{"id":"https://openalex.org/W3175564103","doi":"https://doi.org/10.1109/ipdpsw52791.2021.00037","title":"GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping","display_name":"GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping","publication_year":2021,"publication_date":"2021-06-01","ids":{"openalex":"https://openalex.org/W3175564103","doi":"https://doi.org/10.1109/ipdpsw52791.2021.00037","mag":"3175564103"},"language":"en","primary_location":{"id":"doi:10.1109/ipdpsw52791.2021.00037","doi":"https://doi.org/10.1109/ipdpsw52791.2021.00037","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw52791.2021.00037","pdf_url":null,"source":{"id":"https://openalex.org/S4393918253","display_name":"IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum","issn_l":"2164-7062","issn":["2164-7062"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","is_traditional":true,"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/A5030882331","display_name":"Gulsum Gudukbay Akbulut","orcid":"https://orcid.org/0000-0002-1767-2204","observed_orcids":["https://orcid.org/0000-0002-1767-2204"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gulsum Gudukbay","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104087483","display_name":"Jashwant Raj Gunasekaran","orcid":"https://orcid.org/0000-0001-9607-0131","observed_orcids":["https://orcid.org/0000-0001-9607-0131"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jashwant Raj Gunasekaran","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056312305","display_name":"Yilin Feng","orcid":"https://orcid.org/0000-0002-9927-5658","observed_orcids":["https://orcid.org/0000-0002-9927-5658"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yilin Feng","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007116603","display_name":"Mahmut Kandemir","orcid":"https://orcid.org/0000-0002-9940-9951","observed_orcids":["https://orcid.org/0000-0002-9940-9951"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahmut T. Kandemir","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065292926","display_name":"Anton Nekrutenko","orcid":"https://orcid.org/0000-0002-5987-8032","observed_orcids":["https://orcid.org/0000-0002-5987-8032"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anton Nekrutenko","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054027488","display_name":"Chita R. Das","orcid":"https://orcid.org/0000-0002-4746-7578","observed_orcids":["https://orcid.org/0000-0002-4746-7578"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chita R. Das","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066909672","display_name":"Paul Medvedev","orcid":"https://orcid.org/0000-0003-3143-594X","observed_orcids":["https://orcid.org/0000-0003-3143-594X"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Medvedev","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006559585","display_name":"Bj\u00f6rn Andreas Gr\u00fcning","orcid":"https://orcid.org/0000-0002-3079-6586","observed_orcids":["https://orcid.org/0000-0002-3079-6586","https://orcid.org/0000-0001-7364-821X"]},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bjorn Gruning","raw_affiliation_strings":["University of Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030446017","display_name":"Nate Coraor","orcid":"https://orcid.org/0000-0001-8083-2963","observed_orcids":["https://orcid.org/0000-0001-8083-2963"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nate Coraor","raw_affiliation_strings":["The Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091323463","display_name":"Nathan P. Roach","orcid":"https://orcid.org/0000-0001-9353-4615","observed_orcids":["https://orcid.org/0000-0001-9353-4615"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan Roach","raw_affiliation_strings":["Galaxyworks, Johns Hopkins University, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Galaxyworks, Johns Hopkins University, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006951727","display_name":"Enis Afgan","orcid":"https://orcid.org/0000-0003-0922-6711","observed_orcids":["https://orcid.org/0000-0003-0922-6711"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enis Afgan","raw_affiliation_strings":["Galaxyworks, Johns Hopkins University, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Galaxyworks, Johns Hopkins University, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9531,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.7112069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"194","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6377000212669373,"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":0.6377000212669373,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.23909999430179596,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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":0.093299999833107,"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/galaxies","display_name":"galaxies","score":0.6639999747276306},{"id":"https://openalex.org/keywords/gpu-acceleration","display_name":"GPU acceleration","score":0.6809999942779541},{"id":"https://openalex.org/keywords/job-scheduling","display_name":"job scheduling","score":0.46000000834465027},{"id":"https://openalex.org/keywords/bioinformatics-software","display_name":"bioinformatics software","score":0.6880000233650208},{"id":"https://openalex.org/keywords/genome-assembly","display_name":"genome assembly","score":0.6890000104904175},{"id":"https://openalex.org/keywords/high-performance-computing","display_name":"high-performance computing","score":0.640999972820282},{"id":"https://openalex.org/keywords/cluster-computing","display_name":"cluster