{"id":"https://openalex.org/W1966420492","doi":"https://doi.org/10.1145/1851476.1851551","title":"Optimization of a parallel permutation testing function for the SPRINT R package","display_name":"Optimization of a parallel permutation testing function for the SPRINT R package","publication_year":2010,"publication_date":"2010-06-21","ids":{"openalex":"https://openalex.org/W1966420492","doi":"https://doi.org/10.1145/1851476.1851551","mag":"1966420492"},"language":"en","primary_location":{"id":"doi:10.1145/1851476.1851551","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1851476.1851551","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":true,"oa_status":"green","oa_url":"https://www.research.ed.ac.uk/en/publications/0cd26306-fd50-4c10-b089-0ef1bcdc7957","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089397522","display_name":"Savvas Petrou","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Savvas Petrou","raw_affiliation_strings":["James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK"],"affiliations":[{"raw_affiliation_string":"James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055159868","display_name":"Terence Sloan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Terence M. Sloan","raw_affiliation_strings":["James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK"],"affiliations":[{"raw_affiliation_string":"James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077447220","display_name":"Muriel Mewissen","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Muriel Mewissen","raw_affiliation_strings":["University of Edinburgh, Edinburgh, UK","University of Edinburgh, Edinburgh , UK"],"affiliations":[{"raw_affiliation_string":"University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Edinburgh, Edinburgh , UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064045642","display_name":"Thorsten Forster","orcid":"https://orcid.org/0000-0002-4483-3069"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thorsten Forster","raw_affiliation_strings":["University of Edinburgh, Edinburgh, UK","University of Edinburgh, Edinburgh , UK"],"affiliations":[{"raw_affiliation_string":"University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Edinburgh, Edinburgh , UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103114310","display_name":"Micha\u0142 Piotrowski","orcid":"https://orcid.org/0009-0002-6939-782X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michal Piotrowski","raw_affiliation_strings":["James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK"],"affiliations":[{"raw_affiliation_string":"James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055710686","display_name":"Bartosz Dobrzelecki","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bartosz Dobrzelecki","raw_affiliation_strings":["James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK"],"affiliations":[{"raw_affiliation_string":"James Clerk Maxwell Building, The King's Buildings, Edinburgh, UK","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5089397522"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2643,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5667727,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"516","last_page":"521"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9951000213623047,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9552000164985657,"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":0.7597501277923584},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.7151582837104797},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.7131339907646179},{"id":"https://openalex.org/keywords/permutation","display_name":"Permutation (music)","score":0.7122921943664551},{"id":"https://openalex.org/keywords/sprint","display_name":"Sprint","score":0.5646283626556396},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5574573874473572},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5112736225128174},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4059253931045532},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10620754957199097},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.0736408531665802}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7597501277923584},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7151582837104797},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.7131339907646179},{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.7122921943664551},{"id":"https://openalex.org/C2776868573","wikidata":"https://www.wikidata.org/wiki/Q46855","display_name":"Sprint","level":2,"score":0.5646283626556396},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5574573874473572},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5112736225128174},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4059253931045532},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10620754957199097},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0736408531665802},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/1851476.1851551","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1851476.1851551","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:pure.ed.ac.uk:openaire/0cd26306-fd50-4c10-b089-0ef1bcdc7957","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/0cd26306-fd50-4c10-b089-0ef1bcdc7957","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Petrou, S, Sloan, T, Mewissen, M, Forster, T, Piotrowski, M & Dobrzelecki, B 2010, 'Optimization of a parallel permutation testing function for the SPRINT R package', Paper presented at 19th ACM International Symposium on High Performance Distributed Computing , Chicago, United States, 20/06/10 - 25/06/10 pp. 516-521. https://doi.org/10.1145/1851476.1851551","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/0cd26306-fd50-4c10-b089-0ef1bcdc7957","is_oa":false,"landing_page_url":"http://hdl.handle.net/20.500.11820/0cd26306-fd50-4c10-b089-0ef1bcdc7957","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pure.ed.ac.uk:publications/49d8cf91-a221-44e1-889b-d250a3bda497","is_oa":false,"landing_page_url":"http://www.scopus.com/inward/record.url?scp=80054943286&partnerID=8YFLogxK","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"pmh:oai:pure.ed.ac.uk:openaire/0cd26306-fd50-4c10-b089-0ef1bcdc7957","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/0cd26306-fd50-4c10-b089-0ef1bcdc7957","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Petrou, S, Sloan, T, Mewissen, M, Forster, T, Piotrowski, M & Dobrzelecki, B 2010, 'Optimization of a parallel permutation testing function for the SPRINT R package', Paper presented at 19th ACM International Symposium on High Performance Distributed Computing , Chicago, United States, 20/06/10 - 25/06/10 pp. 516-521. https://doi.org/10.1145/1851476.1851551","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2758612644","display_name":null,"funder_award_id":"WT086696MA","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1537144204","https://openalex.org/W1963916765","https://openalex.org/W1982113214","https://openalex.org/W2010509152","https://openalex.org/W2040588881","https://openalex.org/W2113381189","https://openalex.org/W2166925272","https://openalex.org/W2796856748","https://openalex.org/W6660750587"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W2978247079","https://openalex.org/W2140163842","https://openalex.org/W2148708580","https://openalex.org/W1582436825","https://openalex.org/W1996803181","https://openalex.org/W2979588510"],"abstract_inverted_index":{"The":[0,14,40],"statistical":[1],"language":[2],"R":[3,75],"and":[4,56,78],"Bioconductor":[5],"package":[6,47],"are<br/>favoured":[7],"by":[8,19],"many":[9,26],"biostatisticians":[10],"for":[11,85],"processing":[12],"microarray<br/>data.":[13],"amount":[15],"of":[16,25,87],"data":[17],"produced":[18],"these":[20],"analyses":[21],"has<br/>reached":[22],"the":[23,58],"limits":[24],"common":[27],"bioinformatics":[28],"computing<br/>infrastructures.":[29],"High":[30],"Performance":[31],"Computing":[32],"(HPC)<br/>systems":[33],"offer":[34],"a":[35,46,70],"solution":[36],"to":[37,53,62,89],"this":[38,80],"issue.":[39],"Simple":[41],"Parallel":[42],"R<br/>INTerface":[43],"(SPRINT)":[44],"is":[45],"that":[48],"provides":[49],"biostatisticians<br/>with":[50],"easy":[51],"access":[52],"HPC":[54],"systems":[55],"allows":[57],"addition<br/>of":[59],"parallelized":[60,71],"functions":[61],"R.":[63],"This":[64],"paper":[65],"will":[66],"present<br/>how":[67],"we":[68],"added":[69],"permutation":[72],"testing":[73],"function<br/>in":[74],"using":[76],"SPRINT":[77],"how":[79],"function":[81],"performs":[82],"on":[83],"a<br/>supercomputer":[84],"executions":[86],"up":[88],"512":[90],"processes.":[91]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
