{"id":"https://openalex.org/W2936760626","doi":"https://doi.org/10.1093/bioinformatics/btz278","title":"ORCA: a comprehensive bioinformatics container environment for education and research","display_name":"ORCA: a comprehensive bioinformatics container environment for education and research","publication_year":2019,"publication_date":"2019-04-13","ids":{"openalex":"https://openalex.org/W2936760626","doi":"https://doi.org/10.1093/bioinformatics/btz278","mag":"2936760626","pmid":"https://pubmed.ncbi.nlm.nih.gov/31004474"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz278","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4448/30330604/btz278.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/35/21/4448/30330604/btz278.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028264773","display_name":"Shaun D. Jackman","orcid":"https://orcid.org/0000-0002-9275-5966"},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shaun D Jackman","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":"https://orcid.org/0000-0002-9275-5966","affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079832807","display_name":"Tatyana Mozgacheva","orcid":null},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Tatyana Mozgacheva","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073483194","display_name":"Susie Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Susie Chen","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086971322","display_name":"Brendan O\u2019Huiginn","orcid":null},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Brendan O\u2019Huiginn","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088460142","display_name":"Lance R. Bailey","orcid":null},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lance Bailey","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017539699","display_name":"\u0130nan\u00e7 Birol","orcid":"https://orcid.org/0000-0003-0950-7839"},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Inanc Birol","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100728059","display_name":"Steven J.M. Jones","orcid":"https://orcid.org/0000-0003-3394-2208"},"institutions":[{"id":"https://openalex.org/I4210132220","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210132220"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Steven J M Jones","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer , Vancouver BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer , Vancouver BC, Canada","institution_ids":["https://openalex.org/I4210132220"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100728059"],"corresponding_institution_ids":["https://openalex.org/I4210132220"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.6093,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.64695533,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"21","first_page":"4448","last_page":"4450"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9695000052452087,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9695000052452087,"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":0.00839999970048666,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.006200000178068876,"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/license","display_name":"License","score":0.7094396352767944},{"id":"https://openalex.org/keywords/container","display_name":"Container (type theory)","score":0.6846082210540771},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6831520199775696},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6574786901473999},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6419234275817871},{"id":"https://openalex.org/keywords/debugging","display_name":"Debugging","score":0.6307381987571716},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5167393088340759},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4563371241092682},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.43328702449798584},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3986858129501343},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3704037368297577},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3350337743759155},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11842459440231323},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10253211855888367}],"concepts":[{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.7094396352767944},{"id":"https://openalex.org/C2781018962","wikidata":"https://www.wikidata.org/wiki/Q5164884","display_name":"Container (type theory)","level":2,"score":0.6846082210540771},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6831520199775696},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6574786901473999},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6419234275817871},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.6307381987571716},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5167393088340759},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4563371241092682},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.43328702449798584},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3986858129501343},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3704037368297577},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3350337743759155},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11842459440231323},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10253211855888367},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz278","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4448/30330604/btz278.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:31004474","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31004474","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:5796541","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821186","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz278","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4448/30330604/btz278.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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6000000238418579}],"awards":[{"id":"https://openalex.org/G3761971259","display_name":null,"funder_award_id":"R01HG007182","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320319973","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2936760626.pdf","grobid_xml":"https://content.openalex.org/works/W2936760626.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1964721736","https://openalex.org/W2097288488","https://openalex.org/W2146902212","https://openalex.org/W2604622795","https://openalex.org/W2753370921","https://openalex.org/W2765745983","https://openalex.org/W4251404760"],"related_works":["https://openalex.org/W4286531993","https://openalex.org/W2999281421","https://openalex.org/W2753370921","https://openalex.org/W1878038826","https://openalex.org/W1487119477","https://openalex.org/W2936760626","https://openalex.org/W1988697672","https://openalex.org/W3119028115","https://openalex.org/W1974719404","https://openalex.org/W2097391156"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1,18,34,131,139],"ORCA":[2,19,35,66,106,132,143],"bioinformatics":[3,13,28,75,91,100],"environment":[4,29,36,76],"is":[5,40,135,144],"a":[6,26,38,73,81,98,103],"Docker":[7,43,133],"image":[8,20,134],"that":[9,109,118],"contains":[10],"hundreds":[11],"of":[12,142],"tools":[14],"and":[15,21,32,95,126],"their":[16],"dependencies.":[17],"accompanying":[22],"server":[23,39],"infrastructure":[24],"provide":[25,72,97],"comprehensive":[27],"for":[30,55,85,102],"education":[31,125],"research.":[33,127],"on":[37,90,124],"implemented":[41],"using":[42],"containers,":[44],"but":[45],"without":[46],"requiring":[47],"users":[48],"to":[49,71,77,96],"interact":[50],"directly":[51],"with":[52,63],"Docker,":[53],"suitable":[54],"novices":[56],"who":[57],"may":[58,120],"not":[59],"yet":[60],"have":[61],"familiarity":[62],"managing":[64],"containers.":[65],"has":[67],"been":[68],"used":[69],"successfully":[70],"private":[74],"external":[78],"collaborators":[79],"at":[80,93,137,146],"large":[82],"genome":[83],"institute,":[84],"teaching":[86],"an":[87],"undergraduate":[88],"class":[89],"targeted":[92],"biologists,":[94],"ready-to-go":[99],"suite":[101],"hackathon.":[104],"Using":[105],"eliminates":[107],"time":[108,119],"would":[110],"be":[111,121],"spent":[112,123],"debugging":[113],"software":[114],"installation":[115],"issues,":[116],"so":[117],"better":[122],"AVAILABILITY":[128],"AND":[129],"IMPLEMENTATION:":[130],"available":[136,145],"https://hub.docker.com/r/bcgsc/orca/.":[138],"source":[140],"code":[141],"https://github.com/bcgsc/orca":[147],"under":[148],"the":[149],"MIT":[150],"license.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
