{"id":"https://openalex.org/W2126716774","doi":"https://doi.org/10.1109/ispass.2005.1430554","title":"BioBench: A Benchmark Suite of Bioinformatics Applications","display_name":"BioBench: A Benchmark Suite of Bioinformatics Applications","publication_year":2005,"publication_date":"2005-01-01","ids":{"openalex":"https://openalex.org/W2126716774","doi":"https://doi.org/10.1109/ispass.2005.1430554","mag":"2126716774"},"language":"en","primary_location":{"id":"doi:10.1109/ispass.2005.1430554","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ispass.2005.1430554","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE International Symposium on Performance Analysis of Systems and Software, 2005. ISPASS 2005.","raw_type":"proceedings-article"},"type":"conference-paper","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/A5084412267","display_name":"Kursad Albayraktaroglu","orcid":null},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Albayraktaroglu","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","Dept. of Electr. & Comput. Eng., Maryland Univ., College Park, MD"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Maryland Univ., College Park, MD","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078825915","display_name":"Aamer Jaleel","orcid":"https://orcid.org/0000-0002-5709-2992"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Jaleel","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","Dept. of Electr. & Comput. Eng., Maryland Univ., College Park, MD"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Maryland Univ., College Park, MD","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101551790","display_name":"Xue Wu","orcid":"https://orcid.org/0000-0002-0511-9436"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xue Wu","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081181254","display_name":"M. Franklin","orcid":"https://orcid.org/0000-0002-2650-216X"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Franklin","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","[Department of Electrical and Computer Engineering, University of Maryland College Park, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"[Department of Electrical and Computer Engineering, University of Maryland College Park, USA]","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047597896","display_name":"Bruce Jacob","orcid":"https://orcid.org/0009-0005-3493-8245"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Jacob","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","[Department of Electrical and Computer Engineering, University of Maryland College Park, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"[Department of Electrical and Computer Engineering, University of Maryland College Park, USA]","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110090957","display_name":"Chau\u2010Wen Tseng","orcid":null},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chau-Wen Tseng","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042239243","display_name":"Donald Yeung","orcid":"https://orcid.org/0000-0003-0341-2644"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Yeung","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","[Department of Electrical and Computer Engineering, University of Maryland College Park, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"[Department of Electrical and Computer Engineering, University of Maryland College Park, USA]","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":null,"apc_paid":null,"fwci":9.8738,"has_fulltext":false,"cited_by_count":186,"citation_normalized_percentile":{"value":0.98652713,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"2","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.996999979019165,"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"}},"topics":[{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.996999979019165,"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/T11269","display_name":"Algorithms and Data Compression","score":0.995199978351593,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9941999912261963,"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/spec#","display_name":"Spec#","score":0.9526416063308716},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.8247684240341187},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7809076309204102},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7664215564727783},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5965276956558228},{"id":"https://openalex.org/keywords/microarchitecture","display_name":"Microarchitecture","score":0.4803389310836792},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4741375148296356},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3692944645881653},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3272387981414795},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.27193185687065125},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18166056275367737},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1253361999988556}],"concepts":[{"id":"https://openalex.org/C2778565505","wikidata":"https://www.wikidata.org/wiki/Q2207566","display_name":"Spec#","level":2,"score":0.9526416063308716},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.8247684240341187},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7809076309204102},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7664215564727783},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5965276956558228},{"id":"https://openalex.org/C107598950","wikidata":"https://www.wikidata.org/wiki/Q259864","display_name":"Microarchitecture","level":2,"score":0.4803389310836792},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4741375148296356},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3692944645881653},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3272387981414795},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.27193185687065125},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18166056275367737},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1253361999988556},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/ispass.2005.1430554","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ispass.2005.1430554","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE International Symposium on Performance Analysis of Systems and Software, 2005. ISPASS 2005.","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.486.1059","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.486.1059","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://drum.lib.umd.edu/bitstream/1903/7455/1/BioBench_rights.