{"id":"https://openalex.org/W2054924729","doi":"https://doi.org/10.1145/2649387.2649429","title":"A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy","display_name":"A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy","publication_year":2014,"publication_date":"2014-09-20","ids":{"openalex":"https://openalex.org/W2054924729","doi":"https://doi.org/10.1145/2649387.2649429","mag":"2054924729"},"language":"en","primary_location":{"id":"doi:10.1145/2649387.2649429","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2649387.2649429","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2649387.2649429","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/2649387.2649429","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047833562","display_name":"Luca Pireddu","orcid":"https://orcid.org/0000-0002-4663-5613"},"institutions":[{"id":"https://openalex.org/I172446870","display_name":"University of Cagliari","ror":"https://ror.org/003109y17","country_code":"IT","type":"education","lineage":["https://openalex.org/I172446870"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Luca Pireddu","raw_affiliation_strings":["University of Cagliari, Italy","University Of Cagliari, Italy"],"affiliations":[{"raw_affiliation_string":"University of Cagliari, Italy","institution_ids":["https://openalex.org/I172446870"]},{"raw_affiliation_string":"University Of Cagliari, Italy","institution_ids":["https://openalex.org/I172446870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041142252","display_name":"Simone Leo","orcid":"https://orcid.org/0000-0001-8271-5429"},"institutions":[{"id":"https://openalex.org/I172446870","display_name":"University of Cagliari","ror":"https://ror.org/003109y17","country_code":"IT","type":"education","lineage":["https://openalex.org/I172446870"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Leo","raw_affiliation_strings":["University of Cagliari, Italy","University Of Cagliari, Italy"],"affiliations":[{"raw_affiliation_string":"University of Cagliari, Italy","institution_ids":["https://openalex.org/I172446870"]},{"raw_affiliation_string":"University Of Cagliari, Italy","institution_ids":["https://openalex.org/I172446870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034974535","display_name":"Nicola Soranzo","orcid":"https://orcid.org/0000-0003-3627-5340"},"institutions":[{"id":"https://openalex.org/I2800759272","display_name":"Center for Advanced Studies Research and Development in Sardinia","ror":"https://ror.org/03jdxdk20","country_code":"IT","type":"facility","lineage":["https://openalex.org/I2800759272"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Soranzo","raw_affiliation_strings":["CRS4, Pula, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4, Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073829656","display_name":"Gianluigi Zanetti","orcid":"https://orcid.org/0000-0003-1683-7350"},"institutions":[{"id":"https://openalex.org/I2800759272","display_name":"Center for Advanced Studies Research and Development in Sardinia","ror":"https://ror.org/03jdxdk20","country_code":"IT","type":"facility","lineage":["https://openalex.org/I2800759272"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianluigi Zanetti","raw_affiliation_strings":["CRS4, Pula, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4, Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047833562"],"corresponding_institution_ids":["https://openalex.org/I172446870"],"apc_list":null,"apc_paid":null,"fwci":4.8824,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.95508226,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"184","last_page":"191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9943000078201294,"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":0.9943000078201294,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9847000241279602,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9840999841690063,"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/adapter","display_name":"Adapter (computing)","score":0.784695029258728},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7669229507446289},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6436150074005127},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5357012152671814},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3104930520057678},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2994542121887207}],"concepts":[{"id":"https://openalex.org/C177284502","wikidata":"https://www.wikidata.org/wiki/Q1005390","display_name":"Adapter (computing)","level":2,"score":0.784695029258728},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7669229507446289},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6436150074005127},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5357012152671814},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3104930520057678},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2994542121887207}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2649387.2649429","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2649387.2649429","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2649387.2649429","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/2649387.2649429","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2649387.2649429","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2649387.2649429","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320313987","display_name":"Universit\u00e0 degli Studi di Cagliari","ror":"https://ror.org/003109y17"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2054924729.pdf","grobid_xml":"https://content.openalex.org/works/W2054924729.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W24820730","https://openalex.org/W126044612","https://openalex.org/W1548849615","https://openalex.org/W1780933788","https://openalex.org/W1977046764","https://openalex.org/W2031634592","https://openalex.org/W2050320831","https://openalex.org/W2051039710","https://openalex.org/W2055043387","https://openalex.org/W2063652569","https://openalex.org/W2081930221","https://openalex.org/W2089319449","https://openalex.org/W2097464861","https://openalex.org/W2105805010","https://openalex.org/W2117798581","https://openalex.org/W2136482257","https://openalex.org/W2141978878","https://openalex.org/W2172143128","https://openalex.org/W2172194140","https://openalex.org/W2173213060","https://openalex.org/W2913266250","https://openalex.org/W6808202158"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2133028525","https://openalex.org/W4306381730","https://openalex.org/W4229060448","https://openalex.org/W2981692913","https://openalex.org/W3184035966","https://openalex.org/W3044188621","https://openalex.org/W2160602540","https://openalex.org/W2485605994","https://openalex.org/W3181407718"],"abstract_inverted_index":{"In":[0],"this":[1,21,96],"work":[2],"we":[3],"present":[4],"a":[5,35,41,53,92],"strategy":[6,27],"to":[7,49,63,103],"integrate":[8],"Hadoop-based":[9,83,117],"applications":[10,84],"into":[11],"the":[12,31,47,60,71,105,114,122],"Galaxy":[13,37,88],"platform":[14],"along":[15],"with":[16,128],"an":[17],"extensible":[18],"implementation":[19],"of":[20,33,43,87,108,116,126],"adapter":[22,80,98],"and":[23,57],"related":[24],"utilities.":[25],"The":[26,79],"is":[28],"based":[29],"on":[30,52,66],"idea":[32],"introducing":[34],"new":[36],"datatype":[38],"that":[39],"provides":[40],"layer":[42],"indirection,":[44],"thus":[45],"relaxing":[46],"requirement":[48],"place":[50],"data":[51,62],"Galaxy-accessible":[54],"file":[55],"system":[56],"instead":[58],"allowing":[59],"referenced":[61],"be":[64],"placed":[65],"any":[67],"addressable":[68],"space,":[69],"including":[70],"Hadoop":[72],"Distributed":[73],"File":[74],"System":[75],"or":[76],"Amazon":[77],"S3.":[78],"supports":[81],"using":[82],"as":[85],"part":[86],"workflows.":[89],"We":[90],"demonstrate":[91],"practical":[93],"application":[94],"where":[95],"Hadoop-Galaxy":[97],"was":[99],"used":[100],"at":[101],"CRS4":[102],"accelerate":[104],"bioinformatics":[106],"analysis":[107],"viral":[109],"vector":[110],"integration":[111],"sites":[112],"through":[113],"introduction":[115],"computation":[118],"components,":[119],"while":[120],"keeping":[121],"workflow":[123],"under":[124],"control":[125],"biologists":[127],"little":[129],"specific":[130],"technical":[131],"training.":[132]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
