{"id":"https://openalex.org/W2285697638","doi":"https://doi.org/10.1145/2858656","title":"MASA","display_name":"MASA","publication_year":2016,"publication_date":"2016-02-24","ids":{"openalex":"https://openalex.org/W2285697638","doi":"https://doi.org/10.1145/2858656","mag":"2285697638"},"language":"en","primary_location":{"id":"doi:10.1145/2858656","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2858656","pdf_url":null,"source":{"id":"https://openalex.org/S2483380313","display_name":"ACM Transactions on Parallel Computing","issn_l":"2329-4949","issn":["2329-4949","2329-4957"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Parallel Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/2117/99739","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058639233","display_name":"Edans F. O. Sandes","orcid":"https://orcid.org/0000-0001-9502-7799"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Edans F. De O. Sandes","raw_affiliation_strings":["Department of Computer Science, University of Brasilia, Brazil, CEP"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, Brazil, CEP","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017532574","display_name":"Guillermo Miranda","orcid":null},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Guillermo Miranda","raw_affiliation_strings":["Barcelona Supercomputing Center, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074097057","display_name":"Xavier Martorell","orcid":"https://orcid.org/0000-0002-0417-3430"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Xavier Martorell","raw_affiliation_strings":["Barcelona Supercomputing Center and Universitat Politecnica de Catalunya, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center and Universitat Politecnica de Catalunya, Spain","institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075755125","display_name":"Eduard Ayguad\u00e9","orcid":"https://orcid.org/0000-0002-5146-103X"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Eduard Ayguade","raw_affiliation_strings":["Barcelona Supercomputing Center and Universitat Politecnica de Catalunya, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center and Universitat Politecnica de Catalunya, Spain","institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076465098","display_name":"George Teodoro","orcid":"https://orcid.org/0000-0001-6289-3914"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"George Teodoro","raw_affiliation_strings":["Department of Computer Science, University of Brasilia, Brazil, CEP"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, Brazil, CEP","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005717412","display_name":"Alba Cristina Magalh\u00e3es Alves de Melo","orcid":"https://orcid.org/0000-0001-5191-5209"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alba C. M. A. De Melo","raw_affiliation_strings":["Department of Computer Science, University of Brasilia, Brazil, CEP"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Brasilia, Brazil, CEP","institution_ids":["https://openalex.org/I150729083"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5058639233"],"corresponding_institution_ids":["https://openalex.org/I150729083"],"apc_list":null,"apc_paid":null,"fwci":1.5665,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.82988817,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2","issue":"4","first_page":"1","last_page":"31"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9836999773979187,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9760000109672546,"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/computer-science","display_name":"Computer science","score":0.8693126440048218},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.7878454327583313},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.75447678565979},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.71572345495224},{"id":"https://openalex.org/keywords/dataflow","display_name":"Dataflow","score":0.7046843767166138},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.6721261739730835},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.631696343421936},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.5737231969833374},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5304548144340515},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.44759446382522583},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1456248164176941}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8693126440048218},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.7878454327583313},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.75447678565979},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.71572345495224},{"id":"https://openalex.org/C96324660","wikidata":"https://www.wikidata.org/wiki/Q205446","display_name":"Dataflow","level":2,"score":0.7046843767166138},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.6721261739730835},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.631696343421936},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.5737231969833374},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5304548144340515},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.44759446382522583},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1456248164176941},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2858656","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2858656","pdf_url":null,"source":{"id":"https://openalex.org/S2483380313","display_name":"ACM Transactions on Parallel Computing","issn_l":"2329-4949","issn":["2329-4949","2329-4957"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Parallel Computing","raw_type":"journal-article"},{"id":"pmh:oai:upcommons.upc.edu:2117/99739","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/99739","pdf_url":null,"source":{"id":"https://openalex.org/S4210207057","display_name":"QRU