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.74.2449","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.74.2449","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.eng.umd.edu/~blj/papers/ispass2005.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.79.5786","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.79.5786","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://maggini.eng.umd.edu/pub/biobench.pdf","raw_type":"text"},{"id":"pmh:oai:drum.lib.umd.edu:1903/7455","is_oa":false,"landing_page_url":"http://hdl.handle.net/1903/7455","pdf_url":null,"source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Presentation"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307762","display_name":"International Business Machines Corporation","ror":"https://ror.org/05hh8d621"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1960771887","https://openalex.org/W2015292449","https://openalex.org/W2046621940","https://openalex.org/W2055043387","https://openalex.org/W2094031081","https://openalex.org/W2106882534","https://openalex.org/W2117285153","https://openalex.org/W2125955291","https://openalex.org/W2133904766","https://openalex.org/W2140277987","https://openalex.org/W2151831732","https://openalex.org/W2152331922","https://openalex.org/W2159497035","https://openalex.org/W2168589623","https://openalex.org/W3199943451","https://openalex.org/W4236236547","https://openalex.org/W4249006057","https://openalex.org/W4254879828","https://openalex.org/W6680225039","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W3082894236","https://openalex.org/W2142488884","https://openalex.org/W1838930658","https://openalex.org/W2186315912","https://openalex.org/W4252566889","https://openalex.org/W2168654016","https://openalex.org/W2108305176","https://openalex.org/W2805359884","https://openalex.org/W2810686047","https://openalex.org/W2135158039"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,8,61,114,157,183,221],"bioinformatics":[3,54,77,103,134,212,233],"and":[4,49,79,163,178,197,228,243,256],"the":[5,23,34,39,62,70,90,107,158,219,224],"significant":[6],"increase":[7],"computational":[9],"power":[10],"available":[11,264],"to":[12,18,45,57,110,175,240,265],"researchers":[13,266],"have":[14,85,214],"made":[15,262],"it":[16],"possible":[17],"make":[19],"better":[20],"use":[21],"of":[22,26,41,51,64,73,98,102,133,139,189,223,250],"vast":[24],"amounts":[25],"genetic":[27,42],"data":[28,43,259],"that":[29,128,211,232,245],"has":[30],"been":[31],"collected":[32],"over":[33],"last":[35],"two":[36],"decades.":[37],"As":[38],"uses":[40],"expand":[44],"include":[46],"drug":[47],"discovery":[48],"development":[50],"gene-based":[52],"therapies,":[53],"is":[55],"destined":[56],"take":[58],"its":[59],"place":[60],"forefront":[63],"scientific":[65],"computing":[66],"application":[67,145],"domains.":[68],"Despite":[69],"clear":[71],"importance":[72],"this":[74,115,119,121],"field,":[75],"common":[76,100],"applications":[78,142,156,182,213,220],"their":[80,247],"implication":[81],"on":[82,151,168],"microarchitectural":[83],"design":[84],"received":[86],"scant":[87],"attention":[88],"from":[89,143,218,237],"computer":[91],"architecture":[92],"community":[93],"so":[94],"far.":[95],"The":[96,136,155,252],"availability":[97],"a":[99,125,130,148,169,186],"set":[101,132],"benchmarks":[104],"could":[105],"be":[106,261],"first":[108,137],"step":[109],"motivate":[111],"further":[112],"research":[113],"crucial":[116],"area.":[117],"To":[118],"end,":[120],"paper":[122],"presents":[123],"BioBench,":[124],"benchmark":[126,159],"suite":[127,255],"represents":[129],"diverse":[131],"applications.":[135,154,207],"version":[138],"BioBench":[140,184,254],"includes":[141],"different":[144,216],"domains,":[146],"with":[147],"particular":[149],"emphasis":[150],"mature":[152],"genomics":[153],"are":[160,172],"described":[161],"briefly,":[162],"basic":[164],"execution":[165],"characteristics":[166,217],"obtained":[167],"real":[170],"processor":[171],"presented.":[173],"Compared":[174],"SPEC":[176,179,202,205,226],"INT":[177,203],"FP":[180,206],"benchmarks,":[181],"display":[185],"higher":[187,198],"percentage":[188],"load/store":[190],"instructions,":[191],"almost":[192],"negligible":[193],"floating-point":[194],"operation":[195],"content,":[196],"IPC":[199],"than":[200],"either":[201],"or":[204],"Our":[208],"evaluation":[209],"suggests":[210],"distinctly":[215],"both":[222],"mentioned":[225],"suites;":[227],"our":[229],"findings":[230],"indicate":[231],"workloads":[234],"can":[235],"benefit":[236],"architectural":[238],"improvements":[239],"memory":[241],"bandwidth":[242],"techniques":[244],"exploit":[246],"high":[248],"levels":[249],"ILP.":[251],"entire":[253],"accompanying":[257],"reference":[258],"will":[260],"freely":[263]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":21},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":11}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
