{"id":"https://openalex.org/W3089147664","doi":"https://doi.org/10.1109/compsac48688.2020.00-85","title":"Towards Aggregation Based I/O Optimization for Scaling Bioinformatics Applications","display_name":"Towards Aggregation Based I/O Optimization for Scaling Bioinformatics Applications","publication_year":2020,"publication_date":"2020-07-01","ids":{"openalex":"https://openalex.org/W3089147664","doi":"https://doi.org/10.1109/compsac48688.2020.00-85","mag":"3089147664"},"language":"en","primary_location":{"id":"doi:10.1109/compsac48688.2020.00-85","is_oa":false,"landing_page_url":"https://doi.org/10.1109/compsac48688.2020.00-85","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE 44th Annual Computers, Software, and Applications Conference (COMPSAC)","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/A5030360356","display_name":"Jack Stratton","orcid":null},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jack Stratton","raw_affiliation_strings":["Western Washington University"],"affiliations":[{"raw_affiliation_string":"Western Washington University","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001631971","display_name":"Michael Albert","orcid":"https://orcid.org/0009-0006-0659-7743"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael Albert","raw_affiliation_strings":["Western Washingon University"],"affiliations":[{"raw_affiliation_string":"Western Washingon University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065606222","display_name":"Quentin Jensen","orcid":null},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quentin Jensen","raw_affiliation_strings":["Western Washington University"],"affiliations":[{"raw_affiliation_string":"Western Washington University","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043471059","display_name":"M.T. Ismailov","orcid":null},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Max Ismailov","raw_affiliation_strings":["Western Washington University"],"affiliations":[{"raw_affiliation_string":"Western Washington University","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046109728","display_name":"Filip Jagodzinski","orcid":"https://orcid.org/0000-0001-7783-2241"},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Filip Jagodzinski","raw_affiliation_strings":["Western Washington University"],"affiliations":[{"raw_affiliation_string":"Western Washington University","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002465410","display_name":"Tanzima Islam","orcid":"https://orcid.org/0000-0003-2877-5871"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tanzima Islam","raw_affiliation_strings":["Texas State University"],"affiliations":[{"raw_affiliation_string":"Texas State University","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5030360356"],"corresponding_institution_ids":["https://openalex.org/I52669646"],"apc_list":null,"apc_paid":null,"fwci":0.1542,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52583168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":93},"biblio":{"volume":"8","issue":null,"first_page":"1250","last_page":"1255"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.809501051902771},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6730434894561768},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.621688723564148},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5350236892700195},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.43932023644447327},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4264051020145416},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4163437485694885},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.4162174463272095},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3432254195213318},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3282371163368225},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.20452415943145752},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.18190306425094604},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1806257665157318}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.809501051902771},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6730434894561768},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.621688723564148},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5350236892700195},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.43932023644447327},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4264051020145416},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4163437485694885},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.4162174463272095},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3432254195213318},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3282371163368225},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.20452415943145752},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.18190306425094604},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1806257665157318},{"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":[],"locations_count":1,"locations":[{"id":"doi:10.1109/compsac48688.2020.00-85","is_oa":false,"landing_page_url":"https://doi.org/10.1109/compsac48688.2020.00-85","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE 44th Annual Computers, Software, and Applications Conference (COMPSAC)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W37867413","https://openalex.org/W246421128","https://openalex.org/W1527654363","https://openalex.org/W1548178570","https://openalex.org/W1550602550","https://openalex.org/W1987474460","https://openalex.org/W2003329164","https://openalex.org/W2010628428","https://openalex.org/W2013238066","https://openalex.org/W2032756564","https://openalex.org/W2053632570","https://openalex.org/W2055043387","https://openalex.org/W2077210509","https://openalex.org/W2078837027","https://openalex.org/W2082667898","https://openalex.org/W2101786683","https://openalex.org/W2130479394","https://openalex.org/W2149208773","https://openalex.org/W2151319417","https://openalex.org/W2153457180","https://openalex.org/W2156871002","https://openalex.org/W2166373524","https://openalex.org/W2168292723","https://openalex.org/W2171268876","https://openalex.org/W2464287085","https://openalex.org/W2472368789","https://openalex.org/W2809360952","https://openalex.org/W2940261122","https://openalex.org/W4252909492"],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064","https://openalex.org/W1787170397","https://openalex.org/W4292347844"],"abstract_inverted_index":{"Bioinformatics":[0],"software":[1],"often":[2],"integrates":[3],"multiple":[4],"off-the-shelf":[5],"programs":[6],"into":[7,21],"a":[8,22,114,129],"single":[9],"compute":[10,65,96],"pipeline.":[11,133],"Each":[12],"stand-alone":[13],"program":[14,33],"generates":[15],"output,":[16],"that":[17,34,60],"is":[18,26,35],"frequently":[19],"saved":[20],"plain-text":[23],"file,":[24],"which":[25],"then":[27],"processed":[28,62],"as":[29,101],"input":[30],"by":[31,63],"the":[32,38,42,102,122,152],"responsible":[36],"for":[37],"next":[39],"stage":[40],"of":[41,58,71,79,104,128],"computation.":[43],"Modern":[44],"advances":[45],"in":[46,68],"genome":[47],"sequencing":[48],"and":[49,74,112,125,147,150],"protein":[50,130],"structure":[51],"resolution":[52],"methods":[53],"have":[54],"yielded":[55],"large":[56],"amounts":[57],"data,":[59],"when":[61],"bioinformatics":[64,157],"pipelines,":[66],"results":[67],"vast":[69],"numbers":[70],"file":[72,123],"reads":[73],"writes.":[75],"Since":[76],"computation":[77],"capabilities":[78],"large-scale":[80],"distributed":[81],"systems":[82],"grow":[83],"much":[84],"faster":[85],"than":[86],"their":[87],"I/O":[88,117],"bandwidth,":[89],"processing":[90],"such":[91],"big":[92],"data":[93,105],"using":[94],"these":[95],"pipelines":[97],"will":[98],"not":[99],"scale":[100,155],"amount":[103],"grows.":[106],"For":[107],"this":[108],"work,":[109],"we":[110],"motivate":[111],"demonstrate":[113],"dynamic":[115],"interception-based":[116],"analysis":[118,138,149],"tool":[119,139],"to":[120,144,154],"assess":[121],"read":[124],"write":[126],"characteristics":[127],"mutation":[131],"generation":[132],"We":[134],"discuss":[135],"how":[136],"our":[137],"can":[140],"be":[141],"further":[142],"extended":[143],"apply":[145],"compression":[146],"in-site":[148],"has":[151],"potential":[153],"I/O-intensive":[156],"applications":[158],"on":[159],"high":[160],"performance":[161],"computing":[162],"(HPC)":[163],"systems.":[164]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}