{"id":"https://openalex.org/W4401404710","doi":"https://doi.org/10.1093/bioinformatics/btae486","title":"Galaxy Helm chart: a standardized method for deploying production Galaxy servers","display_name":"Galaxy Helm chart: a standardized method for deploying production Galaxy servers","publication_year":2024,"publication_date":"2024-08-01","ids":{"openalex":"https://openalex.org/W4401404710","doi":"https://doi.org/10.1093/bioinformatics/btae486","pmid":"https://pubmed.ncbi.nlm.nih.gov/39107873"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae486","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae486/58749467/btae486.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae486/58749467/btae486.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001522124","display_name":"Nuwan Goonasekera","orcid":"https://orcid.org/0000-0002-3019-2934"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Nuwan Goonasekera","raw_affiliation_strings":["Australian BioCommons, University of Melbourne , Melbourne, VIC 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0002-3019-2934","affiliations":[{"raw_affiliation_string":"Australian BioCommons, University of Melbourne , Melbourne, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090394262","display_name":"Alexandru Mahmoud","orcid":"https://orcid.org/0000-0002-3779-492X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexandru Mahmoud","raw_affiliation_strings":["Channing Division of Network Medicine, Harvard Medical School , Boston, MA 02115, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Channing Division of Network Medicine, Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012038702","display_name":"Keith Suderman","orcid":"https://orcid.org/0000-0003-0502-4557"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Suderman","raw_affiliation_strings":["Department of Biology, Johns Hopkins University , Baltimore, MD 21210, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Johns Hopkins University , Baltimore, MD 21210, United States","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006951727","display_name":"Enis Afgan","orcid":"https://orcid.org/0000-0003-0922-6711"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enis Afgan","raw_affiliation_strings":["Department of Biology, Johns Hopkins University , Baltimore, MD 21210, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Johns Hopkins University , Baltimore, MD 21210, United States","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5001522124"],"corresponding_institution_ids":["https://openalex.org/I165779595"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9885,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.85684334,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"40","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.5611000061035156,"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":0.5611000061035156,"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/T12127","display_name":"Software System Performance and Reliability","score":0.10109999775886536,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.031700000166893005,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/computer-science","display_name":"Computer science","score":0.676705002784729},{"id":"https://openalex.org/keywords/galaxy","display_name":"Galaxy","score":0.66822749376297},{"id":"https://openalex.org/keywords/chart","display_name":"Chart","score":0.5693523287773132},{"id":"https://openalex.org/keywords/production","display_name":"Production (economics)","score":0.5081675052642822},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.4543416500091553},{"id":"https://openalex.org/keywords/astrophysics","display_name":"Astrophysics","score":0.2904377579689026},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2745855450630188},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17660599946975708},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17129147052764893},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1316525638103485}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.676705002784729},{"id":"https://openalex.org/C98444146","wikidata":"https://www.wikidata.org/wiki/Q318","display_name":"Galaxy","level":2,"score":0.66822749376297},{"id":"https://openalex.org/C190812933","wikidata":"https://www.wikidata.org/wiki/Q28923","display_name":"Chart","level":2,"score":0.5693523287773132},{"id":"https://openalex.org/C2778348673","wikidata":"https://www.wikidata.org/wiki/Q739302","display_name":"Production (economics)","level":2,"score":0.5081675052642822},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.4543416500091553},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.2904377579689026},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2745855450630188},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17660599946975708},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17129147052764893},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1316525638103485},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C139719470","wikidata":"https://www.wikidata.org/wiki/Q39680","display_name":"Macroeconomics","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae486","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae486/58749467/btae486.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:39107873","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39107873","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:11338443","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11338443","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11338443/pdf/btae486.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae486","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae486/58749467/btae486.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6492416188","display_name":null,"funder_award_id":"2005506","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7609855956","display_name":null,"funder_award_id":"U41 HG006620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7895748443","display_name":null,"funder_award_id":"HG006620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8731240734","display_name":null,"funder_award_id":"U24 HG010263","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4401404710.pdf"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2001938458","https://openalex.org/W2087507717","https://openalex.org/W2619713135","https://openalex.org/W2962909145","https://openalex.org/W4206499307","https://openalex.org/W4313880130","https://openalex.org/W4398182689","https://openalex.org/W6806883358"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2092530219","https://openalex.org/W2388464034","https://openalex.org/W2533125852","https://openalex.org/W2140460949","https://openalex.org/W2105580438","https://openalex.org/W2057435755","https://openalex.org/W2390279801","https://openalex.org/W2358668433"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,130,177],"Galaxy":[2,43,61,77,87,124,169,181,196],"application":[3],"is":[4,53,112,132,183],"a":[5,26,32,41,54,57,85,90,121],"popular":[6],"open-source":[7],"framework":[8],"for":[9,56,108,119,158,167,180],"data":[10],"intensive":[11],"sciences,":[12],"counting":[13],"thousands":[14],"of":[15,29,35,40,84,146],"monthly":[16],"users":[17,30],"across":[18],"more":[19,49],"than":[20],"100":[21],"public":[22],"servers.":[23],"To":[24],"support":[25],"growing":[27],"number":[28],"and":[31,59,103,162,193],"greater":[33],"variety":[34],"use":[36],"cases,":[37],"the":[38,76,97,105,114,147,159,164,171,187,194],"complexity":[39],"production-grade":[42,86,123],"installation":[44,88],"has":[45],"also":[46,113],"grown,":[47],"requiring":[48],"administration":[50],"effort.":[51],"There":[52],"need":[55],"rapid":[58,116],"reproducible":[60],"deployment":[62],"method":[63,117],"that":[64,80],"can":[65],"be":[66],"maintained":[67],"at":[68,185,191],"high-availability":[69],"with":[70],"minimal":[71],"maintenance.":[72],"RESULTS:":[73],"We":[74],"describe":[75],"Helm":[78,182,189],"chart":[79,98,131,148],"codifies":[81],"all":[82],"elements":[83],"into":[89],"single":[91],"package.":[92],"Deployable":[93],"on":[94,126,153,170],"Kubernetes":[95],"clusters,":[96],"encapsulates":[99],"supporting":[100],"software":[101],"services":[102,141],"implements":[104],"best-practices":[106],"model":[107],"running":[109,168],"Galaxy.":[110],"It":[111],"most":[115],"available":[118,184],"deploying":[120],"scalable,":[122],"instance":[125],"one's":[127],"own":[128],"infrastructure.":[129],"highly":[133],"configurable,":[134],"allowing":[135],"systems":[136],"administrators":[137],"to":[138],"swap":[139],"dependent":[140],"if":[142],"desired.":[143],"Notable":[144],"uses":[145],"include":[149],"on-demand,":[150],"fully-automated":[151],"deployments":[152],"AnVIL,":[154],"providing":[155],"training":[156],"infrastructure":[157],"Bioconductor":[160],"project,":[161],"as":[163],"AWS-recommended":[165],"solution":[166],"Amazon":[172],"cloud.":[173],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"source":[178],"code":[179],"https://github.com/galaxyproject/galaxy-helm,":[186],"corresponding":[188],"package":[190],"https://github.com/CloudVE/helm-charts,":[192],"required":[195],"container":[197],"image":[198],"https://github.com/galaxyproject/galaxy-docker-k8s.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
