{"id":"https://openalex.org/W4405427401","doi":"https://doi.org/10.1145/3698587.3701354","title":"Impact of the Networking Infrastructure on the Performance of Variant Calling on Human Genomes in Commodity Clusters","display_name":"Impact of the Networking Infrastructure on the Performance of Variant Calling on Human Genomes in Commodity Clusters","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405427401","doi":"https://doi.org/10.1145/3698587.3701354"},"language":"en","primary_location":{"id":"doi:10.1145/3698587.3701354","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701354","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","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/A5071075112","display_name":"Manas Jyoti Das","orcid":"https://orcid.org/0009-0007-9268-4364"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]},{"id":"https://openalex.org/I87547150","display_name":"Southern Illinois University Edwardsville","ror":"https://ror.org/04cqs5j56","country_code":"US","type":"education","lineage":["https://openalex.org/I2801502357","https://openalex.org/I87547150"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Manas Jyoti Das","raw_affiliation_strings":["Southern Illinois Univ. Edwardsville, USA and University of Missouri"],"affiliations":[{"raw_affiliation_string":"Southern Illinois Univ. Edwardsville, USA and University of Missouri","institution_ids":["https://openalex.org/I87547150","https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087950601","display_name":"Praveen Rao","orcid":"https://orcid.org/0000-0002-1859-0438"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Praveen Rao","raw_affiliation_strings":["University of Missouri, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101518641","display_name":"Lisong Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lisong Xu","raw_affiliation_strings":["University of Nebraska-Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"University of Nebraska-Lincoln, USA","institution_ids":["https://openalex.org/I114395901"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071075112"],"corresponding_institution_ids":["https://openalex.org/I76835614","https://openalex.org/I87547150"],"apc_list":null,"apc_paid":null,"fwci":1.3153,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.87550327,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10367","display_name":"Agricultural Innovations and Practices","score":0.977400004863739,"subfield":{"id":"https://openalex.org/subfields/1100","display_name":"General Agricultural and Biological Sciences"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10367","display_name":"Agricultural Innovations and Practices","score":0.977400004863739,"subfield":{"id":"https://openalex.org/subfields/1100","display_name":"General Agricultural and Biological Sciences"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9767000079154968,"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/T11336","display_name":"Energy and Environment Impacts","score":0.9347000122070312,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/commodity","display_name":"Commodity","score":0.6760576963424683},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47582200169563293},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4557303190231323},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.38532453775405884},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15217673778533936},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14339491724967957},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08398336172103882},{"id":"https://openalex.org/keywords/finance","display_name":"Finance","score":0.07132408022880554}],"concepts":[{"id":"https://openalex.org/C2779439359","wikidata":"https://www.wikidata.org/wiki/Q317088","display_name":"Commodity","level":2,"score":0.6760576963424683},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47582200169563293},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4557303190231323},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.38532453775405884},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15217673778533936},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14339491724967957},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08398336172103882},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.07132408022880554}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3698587.3701354","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701354","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6299999952316284,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6752379851","display_name":null,"funder_award_id":"2201583","funder_id":"https://openalex.org/F4320323817","funder_display_name":"Universitas Brawijaya"}],"funders":[{"id":"https://openalex.org/F4320323817","display_name":"Universitas Brawijaya","ror":"https://ror.org/01wk3d929"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1598064945","https://openalex.org/W1904861952","https://openalex.org/W1983587324","https://openalex.org/W2017928178","https://openalex.org/W2022844530","https://openalex.org/W2104846587","https://openalex.org/W2108234281","https://openalex.org/W2121762798","https://openalex.org/W2141978878","https://openalex.org/W2159670728","https://openalex.org/W2160363604","https://openalex.org/W2302703011","https://openalex.org/W2395949150","https://openalex.org/W2396849069","https://openalex.org/W2398924165","https://openalex.org/W2527672088","https://openalex.org/W2785694006","https://openalex.org/W2888300707","https://openalex.org/W2889664156","https://openalex.org/W3024609823","https://openalex.org/W3093528466","https://openalex.org/W3094438816","https://openalex.org/W3211269552","https://openalex.org/W4205170775","https://openalex.org/W4378907379","https://openalex.org/W4386604401","https://openalex.org/W4387848929","https://openalex.org/W4401943814"],"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/W4396696052"],"abstract_inverted_index":{"A":[0],"whole":[1],"genome":[2,41,75],"sequence":[3],"of":[4,10,17,53,61,85,115,126,134,162,169,192],"a":[5,14,21,54,66,73,181,197],"human":[6,40],"can":[7,57,185],"consume":[8],"gigabytes":[9],"storage":[11],"space.":[12],"Analyzing":[13],"large":[15],"number":[16],"such":[18],"sequences":[19],"is":[20,65],"compute":[22],"and":[23,88,99],"memory":[24],"intensive":[25],"process.":[26],"In":[27,43],"this":[28,44],"regard,":[29],"cluster":[30,56,156],"computing":[31],"has":[32],"emerged":[33],"as":[34],"an":[35],"attractive":[36],"solution":[37],"for":[38,180],"large-scale":[39],"analysis.":[42],"paper,":[45],"we":[46],"investigate":[47],"how":[48],"the":[49,59,78,83,90,108,112,124,135,170,176,190],"underlying":[50],"networking":[51],"infrastructure":[52],"commodity":[55],"impact":[58],"performance":[60,84,184],"variant":[62,86,116,163],"calling,":[63],"which":[64],"key":[67],"task":[68],"to":[69,77,123,132,149,159,166],"identify":[70],"variations":[71],"in":[72,93,196],"human's":[74],"compared":[76],"reference":[79],"genome.":[80],"We":[81,103],"measured":[82],"calling":[87,117,164],"analyzed":[89],"network":[91,100,109,153,177],"traffic":[92],"16-node":[94],"clusters":[95],"with":[96,138],"different":[97],"hardware":[98],"bandwidth":[101,140,179],"configurations.":[102],"observed":[104],"that":[105,128],"by":[106],"increasing":[107],"link":[110,178],"bandwidth,":[111],"execution":[113,161],"time":[114],"did":[118],"not":[119],"improve":[120],"significantly":[121],"due":[122,165],"degree":[125],"parallelism":[127],"was":[129],"achievable":[130],"leading":[131,148],"underutilization":[133],"links.":[136],"However,":[137],"low":[139],"links,":[141],"data":[142],"shuffling":[143],"errors":[144],"become":[145],"more":[146],"likely":[147],"failures.":[150],"Furthermore,":[151],"higher":[152],"latency":[154],"among":[155],"nodes":[157],"led":[158],"slower":[160],"lower":[167],"utilization":[168],"processor":[171],"cores.":[172],"By":[173],"appropriately":[174],"choosing":[175],"cluster,":[182],"good":[183],"be":[186],"achieved":[187],"while":[188],"lowering":[189],"price":[191],"processing":[193],"genomes":[194],"especially":[195],"pay-as-you-go":[198],"pricing":[199],"model.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
