{"id":"https://openalex.org/W4409131840","doi":"https://doi.org/10.1109/hpec62836.2024.10938466","title":"On the Scalability of Computing Genomic Diversity Using SparkLeBLAST: A Feasibility Study","display_name":"On the Scalability of Computing Genomic Diversity Using SparkLeBLAST: A Feasibility Study","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4409131840","doi":"https://doi.org/10.1109/hpec62836.2024.10938466"},"language":"en","primary_location":{"id":"doi:10.1109/hpec62836.2024.10938466","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpec62836.2024.10938466","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE High Performance Extreme Computing Conference (HPEC)","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/A5113381396","display_name":"Ritvik Prabhu","orcid":"https://orcid.org/0000-0003-2757-9262"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ritvik Prabhu","raw_affiliation_strings":["Virginia Tech,Department of Computer Science,USA"],"affiliations":[{"raw_affiliation_string":"Virginia Tech,Department of Computer Science,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062060985","display_name":"Bernard Moussad","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard Moussad","raw_affiliation_strings":["Virginia Tech,Department of Computer Science,USA"],"affiliations":[{"raw_affiliation_string":"Virginia Tech,Department of Computer Science,USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103003875","display_name":"Karim Youssef","orcid":"https://orcid.org/0000-0003-4544-9613"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karim Youssef","raw_affiliation_strings":["Center for Applied Scientific Computing, Lawrence Livermore National Laboratory,USA"],"affiliations":[{"raw_affiliation_string":"Center for Applied Scientific Computing, Lawrence Livermore National Laboratory,USA","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042298121","display_name":"Emil Vatai","orcid":"https://orcid.org/0000-0001-7494-5048"},"institutions":[{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Emil Vatai","raw_affiliation_strings":["RIKEN Center for Computational Science,Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Computational Science,Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058539554","display_name":"Wu-chun Feng","orcid":"https://orcid.org/0000-0002-6015-0727"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu-Chun Feng","raw_affiliation_strings":["Virginia Tech,Department of Computer Science,USA"],"affiliations":[{"raw_affiliation_string":"Virginia Tech,Department of Computer Science,USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5113381396"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28221279,"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":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.9071000218391418,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.9071000218391418,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.902999997138977,"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/scalability","display_name":"Scalability","score":0.6936675310134888},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6627932786941528},{"id":"https://openalex.org/keywords/diversity","display_name":"Diversity (politics)","score":0.620191752910614},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.115386962890625}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6936675310134888},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6627932786941528},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.620191752910614},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.115386962890625},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/hpec62836.2024.10938466","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpec62836.2024.10938466","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE High Performance Extreme Computing Conference (HPEC)","raw_type":"proceedings-article"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/142238","is_oa":false,"landing_page_url":"https://hdl.handle.net/10919/142238","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1183173704","display_name":null,"funder_award_id":"1822080","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1494814522","display_name":null,"funder_award_id":"DE_AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G2917824471","display_name":null,"funder_award_id":"DE-AC52-07NA2734","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3140459243","display_name":null,"funder_award_id":"I/UCRC","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3391580208","display_name":null,"funder_award_id":"DE-AC52-07NA2","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G4275066514","display_name":null,"funder_award_id":"CNS-1822080","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4711444667","display_name":null,"funder_award_id":"DE-AC52-07NA2734","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G472215958","display_name":null,"funder_award_id":"1927880","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5816449448","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5964142490","display_name":null,"funder_award_id":"E-AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G6020043373","display_name":null,"funder_award_id":"DE-AC52-07NA2734","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G7806955302","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8374966015","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8658770765","display_name":null,"funder_award_id":"DE-AC52-07NA27","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G991281326","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320331904","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W2014365515","https://openalex.org/W2079942837","https://openalex.org/W2109861188","https://openalex.org/W2136977855","https://openalex.org/W2587970647","https://openalex.org/W2731251882","https://openalex.org/W2886161096","https://openalex.org/W3009109635","https://openalex.org/W3025620739","https://openalex.org/W3039901154","https://openalex.org/W3043722005","https://openalex.org/W3155717024","https://openalex.org/W4236236547","https://openalex.org/W4294147615","https://openalex.org/W4382983551","https://openalex.org/W6606052223"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2389214306"],"abstract_inverted_index":{"Studying":[0],"the":[1,42,60,132,147,164,167,177,192,211],"genomic":[2,33,92],"diversity":[3,34,93],"of":[4,95,106,135,166],"viruses":[5,11],"can":[6,17],"help":[7],"us":[8],"understand":[9],"how":[10,14,82],"evolve":[12],"and":[13,26,46,49,76,85,138,187],"that":[15,157],"evolution":[16],"impact":[18],"human":[19],"health.":[20],"Rather":[21],"than":[22,205],"use":[23],"a":[24,32,38,72,91,100,104,111,125,206],"laborious":[25],"tedious":[27],"wet-lab":[28],"approach":[29],"to":[30,89,115,130,175,195],"conduct":[31],"study,":[35,153],"we":[36,97],"take":[37,88,171],"computational":[39],"approach,":[40],"using":[41,127,183,210],"ubiquitous":[43,212],"NCBI":[44,136,158,213],"BLAST":[45,84,137],"our":[47,154,185],"parallel":[48],"distributed":[50],"SparkLeBLAST,":[51,182],"across":[52],"53":[53],"patients":[54],"(~40,000,000":[55],"query":[56,108,186],"sequences)":[57],"on":[58,103,140,146,162],"Fugaku,":[59],"world's":[61],"fastest":[62],"homogeneous":[63],"supercomputer":[64],"with":[65],"158,976":[66],"nodes,":[67],"where":[68],"each":[69],"code":[70],"contains":[71],"48-core":[73],"A64FX":[74],"processor":[75],"32":[77],"GB":[78],"RAM.":[79],"To":[80],"project":[81,131],"long":[83],"SparkLeBLAST":[86,139],"would":[87,170,190],"complete":[90,176],"study":[94,102],"COVID-19,":[96],"first":[98],"perform":[99],"feasibility":[101,152],"subset":[105],"50":[107],"sequences":[109],"from":[110,149],"single":[112],"COVID-19":[113],"patient":[114],"identify":[116],"bottlenecks":[117],"in":[118,203],"sequence":[119],"alignment":[120],"processing.":[121],"We":[122],"then":[123],"create":[124],"model":[126,155],"Amdahl's":[128],"law":[129],"run":[133],"times":[134],"supercomputing":[141],"systems":[142],"like":[143],"Fugaku.":[144],"Based":[145],"data":[148],"this":[150],"50-sequence":[151],"predicts":[156],"BLAST,":[159],"when":[160],"running":[161],"all":[163],"cores":[165],"Fugaku":[168],"supercomputer,":[169],"approximately":[172],"26.7":[173],"years":[174,197],"full-scale":[178],"study.":[179],"In":[180],"contrast,":[181],"both":[184],"database":[188],"segmentation,":[189],"reduce":[191],"execution":[193],"time":[194],"0.026":[196],"(i.e.,":[198],"22.9":[199],"hours)":[200],"\u2013":[201],"resulting":[202],"more":[204],"10,000\u00d7":[207],"speedup":[208],"over":[209],"BLAST.":[214]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
