{"id":"https://openalex.org/W2983045983","doi":"https://doi.org/10.1093/bioinformatics/btz860","title":"SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems","display_name":"SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems","publication_year":2019,"publication_date":"2019-11-15","ids":{"openalex":"https://openalex.org/W2983045983","doi":"https://doi.org/10.1093/bioinformatics/btz860","mag":"2983045983","pmid":"https://pubmed.ncbi.nlm.nih.gov/31738386"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz860","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz860","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2106.02609","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034685669","display_name":"Filippo Maggioli","orcid":"https://orcid.org/0000-0001-8008-8468"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"F Maggioli","raw_affiliation_strings":["Computer Science Department, Sapienza University of Rome , Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Sapienza University of Rome , Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084753554","display_name":"Toni Mancini","orcid":"https://orcid.org/0000-0003-3355-2170"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"T Mancini","raw_affiliation_strings":["Computer Science Department, Sapienza University of Rome , Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Sapienza University of Rome , Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010524910","display_name":"Enrico Tronci","orcid":"https://orcid.org/0000-0002-0377-3119"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"E Tronci","raw_affiliation_strings":["Computer Science Department, Sapienza University of Rome , Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Sapienza University of Rome , Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5084753554"],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7176,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.85101687,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"36","issue":"7","first_page":"2165","last_page":"2172"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9980000257492065,"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":0.9980000257492065,"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/T13286","display_name":"Modeling and Simulation Systems","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.9872000217437744,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9963934421539307},{"id":"https://openalex.org/keywords/modelica","display_name":"Modelica","score":0.9096152186393738},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7589700222015381},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5748595595359802},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41811835765838623},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4112018346786499},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.38199734687805176},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.32146063446998596},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11866137385368347},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.07891485095024109}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9963934421539307},{"id":"https://openalex.org/C37785467","wikidata":"https://www.wikidata.org/wiki/Q385325","display_name":"Modelica","level":2,"score":0.9096152186393738},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7589700222015381},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5748595595359802},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41811835765838623},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4112018346786499},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.38199734687805176},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.32146063446998596},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11866137385368347},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.07891485095024109}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz860","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz860","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31738386","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31738386","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:arXiv.org:2106.02609","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2106.02609","pdf_url":"https://arxiv.org/pdf/2106.02609","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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:iris.uniroma1.it:11573/1356836","is_oa":false,"landing_page_url":"http://hdl.handle.net/11573/1356836","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2106.02609","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2106.02609","pdf_url":"https://arxiv.org/pdf/2106.02609","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W98354153","https://openalex.org/W252848119","https://openalex.org/W431902837","https://openalex.org/W1963943927","https://openalex.org/W1978520001","https://openalex.org/W2002900603","https://openalex.org/W2034375827","https://openalex.org/W2086894550","https://openalex.org/W2098367419","https://openalex.org/W2102653059","https://openalex.org/W2104759754","https://openalex.org/W2107062718","https://openalex.org/W2107426858","https://openalex.org/W2124436671","https://openalex.org/W2132844121","https://openalex.org/W2150908245","https://openalex.org/W2153710377","https://openalex.org/W2161088429","https://openalex.org/W2168798915","https://openalex.org/W2248858308","https://openalex.org/W2294128886","https://openalex.org/W2344850968","https://openalex.org/W2566646675","https://openalex.org/W2583964271","https://openalex.org/W2742779439","https://openalex.org/W2782744517","https://openalex.org/W2885434610","https://openalex.org/W2902868425","https://openalex.org/W2908029862","https://openalex.org/W2916475656","https://openalex.org/W2947660247","https://openalex.org/W3105134387","https://openalex.org/W4232840679","https://openalex.org/W4237725837","https://openalex.org/W4244457856","https://openalex.org/W6813711271"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W3041939341"],"abstract_inverted_index":{"SBML2Modelica":[0],"is":[1,6],"written":[2],"in":[3],"Java":[4],"and":[5],"freely":[7],"available":[8],"for":[9],"non-commercial":[10],"use":[11],"at":[12],"https://bitbucket.org/mclab/sbml2modelica.":[13]},"counts_by_year":[{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
