://openalex.org/W2273096596","https://openalex.org/W2306286459","https://openalex.org/W2330602748","https://openalex.org/W2346042384","https://openalex.org/W2401316178","https://openalex.org/W2621199550","https://openalex.org/W2740081098","https://openalex.org/W2783589141","https://openalex.org/W2947028229","https://openalex.org/W2949375583","https://openalex.org/W4302138509","https://openalex.org/W4302331569","https://openalex.org/W4367184870","https://openalex.org/W4399636501"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W4393677513","https://openalex.org/W2549786917","https://openalex.org/W3204758414"],"abstract_inverted_index":{"Stochastic":[0],"mechanistic":[1],"epidemiological":[2,96],"models":[3,28],"largely":[4],"contribute":[5,121],"to":[6,22,58,71,90,122,179,186,195,219],"better":[7],"understand":[8],"pathogen":[9],"emergence":[10],"and":[11,13,51,53,75,149,154,169,192,242,254,270],"spread,":[12],"assess":[14],"control":[15],"strategies":[16],"at":[17,127,182],"various":[18],"scales":[19,184],"(from":[20,177],"within-host":[21],"transnational":[23],"scale).":[24],"However,":[25],"developing":[26],"realistic":[27],"which":[29],"involve":[30],"multi-disciplinary":[31],"knowledge":[32],"integration":[33],"faces":[34],"three":[35],"major":[36],"challenges":[37],"in":[38,226,246],"predictive":[39],"epidemiology:":[40],"lack":[41],"of":[42,94,130,162,190,204,210,223],"readability":[43],"once":[44],"translated":[45],"into":[46],"simulation":[47,141,155],"code,":[48],"low":[49],"reproducibility":[50],"reusability,":[52],"long":[54],"development":[55],"time":[56,60],"compared":[57],"outbreak":[59],"scale.":[61],"We":[62],"introduce":[63],"here":[64,201],"EMULSION,":[65],"an":[66,95],"artificial":[67,164],"intelligence-based":[68],"software":[69],"intended":[70],"address":[72],"those":[73],"issues":[74],"help":[76],"modellers":[77],"focus":[78],"on":[79,159,251],"model":[80,97,131,147,212,220,238],"design":[81],"rather":[82],"than":[83],"programming.":[84],"EMULSION":[85,139,191,214,229,249],"defines":[86],"a":[87,103,231,268],"domain-specific":[88],"language":[89,153],"make":[91],"all":[92],"components":[93],"(structure,":[98],"processes,":[99],"parameters\u2026)":[100],"explicit":[101],"as":[102],"structured":[104],"text":[105],"file.":[106],"This":[107],"file":[108],"is":[109,134,215,257],"readable":[110],"by":[111,138],"scientists":[112],"from":[113],"other":[114],"fields":[115],"(epidemiologists,":[116],"biologists,":[117],"economists),":[118],"who":[119],"can":[120],"validate":[123],"or":[124],"revise":[125],"assumptions":[126],"any":[128,144],"stage":[129],"development.":[132],"It":[133,256],"then":[135],"automatically":[136],"processed":[137],"generic":[140],"engine,":[142],"preventing":[143],"discrepancy":[145],"between":[146],"description":[148],"implementation.":[150],"The":[151,188],"modelling":[152,175,198],"architecture":[156],"both":[157],"rely":[158],"the":[160,221],"combination":[161],"advanced":[163],"intelligence":[165],"methods":[166],"(knowledge":[167],"representation":[168],"multi-level":[170],"agent-based":[171],"simulation),":[172],"allowing":[173],"several":[174,183,224],"paradigms":[176],"compartment-":[178],"individual-based":[180],"models)":[181],"(up":[185],"metapopulation).":[187],"flexibility":[189],"its":[193],"capability":[194],"support":[196],"iterative":[197],"are":[199,273],"illustrated":[200],"through":[202],"examples":[203,272],"progressive":[205],"complexity,":[206],"including":[207],"late":[208],"revisions":[209],"core":[211],"assumptions.":[213],"also":[216],"currently":[217],"used":[218],"spread":[222],"diseases":[225],"real":[227],"pathosystems.":[228],"provides":[230],"command-line":[232],"tool":[233],"for":[234],"checking":[235],"models,":[236],"producing":[237],"diagrams,":[239],"running":[240],"simulations,":[241],"plotting":[243],"outputs.":[244],"Written":[245],"Python":[247],"3,":[248],"runs":[250],"Linux,":[252],"MacOS,":[253],"Windows.":[255],"released":[258],"under":[259],"Apache-2.0":[260],"license.":[261],"A":[262],"comprehensive":[263],"documentation":[264],"with":[265],"installation":[266],"instructions,":[267],"tutorial":[269],"many":[271],"available":[274],"from:":[275],"https://sourcesup.renater.fr/www/emulsion-public.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
