{"id":"https://openalex.org/W2951522607","doi":"https://doi.org/10.1093/bioinformatics/btac770","title":"libRoadRunner 2.0: a high performance SBML simulation and analysis library","display_name":"libRoadRunner 2.0: a high performance SBML simulation and analysis library","publication_year":2022,"publication_date":"2022-12-07","ids":{"openalex":"https://openalex.org/W2951522607","doi":"https://doi.org/10.1093/bioinformatics/btac770","mag":"2951522607","pmid":"https://pubmed.ncbi.nlm.nih.gov/36478036"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac770","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac770","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac770/48520701/btac770.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac770/48520701/btac770.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110621022","display_name":"Ciaran Welsh","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ciaran Welsh","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038610034","display_name":"Jin Xu","orcid":"https://orcid.org/0000-0001-6738-9979"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jin Xu","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucian Smith","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012727458","display_name":"Matthias K\u00f6nig","orcid":"https://orcid.org/0000-0003-1725-179X"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias K\u00f6nig","raw_affiliation_strings":["Institute of Biology, Institute of Theoretical Biology, Humboldt-University Berlin , Berlin 10115, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Biology, Institute of Theoretical Biology, Humboldt-University Berlin , Berlin 10115, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009998609","display_name":"Kiri Choi","orcid":"https://orcid.org/0000-0002-0156-8410"},"institutions":[{"id":"https://openalex.org/I125608817","display_name":"Korea Institute for Advanced Study","ror":"https://ror.org/041hz9568","country_code":"KR","type":"facility","lineage":["https://openalex.org/I125608817"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kiri Choi","raw_affiliation_strings":["School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Republic of Korea","institution_ids":["https://openalex.org/I125608817"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Herbert M Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5044484291"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5526,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.94061791,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9954000115394592,"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":0.9954000115394592,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.9886000156402588,"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":0.9786542654037476},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7826638221740723},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.520310640335083},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.29548895359039307},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.22799411416053772},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.05855762958526611}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9786542654037476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7826638221740723},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.520310640335083},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.29548895359039307},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.22799411416053772},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.05855762958526611}],"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac770","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac770","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac770/48520701/btac770.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36478036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36478036","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:pubmedcentral.nih.gov:9825722","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825722","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac770","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac770","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac770/48520701/btac770.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6321517409","display_name":null,"funder_award_id":"1933453","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951522607.pdf","grobid_xml":"https://content.openalex.org/works/W2951522607.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W115452890","https://openalex.org/W985699466","https://openalex.org/W1491178396","https://openalex.org/W1493349649","https://openalex.org/W1510479004","https://openalex.org/W1512003720","https://openalex.org/W1663066714","https://openalex.org/W1978864877","https://openalex.org/W1979565917","https://openalex.org/W1995091049","https://openalex.org/W2012638722","https://openalex.org/W2034375827","https://openalex.org/W2040163651","https://openalex.org/W2054877682","https://openalex.org/W2061364094","https://openalex.org/W2077587321","https://openalex.org/W2081781433","https://openalex.org/W2097240335","https://openalex.org/W2097319997","https://openalex.org/W2098367419","https://openalex.org/W2102653059","https://openalex.org/W2104759754","https://openalex.org/W2109990759","https://openalex.org/W2125615370","https://openalex.org/W2134221731","https://openalex.org/W2136970290","https://openalex.org/W2149146154","https://openalex.org/W2150908245","https://openalex.org/W2153185479","https://openalex.org/W2155321250","https://openalex.org/W2161088429","https://openalex.org/W2164653071","https://openalex.org/W2166751342","https://openalex.org/W2170032647","https://openalex.org/W2472803348","https://openalex.org/W2785514490","https://openalex.org/W2884300959","https://openalex.org/W2897722020","https://openalex.org/W2916475656","https://openalex.org/W2949797623","https://openalex.org/W2983045983","https://openalex.org/W2988361147","https://openalex.org/W2989997158","https://openalex.org/W3048335229","https://openalex.org/W3080133182","https://openalex.org/W3121429485","https://openalex.org/W3134089816","https://openalex.org/W3159249481","https://openalex.org/W3200565866","https://openalex.org/W3217107425","https://openalex.org/W3217272007","https://openalex.org/W4205129776","https://openalex.org/W4205450773","https://openalex.org/W6770460946"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1568154633","https://openalex.org/W1833372769","https://openalex.org/W1994518768","https://openalex.org/W2082621456","https://openalex.org/W104010570","https://openalex.org/W2150908245","https://openalex.org/W2069162648"],"abstract_inverted_index":{"libRoadRunner":[0],"binary":[1],"distributions":[2],"for":[3,36],"Windows,":[4],"Mac":[5],"OS":[6],"and":[7,10,15,22],"Linux,":[8],"Julia":[9],"Python":[11,23],"bindings,":[12],"source":[13,31],"code":[14,32],"documentation":[16],"are":[17,25],"all":[18],"available":[19,27],"at":[20],"https://github.com/sys-bio/roadrunner,":[21],"bindings":[24],"also":[26],"via":[28],"pip.":[29],"The":[30,58],"can":[33],"be":[34],"compiled":[35],"the":[37,55,63],"supported":[38,47],"systems":[39],"as":[40,42,51],"well":[41],"in":[43],"principle":[44],"any":[45],"system":[46],"by":[48],"LLVM-13,":[49],"such":[50],"ARM-based":[52],"computers":[53],"like":[54],"Raspberry":[56],"Pi.":[57],"library":[59],"is":[60],"licensed":[61],"under":[62],"Apache":[64],"License":[65],"Version":[66],"2.0.":[67]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
