{"id":"https://openalex.org/W2949433290","doi":"https://doi.org/10.1093/bioinformatics/btz379","title":"Tibanna: software for scalable execution of portable pipelines on the cloud","display_name":"Tibanna: software for scalable execution of portable pipelines on the cloud","publication_year":2019,"publication_date":"2019-04-30","ids":{"openalex":"https://openalex.org/W2949433290","doi":"https://doi.org/10.1093/bioinformatics/btz379","mag":"2949433290","pmid":"https://pubmed.ncbi.nlm.nih.gov/31077294"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz379","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz379","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6931271","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100443294","display_name":"Soohyun Lee","orcid":"https://orcid.org/0000-0002-3594-6213"},"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":"Soohyun Lee","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103852861","display_name":"Jeremy Johnson","orcid":null},"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":"Jeremy Johnson","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051116389","display_name":"Carl Vitzthum","orcid":"https://orcid.org/0000-0002-3075-2305"},"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":"Carl Vitzthum","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006160672","display_name":"Koray K\u0131rl\u0131","orcid":"https://orcid.org/0000-0002-2289-0652"},"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":"Koray K\u0131rl\u0131","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084957565","display_name":"B. Alver","orcid":"https://orcid.org/0000-0002-5019-7652"},"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":true,"raw_author_name":"Burak H Alver","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022028438","display_name":"Peter J. Park","orcid":"https://orcid.org/0000-0001-9378-960X"},"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":true,"raw_author_name":"Peter J Park","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5022028438","https://openalex.org/A5084957565"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.769,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.70847953,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"35","issue":"21","first_page":"4424","last_page":"4426"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4551999866962433,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4551999866962433,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.23759999871253967,"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":0.14749999344348907,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8647410869598389},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6870477199554443},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6647335290908813},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.6225435733795166},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.594368040561676},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5716040730476379},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5269715785980225},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.5057985782623291},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.49561989307403564},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4643697142601013},{"id":"https://openalex.org/keywords/terabyte","display_name":"Terabyte","score":0.4630140960216522},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.45289838314056396},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4473940432071686},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.43567946553230286},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.42161113023757935},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37448370456695557}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8647410869598389},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6870477199554443},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6647335290908813},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.6225435733795166},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.594368040561676},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5716040730476379},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5269715785980225},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5057985782623291},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.49561989307403564},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4643697142601013},{"id":"https://openalex.org/C199683683","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Terabyte","level":2,"score":0.4630140960216522},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.45289838314056396},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4473940432071686},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.43567946553230286},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.42161113023757935},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37448370456695557},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"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":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz379","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz379","pdf_url":null,"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":"pmid:31077294","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31077294","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:6931271","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6931271","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6931271","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6931271","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2110417468","https://openalex.org/W2161645441","https://openalex.org/W2584394140","https://openalex.org/W2605897695","https://openalex.org/W2607211817","https://openalex.org/W2613409207","https://openalex.org/W2762888391","https://openalex.org/W2786998058","https://openalex.org/W2963268312","https://openalex.org/W6744938664","https://openalex.org/W6748436567"],"related_works":["https://openalex.org/W4226323523","https://openalex.org/W2557718140","https://openalex.org/W67092138","https://openalex.org/W3201519406","https://openalex.org/W4225687299","https://openalex.org/W2789551765","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W4211197663","https://openalex.org/W2491403535"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"introduce":[2],"Tibanna,":[3],"an":[4],"open-source":[5],"software":[6],"tool":[7],"for":[8,79,105],"automated":[9],"execution":[10],"of":[11,41,45,84,103],"bioinformatics":[12],"pipelines":[13],"on":[14,118],"Amazon":[15],"Web":[16],"Services":[17],"(AWS).":[18],"Tibanna":[19,75],"accepts":[20],"reproducible":[21],"and":[22,35,43,57,69,91],"portable":[23],"pipeline":[24],"standards":[25],"including":[26,87],"Common":[27],"Workflow":[28,31],"Language":[29,33],"(CWL),":[30],"Description":[32],"(WDL)":[34],"Docker.":[36],"It":[37],"adopts":[38],"a":[39,50,82],"strategy":[40],"isolation":[42],"optimization":[44],"individual":[46],"executions,":[47],"combined":[48],"with":[49,81,89],"serverless":[51],"scheduling":[52],"approach.":[53],"Pipelines":[54],"are":[55,126],"executed":[56],"monitored":[58],"using":[59],"local":[60],"commands":[61],"or":[62],"the":[63,106],"Python":[64],"Application":[65],"Programming":[66],"Interface":[67],"(API)":[68],"cloud":[70],"configuration":[71],"is":[72,76,116],"automatically":[73],"handled.":[74],"well":[77],"suited":[78],"projects":[80],"range":[83],"computational":[85],"requirements,":[86],"those":[88],"large":[90],"widely":[92],"fluctuating":[93],"loads.":[94],"Notably,":[95],"it":[96],"has":[97],"been":[98],"used":[99],"to":[100],"process":[101],"terabytes":[102],"data":[104,125],"4D":[107],"Nucleome":[108],"(4DN)":[109],"Network.":[110],"AVAILABILITY":[111],"AND":[112],"IMPLEMENTATION:":[113],"Source":[114],"code":[115],"available":[117,127],"GitHub":[119],"at":[120,128],"https://github.com/4dn-dcic/tibanna.":[121],"SUPPLEMENTARY":[122],"INFORMATION:":[123],"Supplementary":[124],"Bioinformatics":[129],"online.":[130]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