computing","score":0.37700000405311584}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8298875093460083},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6306886672973633},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5139769911766052},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4673357903957367},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.44963639974594116},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.44775480031967163},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4384710192680359},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.4295244812965393},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.42839616537094116},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.362583190202713},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34948980808258057},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2356191873550415},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.2093239724636078},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10013484954833984}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/ipdpsw52791.2021.00037","doi":"https://doi.org/10.1109/ipdpsw52791.2021.00037","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdpsw52791.2021.00037","pdf_url":null,"source":{"id":"https://openalex.org/S4393918253","display_name":"IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum","issn_l":"2164-7062","issn":["2164-7062"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)","raw_type":"proceedings-article"},{"id":"pmh:oai:freidok.uni-freiburg.de:279282","doi":null,"is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/279282","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). - Piscataway, NJ, 2021. - 194-203, ISBN: 978-1-6654-3577-2","raw_type":"article_in_conference_proceedings"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W151564507","https://openalex.org/W1667652561","https://openalex.org/W1965522578","https://openalex.org/W2005457816","https://openalex.org/W2013173369","https://openalex.org/W2018580582","https://openalex.org/W2024872854","https://openalex.org/W2142549260","https://openalex.org/W2163112106","https://openalex.org/W2464597840","https://openalex.org/W2575750030","https://openalex.org/W2775139887","https://openalex.org/W2781907349","https://openalex.org/W2807042094","https://openalex.org/W2917207851","https://openalex.org/W3092929313","https://openalex.org/W4226251181","https://openalex.org/W4237761118","https://openalex.org/W4250981202"],"related_works":["https://openalex.org/W6912940995","https://openalex.org/W6939714891","https://openalex.org/W4229608894","https://openalex.org/W6911945956","https://openalex.org/W1997795555","https://openalex.org/W2776388614","https://openalex.org/W4226051960","https://openalex.org/W23318890","https://openalex.org/W3029928583","https://openalex.org/W2015552471"],"abstract_inverted_index":{"Galaxy":[0,33,75,104,139,143],"is":[1,7],"an":[2],"open-source":[3],"web-based":[4],"framework":[5,35,105],"that":[6,140],"widely":[8],"used":[9],"for":[10,58,95],"performing":[11],"computational":[12,22,92],"analyses":[13],"in":[14,74,82,138,173],"diverse":[15],"application":[16],"domains,":[17],"such":[18,42],"as":[19,43],"genome":[20],"assembly,":[21],"chemistry,":[23],"ecology,":[24],"and":[25,49,110,126,134,160,180],"epigenetics,":[26],"to":[27,145,195],"name":[28],"a":[29,89,130,149],"few.":[30],"The":[31],"current":[32,103],"software":[34],"runs":[36],"on":[37,148,163,170],"several":[38],"high-performance":[39],"computing":[40],"platforms":[41],"on-premise":[44],"clusters,":[45],"public":[46],"data":[47],"centers,":[48],"national":[50],"lab":[51],"supercomputers.":[52],"These":[53],"infrastructures":[54],"also":[55],"provide":[56],"support":[57,108],"state-of-the-art":[59],"accelerators":[60],"like":[61],"Graphical":[62],"Processing":[63],"Units":[64],"(GPUs).":[65],"When":[66],"coupled":[67],"with":[68],"accelerator":[69],"support,":[70],"the":[71,102,118,142,154,171,174,189,197,205,213,219],"tools":[72,98,113,144,159,194],"executing":[73],"can":[76],"benefit":[77],"from":[78,114],"massive":[79],"performance":[80,119],"gains":[81],"terms":[83],"of":[84,117,156,188,199],"computation":[85,132],"time,":[86],"thereby":[87],"allowing":[88],"more":[90],"robust":[91],"analysis":[93],"environment":[94],"researchers.":[96],"Despite":[97],"having":[99],"GPU":[100,167,201],"capabilities,":[101],"does":[106],"not":[107],"GPUs,":[109],"thus":[111],"prevents":[112],"taking":[115],"advantage":[116],"benefits":[120,198],"offered":[121],"by":[122],"GPUs.":[123],"We":[124,184],"present":[125],"experimentally":[127],"evaluate":[128],"GYAN,":[129],"GPU-aware":[131],"mapping":[133],"orchestration":[135],"functionality":[136],"implemented":[137],"allows":[141],"be":[146],"executed":[147],"GPU-enabled":[150],"cluster.":[151,175],"GYAN":[152,176],"has":[153],"capability":[155],"identifying":[157],"GPU-supported":[158],"scheduling":[161],"them":[162],"single":[164],"or":[165],"multiple":[166],"nodes":[168],"based":[169],"availability":[172],"supports":[177],"both":[178],"native":[179],"containerized":[181],"tool":[182,208,223],"execution.":[183],"performed":[185],"extensive":[186],"evaluations":[187],"implementation":[190],"using":[191,200],"popular":[192],"bio-engineering":[193],"demonstrate":[196],"technologies.":[202],"For":[203],"example,":[204],"Racon":[206],"consensus":[207],"executes":[209],"~2\u00d7":[210],"faster":[211],"than":[212],"regular":[214],"baseline":[215],"CPU-only":[216],"jobs,":[217],"while":[218],"Bonito":[220],"base":[221],"calling":[222],"shows":[224],"~50\u00d7":[225],"speedup.":[226]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2021-07-05T00:00:00"}