{"id":"https://openalex.org/W2031740815","doi":"https://doi.org/10.1145/1851476.1851550","title":"Data parallelism in bioinformatics workflows using Hydra","display_name":"Data parallelism in bioinformatics workflows using Hydra","publication_year":2010,"publication_date":"2010-06-21","ids":{"openalex":"https://openalex.org/W2031740815","doi":"https://doi.org/10.1145/1851476.1851550","mag":"2031740815"},"language":"en","primary_location":{"id":"doi:10.1145/1851476.1851550","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1851476.1851550","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing","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/A5103553263","display_name":"F\u00e1bio Coutinho","orcid":null},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"F\u00e1bio Coutinho","raw_affiliation_strings":["Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027399495","display_name":"Eduardo Ogasawara","orcid":"https://orcid.org/0000-0002-0466-0626"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Eduardo Ogasawara","raw_affiliation_strings":["Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050455034","display_name":"Daniel de Oliveira","orcid":"https://orcid.org/0000-0001-9346-7651"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Daniel de Oliveira","raw_affiliation_strings":["Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031131350","display_name":"Vanessa Braganholo","orcid":"https://orcid.org/0000-0002-1184-8192"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Vanessa Braganholo","raw_affiliation_strings":["Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101722865","display_name":"Alexandre A. B. Lima","orcid":"https://orcid.org/0000-0001-7486-0415"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alexandre A. B. Lima","raw_affiliation_strings":["Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024614936","display_name":"Alberto M. R. D\u00e1vila","orcid":"https://orcid.org/0000-0002-6918-7673"},"institutions":[{"id":"https://openalex.org/I52325","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08","country_code":"BR","type":"facility","lineage":["https://openalex.org/I52325"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alberto M. R. D\u00e1vila","raw_affiliation_strings":["Oswaldo Cruz Institute -- FIOCRUZ -- Rio de Janeiro Brazil"],"affiliations":[{"raw_affiliation_string":"Oswaldo Cruz Institute -- FIOCRUZ -- Rio de Janeiro Brazil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039896734","display_name":"Marta Mattoso","orcid":"https://orcid.org/0000-0002-0870-3371"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marta Mattoso","raw_affiliation_strings":["Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Rio de Janeiro - Rio de Janeiro -- Brazil","institution_ids":["https://openalex.org/I122140584"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5103553263"],"corresponding_institution_ids":["https://openalex.org/I122140584"],"apc_list":null,"apc_paid":null,"fwci":11.4338,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.97971911,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"507","last_page":"515"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9998999834060669,"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":0.9998999834060669,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9983999729156494,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.982699990272522,"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":0.8669611215591431},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8579517602920532},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.6040016412734985},{"id":"https://openalex.org/keywords/middleware","display_name":"Middleware (distributed applications)","score":0.5671525001525879},{"id":"https://openalex.org/keywords/task-parallelism","display_name":"Task parallelism","score":0.550135612487793},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.46113336086273193},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4522625803947449},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.43842145800590515},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.423300176858902},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3303842842578888},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3226662576198578},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.31751781702041626},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22077873349189758}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8669611215591431},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8579517602920532},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.6040016412734985},{"id":"https://openalex.org/C169468491","wikidata":"https://www.wikidata.org/wiki/Q146923","display_name":"Middleware (distributed