{"id":"https://openalex.org/W4308336157","doi":"https://doi.org/10.21105/joss.04742","title":"basilisk: a Bioconductor package for managing Pythonenvironments","display_name":"basilisk: a Bioconductor package for managing Pythonenvironments","publication_year":2022,"publication_date":"2022-11-04","ids":{"openalex":"https://openalex.org/W4308336157","doi":"https://doi.org/10.21105/joss.04742"},"language":"en","primary_location":{"id":"doi:10.21105/joss.04742","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.04742","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.04742.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.04742.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072824003","display_name":"Aaron T. L. Lun","orcid":"https://orcid.org/0000-0002-3564-4813"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Aaron T. L. Lun","raw_affiliation_strings":["Genentech Inc., South San Francisco, USA"],"raw_orcid":"https://orcid.org/0000-0002-3564-4813","affiliations":[{"raw_affiliation_string":"Genentech Inc., South San Francisco, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5072824003"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.5924,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.95842187,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"79","first_page":"4742","last_page":"4742"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.944599986076355,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.944599986076355,"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/T13650","display_name":"Computational Physics and Python Applications","score":0.9147999882698059,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8873469233512878},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.830896258354187},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5502195954322815},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5406614542007446},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3950384557247162},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21819236874580383}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8873469233512878},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.830896258354187},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5502195954322815},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5406614542007446},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3950384557247162},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21819236874580383},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.04742","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.04742","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.04742.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.04742","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.04742","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.04742.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4308336157.pdf","grobid_xml":"https://content.openalex.org/works/W4308336157.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W4225152484","https://openalex.org/W4399636375","https://openalex.org/W6963017890","https://openalex.org/W6991581718"],"related_works":["https://openalex.org/W2164960035","https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W1906486629","https://openalex.org/W3045904767","https://openalex.org/W4318619745","https://openalex.org/W3021560500","https://openalex.org/W2166247150","https://openalex.org/W4243252198","https://openalex.org/W4308336157"],"abstract_inverted_index":{"basilisk":[0,21,46],"is":[1],"an":[2],"R/Bioconductor":[3],"package":[4,12,65],"for":[5,34,41,72],"managing":[6],"Python":[7,28,52,62,75],"environments":[8],"within":[9],"the":[10,39,78],"Bioconductor":[11,17,79],"ecosystem.":[13],"Developers":[14],"of":[15,51,74],"other":[16],"packages":[18],"can":[19],"use":[20],"to":[22,67],"automatically":[23],"provision":[24],"and":[25],"load":[26],"custom":[27],"environments,":[29],"providing":[30],"a":[31,69],"streamlined":[32],"experience":[33],"their":[35],"end-users":[36],"by":[37],"avoiding":[38],"need":[40],"any":[42],"manual":[43],"system":[44],"configuration.":[45],"also":[47],"enables":[48],"robust":[49],"execution":[50],"code":[53,80],"via":[54],"reticulate":[55],"in":[56],"complex":[57],"analysis":[58],"workflows":[59],"involving":[60],"multiple":[61],"environments.":[63],"This":[64],"aims":[66],"provide":[68],"standardized":[70],"mechanism":[71],"integration":[73],"functionality":[76],"into":[77],"base.":[81]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2025-10-10T00:00:00"}
