{"id":"https://openalex.org/W2033643965","doi":"https://doi.org/10.1109/hpcsim.2014.6903742","title":"An automated infrastructure to support high-throughput bioinformatics","display_name":"An automated infrastructure to support high-throughput bioinformatics","publication_year":2014,"publication_date":"2014-07-01","ids":{"openalex":"https://openalex.org/W2033643965","doi":"https://doi.org/10.1109/hpcsim.2014.6903742","mag":"2033643965"},"language":"en","primary_location":{"id":"doi:10.1109/hpcsim.2014.6903742","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpcsim.2014.6903742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 International Conference on High Performance Computing & Simulation (HPCS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086775972","display_name":"Gianmauro Cuccuru","orcid":"https://orcid.org/0000-0002-5335-545X"},"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":true,"raw_author_name":"Gianmauro Cuccuru","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"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/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":"Simone Leo","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047695542","display_name":"Luca Lianas","orcid":"https://orcid.org/0000-0002-7123-6948"},"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":"Luca Lianas","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086776266","display_name":"Michele Muggiri","orcid":null},"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":"Michele Muggiri","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019342840","display_name":"Andr\u00e9a Pinna","orcid":"https://orcid.org/0000-0002-2388-7404"},"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":"Andrea Pinna","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047833562","display_name":"Luca Pireddu","orcid":"https://orcid.org/0000-0002-4663-5613"},"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":"Luca Pireddu","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057833674","display_name":"Paolo Uva","orcid":"https://orcid.org/0000-0002-9524-8492"},"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":"Paolo Uva","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030573407","display_name":"Andrea Angius","orcid":"https://orcid.org/0000-0003-2596-6461"},"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":"Andrea Angius","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023364868","display_name":"Giorgio Fotia","orcid":null},"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":"Giorgio Fotia","raw_affiliation_strings":["CRS4 Pula, Italy","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, 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","CRS4, Pula, CA, Italy"],"affiliations":[{"raw_affiliation_string":"CRS4 Pula, Italy","institution_ids":["https://openalex.org/I2800759272"]},{"raw_affiliation_string":"CRS4, Pula, CA, Italy","institution_ids":["https://openalex.org/I2800759272"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5086775972"],"corresponding_institution_ids":["https://openalex.org/I2800759272"],"apc_list":null,"apc_paid":null,"fwci":4.0686,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.94671991,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"600","last_page":"607"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.998199999332428,"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":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9927999973297119,"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":0.7884336709976196},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.6417026519775391},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.632177472114563},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.6151718497276306},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5978633165359497},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5595828890800476},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.5020797252655029},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.47865211963653564},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.40646275877952576},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.324749231338501},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2876865267753601},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13239583373069763},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10293352603912354}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7884336709976196},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.6417026519775391},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.632177472114563},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.6151718497276306},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5978633165359497},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5595828890800476},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.5020797252655029},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.47865211963653564},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40646275877952576},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.324749231338501},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2876865267753601},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13239583373069763},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10293352603912354},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/hpcsim.2014.6903742","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpcsim.2014.6903742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 International Conference on High Performance Computing & Simulation (HPCS)","raw_type":"proceedings-article"},{"id":"pmh:oai:iris.unica.it:11584/85072","is_oa":false,"landing_page_url":"http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6903742&tag=1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196293","display_name":"UNICA IRIS Institutional Research Information System (University of Cagliari)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172446870","host_organization_name":"University of Cagliari","host_organization_lineage":["https://openalex.org/I172446870"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.6499999761581421,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1548849615","https://openalex.org/W1598064945","https://openalex.org/W1967841763","https://openalex.org/W1974694769","https://openalex.org/W1990073900","https://openalex.org/W2015873366","https://openalex.org/W2019971954","https://openalex.org/W2031634592","https://openalex.org/W2040959789","https://openalex.org/W2050616093","https://openalex.org/W2051039710","https://openalex.org/W2061906497","https://openalex.org/W2063652569","https://openalex.org/W2071533485","https://openalex.org/W2081930221","https://openalex.org/W2089319449","https://openalex.org/W2096192437","https://openalex.org/W2096394186","https://openalex.org/W2098380237","https://openalex.org/W2102231480","https://openalex.org/W2108370395","https://openalex.org/W2116797609","https://openalex.org/W2117798581","https://openalex.org/W2120090897","https://openalex.org/W2127093546","https://openalex.org/W2136482257","https://openalex.org/W2141978878","https://openalex.org/W2144610372","https://openalex.org/W4298068285"],"related_works":["https://openalex.org/W4389670110","https://openalex.org/W2187546663","https://openalex.org/W2429057255","https://openalex.org/W148745890","https://openalex.org/W2611942503","https://openalex.org/W2899790217","https://openalex.org/W1576092969","https://openalex.org/W4315621326","https://openalex.org/W2598865957","https://openalex.org/W2359178629"],"abstract_inverted_index":{"The":[0,117],"number":[1,75],"of":[2,46,76,104,107],"domains":[3],"affected":[4],"by":[5,61,86,111,125],"the":[6,24,47,98,102,105,108,112,136],"big":[7],"data":[8,27,55,109,138],"phenomenon":[9],"is":[10,43],"constantly":[11],"increasing,":[12],"both":[13],"in":[14,101],"science":[15],"and":[16,79,84],"industry,":[17],"with":[18,36,53],"high-throughput":[19],"DNA":[20],"sequencers":[21],"being":[22],"among":[23],"most":[25],"massive":[26],"producers.":[28],"Building":[29],"analysis":[30,106,147],"frameworks":[31],"that":[32,133],"can":[33,134],"keep":[34],"up":[35],"such":[37],"a":[38,73,131],"high":[39],"production":[40],"rate,":[41],"however,":[42],"only":[44],"part":[45],"problem:":[48],"current":[49],"challenges":[50],"include":[51],"dealing":[52],"articulated":[54],"repositories":[56],"where":[57,68],"objects":[58],"are":[59],"connected":[60],"multiple":[62],"relationships,":[63],"managing":[64],"complex":[65],"processing":[66],"pipelines":[67],"each":[69],"step":[70],"depends":[71],"on":[72],"large":[74],"configuration":[77],"parameters":[78],"ensuring":[80],"reproducibility,":[81],"error":[82],"control":[83],"usability":[85],"non-technical":[87],"staff.":[88],"Here":[89],"we":[90],"describe":[91],"an":[92],"automated":[93],"infrastructure":[94],"built":[95],"to":[96,145],"address":[97],"above":[99],"issues":[100],"context":[103],"produced":[110],"CRS4":[113],"next-generation":[114],"sequencing":[115],"facility.":[116],"system":[118],"integrates":[119],"open":[120],"source":[121],"tools,":[122],"either":[123],"written":[124],"us":[126],"or":[127],"publicly":[128],"available,":[129],"into":[130],"framework":[132],"handle":[135],"whole":[137],"transformation":[139],"process,":[140],"from":[141],"raw":[142],"sequencer":[143],"output":[144],"primary":[146],"results.":[148]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}