{"id":"https://openalex.org/W2419000639","doi":"https://doi.org/10.1093/bioinformatics/btw353","title":"Rule-based modeling with Virtual Cell","display_name":"Rule-based modeling with Virtual Cell","publication_year":2016,"publication_date":"2016-06-09","ids":{"openalex":"https://openalex.org/W2419000639","doi":"https://doi.org/10.1093/bioinformatics/btw353","mag":"2419000639","pmid":"https://pubmed.ncbi.nlm.nih.gov/27497444"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw353","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw353","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2880/24406881/btw353.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2880/24406881/btw353.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027644564","display_name":"James C. Schaff","orcid":"https://orcid.org/0000-0003-3286-7736"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James C. Schaff","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075363923","display_name":"Dan Vasilescu","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan Vasilescu","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066544731","display_name":"Ion I. Moraru","orcid":"https://orcid.org/0000-0002-3746-9676"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ion I. Moraru","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019048997","display_name":"Leslie M. Loew","orcid":"https://orcid.org/0000-0002-1851-4646"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leslie M. Loew","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107139754","display_name":"Michael L. Blinov","orcid":"https://orcid.org/0000-0002-9363-9705"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael L. Blinov","raw_affiliation_strings":["R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5107139754"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8868,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.90950918,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"18","first_page":"2880","last_page":"2882"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8920999765396118,"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":0.8920999765396118,"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/T12029","display_name":"DNA and Biological Computing","score":0.019700000062584877,"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":0.01209999993443489,"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/computer-science","display_name":"Computer science","score":0.8666387796401978},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.8618820905685425},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5782006978988647},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5469304919242859},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4691076874732971},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.45584601163864136},{"id":"https://openalex.org/keywords/virtual-machine","display_name":"Virtual machine","score":0.45559266209602356},{"id":"https://openalex.org/keywords/virtual-laboratory","display_name":"Virtual Laboratory","score":0.45137304067611694},{"id":"https://openalex.org/keywords/modeling-language","display_name":"Modeling language","score":0.4299708604812622}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8666387796401978},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.8618820905685425},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5782006978988647},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5469304919242859},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4691076874732971},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.45584601163864136},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.45559266209602356},{"id":"https://openalex.org/C2777609615","wikidata":"https://www.wikidata.org/wiki/Q2527919","display_name":"Virtual Laboratory","level":2,"score":0.45137304067611694},{"id":"https://openalex.org/C179603123","wikidata":"https://www.wikidata.org/wiki/Q1941921","display_name":"Modeling language","level":3,"score":0.4299708604812622},{"id":"https://openalex.org/C49774154","wikidata":"https://www.wikidata.org/wiki/Q131765","display_name":"Multimedia","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw353","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw353","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2880/24406881/btw353.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5018377","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5018377","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:27497444","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27497444","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:open-archive.highwire.org:bioinfo:32/18/2880","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/18/2880","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw353","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw353","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/18/2880/24406881/btw353.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1442390677","display_name":null,"funder_award_id":"R01 GM095485","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3030034556","display_name":null,"funder_award_id":"P41 GM103313","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1745503682","https://openalex.org/W1870430550","https://openalex.org/W2023568310","https://openalex.org/W2040890820","https://openalex.org/W2069941324","https://openalex.org/W2081098704","https://openalex.org/W2097240335","https://openalex.org/W2097319997","https://openalex.org/W2121490181","https://openalex.org/W2144063122","https://openalex.org/W2159629828","https://openalex.org/W2163493106","https://openalex.org/W2175715045","https://openalex.org/W2916475656","https://openalex.org/W4231917197","https://openalex.org/W6667917037","https://openalex.org/W6813711271"],"related_works":["https://openalex.org/W2086733238","https://openalex.org/W4235530921","https://openalex.org/W3017187763","https://openalex.org/W270927586","https://openalex.org/W212372412","https://openalex.org/W4313142237","https://openalex.org/W4253023131","https://openalex.org/W950049861","https://openalex.org/W4312816704","https://openalex.org/W83892589"],"abstract_inverted_index":{"UNLABELLED:":[0],"Rule-based":[1],"modeling":[2,34,58,81],"is":[3,48,170,177],"invaluable":[4],"when":[5],"the":[6,39,76,119,134,157,164,173],"number":[7],"of":[8,41,103],"possible":[9],"species":[10],"and":[11,30,35,105,131,143,149,168],"reactions":[12],"in":[13,71],"a":[14,43,57,72,100,108,114],"model":[15,65,85,109],"become":[16],"too":[17],"large":[18,101],"to":[19,50,98],"allow":[20],"convenient":[21],"manual":[22],"specification.":[23],"The":[24,140],"popular":[25],"rule-based":[26,64],"software":[27],"tools":[28],"BioNetGen":[29],"NFSim":[31,120],"provide":[32],"powerful":[33],"simulation":[36,69,121],"capabilities":[37],"at":[38,133,163,179,189],"cost":[40],"learning":[42],"complex":[44],"scripting":[45],"language":[46],"which":[47],"used":[49],"specify":[51],"these":[52],"models.":[53],"Here,":[54],"we":[55],"introduce":[56],"tool":[59],"that":[60],"combines":[61],"new":[62],"graphical":[63],"specification":[66],"with":[67,93],"existing":[68],"engines":[70],"seamless":[73],"way":[74],"within":[75,172],"familiar":[77],"Virtual":[78,135,165],"Cell":[79,136,166],"(VCell)":[80],"environment.":[82],"A":[83],"mathematical":[84],"can":[86,110],"be":[87,111],"built":[88],"integrating":[89],"explicit":[90],"reaction":[91,94],"networks":[92],"rules.":[95],"In":[96],"addition":[97],"offering":[99],"choice":[102],"ODE":[104],"stochastic":[106],"solvers,":[107],"simulated":[112],"using":[113],"network":[115],"free":[116],"approach":[117],"through":[118],"engine.":[122],"AVAILABILITY":[123],"AND":[124],"IMPLEMENTATION:":[125],"Available":[126],"as":[127],"VCell":[128],"(versions":[129],"6.0":[130],"later)":[132],"web":[137],"site":[138],"(http://vcell.org/).":[139],"application":[141],"installs":[142],"runs":[144],"on":[145,156],"all":[146],"major":[147],"platforms":[148],"does":[150],"not":[151],"require":[152],"registration":[153],"for":[154],"use":[155],"user's":[158],"computer.":[159],"Tutorials":[160],"are":[161,187],"available":[162,178,188],"website":[167],"Help":[169],"provided":[171],"software.":[174],"Source":[175],"code":[176],"Sourceforge.":[180],"CONTACT:":[181],"vcell_support@uchc.edu":[182],"SUPPLEMENTARY":[183],"INFORMATION:":[184],"Supplementary":[185],"data":[186],"Bioinformatics":[190],"online.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}