Quaderns de Recerca en Urbanisme","issn_l":"2014-9689","issn":["2014-9689","2385-6777"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310322448","host_organization_name":"Q71272178","host_organization_lineage":["https://openalex.org/P4310322448"],"host_organization_lineage_names":["Q71272178"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:upcommons.upc.edu:2117/99739","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/99739","pdf_url":null,"source":{"id":"https://openalex.org/S4210207057","display_name":"QRU Quaderns de Recerca en Urbanisme","issn_l":"2014-9689","issn":["2014-9689","2385-6777"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310322448","host_organization_name":"Q71272178","host_organization_lineage":["https://openalex.org/P4310322448"],"host_organization_lineage_names":["Q71272178"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.49000000953674316}],"awards":[{"id":"https://openalex.org/G4054932317","display_name":null,"funder_award_id":"TIN2012-34557","funder_id":"https://openalex.org/F4320323737","funder_display_name":"Ministerio de Ciencia y Tecnolog\u00eda"},{"id":"https://openalex.org/G6683393770","display_name":null,"funder_award_id":"313931/2013-5,305208/2014-4,446297/2014-3","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G8199932365","display_name":null,"funder_award_id":"SGR1051","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"}],"funders":[{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320323737","display_name":"Ministerio de Ciencia y Tecnolog\u00eda","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1577019216","https://openalex.org/W1585577780","https://openalex.org/W1592614241","https://openalex.org/W1850429294","https://openalex.org/W1986228396","https://openalex.org/W1995106824","https://openalex.org/W2011652244","https://openalex.org/W2015915218","https://openalex.org/W2017972683","https://openalex.org/W2021342241","https://openalex.org/W2023226967","https://openalex.org/W2024704296","https://openalex.org/W2040528486","https://openalex.org/W2052601433","https://openalex.org/W2052870002","https://openalex.org/W2055043387","https://openalex.org/W2065461987","https://openalex.org/W2065783991","https://openalex.org/W2066732554","https://openalex.org/W2068448872","https://openalex.org/W2069453784","https://openalex.org/W2074231493","https://openalex.org/W2075871133","https://openalex.org/W2077252523","https://openalex.org/W2081977490","https://openalex.org/W2087064593","https://openalex.org/W2098232690","https://openalex.org/W2108215151","https://openalex.org/W2109710144","https://openalex.org/W2111953042","https://openalex.org/W2115324785","https://openalex.org/W2115965694","https://openalex.org/W2116377941","https://openalex.org/W2116567188","https://openalex.org/W2139596748","https://openalex.org/W2140917900","https://openalex.org/W2142677441","https://openalex.org/W2146379626","https://openalex.org/W2162256669","https://openalex.org/W2165654401","https://openalex.org/W2166292076","https://openalex.org/W2170896626","https://openalex.org/W2184473133","https://openalex.org/W3105244973","https://openalex.org/W3148748026","https://openalex.org/W3214380909","https://openalex.org/W6675949863"],"related_works":["https://openalex.org/W2293118914","https://openalex.org/W2356602486","https://openalex.org/W2998381397","https://openalex.org/W4236419692","https://openalex.org/W2171015181","https://openalex.org/W2621501241","https://openalex.org/W2208757713","https://openalex.org/W3177128669","https://openalex.org/W2991848348","https://openalex.org/W2352639277"],"abstract_inverted_index":{"Biological":[0],"sequence":[1,17,60],"alignment":[2,18,61],"is":[3,78,147],"a":[4,48,96,111],"very":[5,148],"popular":[6],"application":[7],"in":[8,70,124],"Bioinformatics,":[9],"used":[10],"routinely":[11],"worldwide.":[12],"Many":[13],"implementations":[14,30,132],"of":[15,58,85,99,152,175],"biological":[16,59],"algorithms":[19],"have":[20],"been":[21],"proposed":[22,165],"for":[23,133],"multicores,":[24],"GPUs,":[25],"FPGAs":[26],"and":[27,45,50,68,102,136,140],"CellBEs.":[28],"These":[29],"are":[31],"platform-specific;":[32],"porting":[33],"them":[34],"to":[35,80,120,170,173],"other":[36],"systems":[37],"requires":[38],"considerable":[39],"programming":[40],"effort.":[41],"This":[42],"article":[43],"proposes":[44],"evaluates":[46],"MASA,":[47],"flexible":[49],"customizable":[51],"software":[52],"architecture":[53],"that":[54,145,159],"enables":[55],"the":[56,83,163,176,180],"execution":[57],"applications":[62],"with":[63,74],"three":[64],"variants":[65],"(local,":[66],"global,":[67],"semiglobal)":[69],"multiple":[71,104],"hardware/software":[72],"platforms":[73],"block":[75,100,155,166],"pruning,":[76,167],"which":[77,116],"able":[79,169],"reduce":[81],"significantly":[82,161],"amount":[84],"data":[86],"processed.":[87],"To":[88],"attain":[89],"our":[90,153],"flexibility":[91],"goals,":[92],"we":[93],"also":[94],"propose":[95],"generic":[97,154],"version":[98],"pruning":[101,156],"developed":[103],"parallelization":[105,183],"strategies":[106],"as":[107],"building":[108],"blocks,":[109],"including":[110],"new":[112,181],"asynchronous":[113],"dataflow-based":[114,182],"parallelization,":[115],"may":[117],"be":[118],"combined":[119],"implement":[121],"efficient":[122],"aligners":[123],"different":[125],"platforms.":[126],"We":[127],"provide":[128],"four":[129],"MASA":[130,146],"aligner":[131],"multicores":[134],"(OmpSs":[135],"OpenMP),":[137],"GPU":[138],"(CUDA),":[139],"Intel":[141],"Phi":[142],"(OpenMP),":[143],"showing":[144],"flexible.":[149],"The":[150],"evaluation":[151],"strategy":[157],"shows":[158],"it":[160],"outperforms":[162],"previously":[164],"being":[168],"prune":[171],"up":[172],"66.5%":[174],"cells":[177],"when":[178],"using":[179],"strategy.":[184]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}