applications)","level":2,"score":0.5671525001525879},{"id":"https://openalex.org/C42992933","wikidata":"https://www.wikidata.org/wiki/Q691169","display_name":"Task parallelism","level":3,"score":0.550135612487793},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.46113336086273193},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4522625803947449},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.43842145800590515},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.423300176858902},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3303842842578888},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3226662576198578},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.31751781702041626},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22077873349189758},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/1851476.1851550","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1851476.1851550","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.227.1991","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.227.1991","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://salsahpc.indiana.edu/ECMLS2010/papers/063.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1512650735","https://openalex.org/W1583683058","https://openalex.org/W1867390120","https://openalex.org/W1983704199","https://openalex.org/W1994174225","https://openalex.org/W2034551584","https://openalex.org/W2056771108","https://openalex.org/W2066460177","https://openalex.org/W2083564402","https://openalex.org/W2083792262","https://openalex.org/W2091257550","https://openalex.org/W2100948378","https://openalex.org/W2103803358","https://openalex.org/W2119805896","https://openalex.org/W2123130398","https://openalex.org/W2123663722","https://openalex.org/W2125320251","https://openalex.org/W2131229759","https://openalex.org/W2137653635","https://openalex.org/W2141088026","https://openalex.org/W2145154883","https://openalex.org/W2146917903","https://openalex.org/W2154055222","https://openalex.org/W2158502782","https://openalex.org/W2158527924","https://openalex.org/W2162528252","https://openalex.org/W2167500728","https://openalex.org/W2168281637","https://openalex.org/W2173213060","https://openalex.org/W2190206719","https://openalex.org/W2243768821","https://openalex.org/W2254543411","https://openalex.org/W4253109001","https://openalex.org/W6630572918"],"related_works":["https://openalex.org/W2375304607","https://openalex.org/W2391168633","https://openalex.org/W2035995658","https://openalex.org/W2353477037","https://openalex.org/W1574425962","https://openalex.org/W2385499106","https://openalex.org/W2354357087","https://openalex.org/W2352774566","https://openalex.org/W4243836028","https://openalex.org/W2376671203"],"abstract_inverted_index":{"Large":[0],"scale":[1],"bioinformatics":[2,53,149,167],"experiments":[3,54],"are":[4,35],"usually":[5],"composed":[6],"by":[7,14,127],"a":[8,15,66,129,159],"set":[9],"of":[10,17,80,98,182],"data":[11,63,100,145,164],"flows":[12],"generated":[13],"chain":[16],"activities":[18],"(programs":[19],"or":[20],"services)":[21],"that":[22,162],"may":[23],"be":[24],"modeled":[25],"as":[26],"scientific":[27],"workflows.":[28,168],"Current":[29],"Scientific":[30],"Workflow":[31],"Management":[32],"Systems":[33],"(SWfMS)":[34],"used":[36,69],"to":[37,41,55,70,116,134,155],"orchestrate":[38],"these":[39],"workflows":[40,172],"control":[42],"and":[43,73,123,151],"monitor":[44],"the":[45,118,121,124,179],"whole":[46],"execution.":[47],"It":[48],"is":[49,65,104],"very":[50,57],"common":[51,67],"in":[52,89,101,148,166],"process":[56],"large":[58],"datasets.":[59],"In":[60],"this":[61],"way,":[62],"parallelism":[64,146,165],"approach":[68],"increase":[71],"performance":[72,91,176],"reduce":[74],"overall":[75],"execution":[76],"time.":[77],"However,":[78],"most":[79],"current":[81],"SWfMS":[82,122],"still":[83,105],"lack":[84],"on":[85],"supporting":[86],"parallel":[87],"executions":[88,137],"high":[90],"computing":[92],"(HPC)":[93],"environments.":[94],"Additionally":[95],"keeping":[96],"track":[97],"provenance":[99,184],"distributed":[102,140,183],"environments":[103],"an":[106,153],"open,":[107],"yet":[108],"important":[109],"problem.":[110],"Recently,":[111],"Hydra":[112,156],"middleware":[113,157],"was":[114],"proposed":[115],"bridge":[117],"gap":[119],"between":[120],"HPC":[125],"environment,":[126],"providing":[128],"transparent":[130],"way":[131],"for":[132],"scientists":[133],"parallelize":[135],"workflow":[136],"while":[138],"capturing":[139],"provenance.":[141],"This":[142],"paper":[143],"analyzes":[144],"scenarios":[147],"domain":[150],"presents":[152],"extension":[154],"through":[158],"specific":[160],"cartridge":[161],"promotes":[163],"Experimental":[169],"results":[170],"using":[171],"with":[173,178],"BLAST":[174],"show":[175],"gains":[177],"additional":[180],"benefits":[181],"support.":[185]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
