{"id":"https://openalex.org/W4400798813","doi":"https://doi.org/10.1145/3626203.3670559","title":"nf-core on Open OnDemand: community-curated bioinformatics pipelines for everyone","display_name":"nf-core on Open OnDemand: community-curated bioinformatics pipelines for everyone","publication_year":2024,"publication_date":"2024-07-17","ids":{"openalex":"https://openalex.org/W4400798813","doi":"https://doi.org/10.1145/3626203.3670559"},"language":"en","primary_location":{"id":"doi:10.1145/3626203.3670559","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3626203.3670559","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing 2024: Human Powered Computing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3626203.3670559","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100387026","display_name":"Yucheng Zhang","orcid":"https://orcid.org/0000-0001-6802-009X"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yucheng Zhang","raw_affiliation_strings":["Research Technology, Tufts University, USA"],"affiliations":[{"raw_affiliation_string":"Research Technology, Tufts University, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000013516","display_name":"Payas Bhutra","orcid":"https://orcid.org/0009-0005-0022-2492"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Payas Bhutra","raw_affiliation_strings":["Rosen Center for Advanced Computing, Purdue University, USA"],"affiliations":[{"raw_affiliation_string":"Rosen Center for Advanced Computing, Purdue University, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100372240","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-9126-2692"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xue Li","raw_affiliation_strings":["Research Technology, Tufts University, USA"],"affiliations":[{"raw_affiliation_string":"Research Technology, Tufts University, USA","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100387026"],"corresponding_institution_ids":["https://openalex.org/I121934306"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12190761,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994999766349792,"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":0.9994999766349792,"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/T11937","display_name":"Research Data Management Practices","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9948999881744385,"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":0.5236458778381348},{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.503750741481781},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.10835874080657959}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5236458778381348},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.503750741481781},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.10835874080657959}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3626203.3670559","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3626203.3670559","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing 2024: Human Powered Computing","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3626203.3670559","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3626203.3670559","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing 2024: Human Powered Computing","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W2605897695","https://openalex.org/W2804145951","https://openalex.org/W3006653136"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"The":[0,156,174],"standardization,":[1],"portability,":[2],"and":[3,120,129,195,213,232],"reproducibility":[4],"of":[5,34,44,68,80,91,103,163,176,204],"analysis":[6,36],"pipelines":[7,37,51,82,115,149,206],"in":[8,25],"bioinformatics":[9,35,61,111,143],"is":[10,63,73],"a":[11,18,31,192],"well-known":[12],"challenge.":[13],"To":[14,132],"tackle":[15],"this":[16],"issue,":[17],"community-driven":[19],"initiative":[20],"called":[21],"nf-core":[22,46,71,81,114,148,164,205,214],"was":[23],"launched":[24],"2018.":[26],"It":[27],"aims":[28],"to":[29,55,98,109,136,168,184,200,226,235],"collect":[30],"curated":[32],"set":[33],"built":[38],"using":[39],"nextflow.":[40],"At":[41,57],"the":[42,60,66,78,89,104,134,151,161,202],"time":[43],"writing,":[45],"encompasses":[47],"over":[48],"100":[49],"well-maintained":[50],"that":[52],"are":[53,94,116,123],"ready":[54],"use.":[56],"Tufts":[58,223],"University,":[59,224],"community":[62],"well-established,":[64],"yet":[65],"use":[67,203],"nextflow":[69,130,212],"or":[70],"pipeline":[72],"limited.":[74],"Two":[75],"barriers":[76,135],"impede":[77],"adoption":[79],"into":[83,150,187,217,238],"research":[84],"workflows":[85],"by":[86],"users.":[87],"Firstly,":[88],"advantages":[90],"these":[92,177,230],"tools":[93,128,231],"not":[95,124],"effectively":[96],"communicated":[97],"researchers,":[99],"leaving":[100],"many":[101,121],"unaware":[102],"benefits":[105],"they":[106],"can":[107],"bring":[108],"their":[110,188,239],"research.":[112,240],"Secondly,":[113],"based":[117],"on":[118],"nextflow,":[119],"users":[122,139,167,228],"familiar":[125],"with":[126,142,171,229],"command-line":[127,144],"syntax.":[131],"reduce":[133],"entry":[137],"for":[138],"less":[140],"experienced":[141],"tools,":[145],"we":[146,209],"integrated":[147],"Open":[152],"OnDemand":[153],"(OOD)":[154],"platform.":[155],"OOD":[157,178],"web":[158],"interface":[159],"streamlines":[160],"execution":[162],"pipelines,":[165],"allowing":[166],"launch":[169],"analyses":[170],"minimal":[172],"effort.":[173],"availability":[175],"apps":[179],"also":[180],"enables":[181],"faculty":[182],"members":[183],"incorporate":[185],"them":[186,234,237],"classes,":[189],"which":[190],"creates":[191],"more":[193],"efficient":[194],"productive":[196],"learning":[197],"environment.":[198],"Additionally,":[199],"promote":[201],"among":[207],"users,":[208],"have":[210],"incorporated":[211],"training":[215],"sessions":[216],"our":[218],"regular":[219],"workshop":[220],"series":[221],"at":[222],"aiming":[225],"familiarize":[227],"inspire":[233],"integrate":[236]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
