{"id":"https://openalex.org/W1975904117","doi":"https://doi.org/10.1145/2488551.2488581","title":"A dynamic pipeline for RNA sequencing on multicore processors","display_name":"A dynamic pipeline for RNA sequencing on multicore processors","publication_year":2013,"publication_date":"2013-09-11","ids":{"openalex":"https://openalex.org/W1975904117","doi":"https://doi.org/10.1145/2488551.2488581","mag":"1975904117"},"language":"en","primary_location":{"id":"doi:10.1145/2488551.2488581","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2488551.2488581","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 20th European MPI Users' Group Meeting","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/A5018719028","display_name":"H\u00e8ctor Mart\u00ednez","orcid":"https://orcid.org/0000-0001-5891-4479"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"H\u00e9ctor Mart\u00ednez","raw_affiliation_strings":["Universidad Jaume I, Castell\u00f3n, Spain"],"affiliations":[{"raw_affiliation_string":"Universidad Jaume I, Castell\u00f3n, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005495520","display_name":"Joaqu\u00edn T\u00e1rraga","orcid":null},"institutions":[{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Joaqu\u00edn T\u00e1rraga","raw_affiliation_strings":["Centro de Investigaci\u00f3n, Pr\u00edncipe Felipe, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaci\u00f3n, Pr\u00edncipe Felipe, Valencia, Spain","institution_ids":["https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068938981","display_name":"Ignacio Medina","orcid":"https://orcid.org/0000-0003-0095-670X"},"institutions":[{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Ignacio Medina","raw_affiliation_strings":["Centro de Investigaci\u00f3n, Pr\u00edncipe Felipe, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaci\u00f3n, Pr\u00edncipe Felipe, Valencia, Spain","institution_ids":["https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090675958","display_name":"Sergio Barrachina","orcid":"https://orcid.org/0000-0003-4642-7467"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Sergio Barrachina","raw_affiliation_strings":["Universidad Jaume I, Castell\u00f3n, Spain"],"affiliations":[{"raw_affiliation_string":"Universidad Jaume I, Castell\u00f3n, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101773656","display_name":"Maribel Castillo","orcid":"https://orcid.org/0000-0002-2826-3086"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Maribel Castillo","raw_affiliation_strings":["Universidad Jaume I, Castell\u00f3n, Spain"],"affiliations":[{"raw_affiliation_string":"Universidad Jaume I, Castell\u00f3n, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074140420","display_name":"Joaqu\u0131\u0301n Dopazo","orcid":"https://orcid.org/0000-0003-3318-120X"},"institutions":[{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Joaqu\u00edn Dopazo","raw_affiliation_strings":["Centro de Investigaci\u00f3n, Pr\u00edncipe Felipe, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaci\u00f3n, Pr\u00edncipe Felipe, Valencia, Spain","institution_ids":["https://openalex.org/I4210165109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012806004","display_name":"Enrique S. Quintana\u2013Ort\u0301\u0131","orcid":"https://orcid.org/0000-0002-5454-165X"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Enrique S. Quintana-Ort\u00ed","raw_affiliation_strings":["Universidad Jaume I, Castell\u00f3n, Spain"],"affiliations":[{"raw_affiliation_string":"Universidad Jaume I, Castell\u00f3n, Spain","institution_ids":["https://openalex.org/I10902133"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5018719028"],"corresponding_institution_ids":["https://openalex.org/I10902133"],"apc_list":null,"apc_paid":null,"fwci":0.8773,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.72583793,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"235","last_page":"240"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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":0.993399977684021,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9822999835014343,"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/multi-core-processor","display_name":"Multi-core processor","score":0.8217188119888306},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8016293048858643},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7911020517349243},{"id":"https://openalex.org/keywords/posix-threads","display_name":"POSIX Threads","score":0.7348966598510742},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7189284563064575},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6332729458808899},{"id":"https://openalex.org/keywords/posix","display_name":"POSIX","score":0.4590733051300049},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2958054840564728},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.21820014715194702},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07019615173339844}],"concepts":[{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.8217188119888306},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8016293048858643},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7911020517349243},{"id":"https://openalex.org/C41138395","wikidata":"https://www.wikidata.org/wiki/Q928112","display_name":"POSIX Threads","level":3,"score":0.7348966598510742},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7189284563064575},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6332729458808899},{"id":"https://openalex.org/C532756234","wikidata":"https://www.wikidata.org/wiki/Q14658","display_name":"POSIX","level":2,"score":0.4590733051300049},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2958054840564728},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.21820014715194702},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07019615173339844},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2488551.2488581","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2488551.2488581","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 20th European MPI Users' Group Meeting","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1488229309","https://openalex.org/W1492601037","https://openalex.org/W1555915743","https://openalex.org/W2055770801","https://openalex.org/W2087064593","https://openalex.org/W2093931624","https://openalex.org/W2097065948","https://openalex.org/W2100955902","https://openalex.org/W2124985265","https://openalex.org/W2165606466","https://openalex.org/W2170551349"],"related_works":["https://openalex.org/W4230580429","https://openalex.org/W1901085887","https://openalex.org/W2556689029","https://openalex.org/W614734992","https://openalex.org/W4243833290","https://openalex.org/W2049324807","https://openalex.org/W4243850526","https://openalex.org/W2397962676","https://openalex.org/W2104952251","https://openalex.org/W2328678367"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,36,49,57,77,83,99],"concurrent":[3],"algorithm":[4],"for":[5,95],"mapping":[6],"short":[7],"and":[8,62],"long":[9],"RNA":[10],"sequences":[11],"on":[12,22,53,82],"multicore":[13,84],"processors.":[14],"Our":[15],"solution":[16],"processes":[17],"the":[18,32,43],"data,":[19],"initially":[20],"stored":[21],"disk,":[23],"in":[24,76],"batches":[25],"of":[26,35,42,72,104],"reads":[27],"which":[28],"are":[29],"passed":[30],"between":[31,60],"consecutive":[33],"stages":[34],"pipeline.":[37,79],"A":[38],"major":[39],"operational":[40],"reorganization":[41,89],"original":[44],"static":[45],"pipeline,":[46],"combined":[47],"with":[48,98],"complete":[50],"reimplementation":[51],"based":[52],"POSIX":[54],"threads,":[55],"renders":[56],"dissociated":[58],"execution":[59],"threads":[61,67],"stages/task":[63],"types,":[64],"so":[65],"that":[66,87],"can":[68],"compute":[69],"any":[70],"type":[71],"pending":[73],"task":[74],"resulting":[75],"dynamic":[78],"The":[80],"experiments":[81],"platform":[85],"reveal":[86],"this":[88],"yields":[90],"significantly":[91],"higher":[92],"performance,":[93],"specially":[94],"architectures":[96],"equipped":[97],"small":[100],"to":[101],"moderate":[102],"number":[103],"cores.":[105]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}