{"id":"https://openalex.org/W2970106630","doi":"https://doi.org/10.1109/cloud.2019.00083","title":"Scalable Pathogen Pipeline Platform (SP^3): Enabling Unified Genomic Data Analysis with Elastic Cloud Computing","display_name":"Scalable Pathogen Pipeline Platform (SP^3): Enabling Unified Genomic Data Analysis with Elastic Cloud Computing","publication_year":2019,"publication_date":"2019-07-01","ids":{"openalex":"https://openalex.org/W2970106630","doi":"https://doi.org/10.1109/cloud.2019.00083","mag":"2970106630"},"language":"en","primary_location":{"id":"doi:10.1109/cloud.2019.00083","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cloud.2019.00083","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE 12th International Conference on Cloud Computing (CLOUD)","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/A5082592955","display_name":"Fan Yang-Turner","orcid":"https://orcid.org/0000-0001-9455-6787"},"institutions":[{"id":"https://openalex.org/I2802742124","display_name":"John Radcliffe Hospital","ror":"https://ror.org/0080acb59","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802742124","https://openalex.org/I4210127145","https://openalex.org/I4210147381"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Fan Yang-Turner","raw_affiliation_strings":["NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom","institution_ids":["https://openalex.org/I2802742124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086828108","display_name":"Denis Volk","orcid":null},"institutions":[{"id":"https://openalex.org/I2802742124","display_name":"John Radcliffe Hospital","ror":"https://ror.org/0080acb59","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802742124","https://openalex.org/I4210127145","https://openalex.org/I4210147381"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Denis Volk","raw_affiliation_strings":["NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom","institution_ids":["https://openalex.org/I2802742124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025309888","display_name":"Philip W. Fowler","orcid":"https://orcid.org/0000-0003-0912-4483"},"institutions":[{"id":"https://openalex.org/I2802742124","display_name":"John Radcliffe Hospital","ror":"https://ror.org/0080acb59","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802742124","https://openalex.org/I4210127145","https://openalex.org/I4210147381"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Philip Fowler","raw_affiliation_strings":["NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom","institution_ids":["https://openalex.org/I2802742124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064078365","display_name":"Jeremy Swann","orcid":"https://orcid.org/0000-0002-1475-8248"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jeremy Swann","raw_affiliation_strings":["NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom","institution_ids":["https://openalex.org/I348769827","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084609233","display_name":"Matthew Bull","orcid":"https://orcid.org/0000-0002-8701-0417"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew Bull","raw_affiliation_strings":["School of Biosciences, Cardiff University, Cardiff, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Cardiff University, Cardiff, United Kingdom","institution_ids":["https://openalex.org/I79510175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041276359","display_name":"Sarah Hoosdally","orcid":"https://orcid.org/0000-0001-7375-6907"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah Hoosdally","raw_affiliation_strings":["Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028687331","display_name":"Thomas R. Connor","orcid":"https://orcid.org/0000-0003-2394-6504"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thomas Connor","raw_affiliation_strings":["School of Biosciences, Cardiff University, Cardiff, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Cardiff University, Cardiff, United Kingdom","institution_ids":["https://openalex.org/I79510175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026480684","display_name":"Tim Peto","orcid":"https://orcid.org/0000-0003-3477-8307"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tim Peto","raw_affiliation_strings":["NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom","institution_ids":["https://openalex.org/I348769827","https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089282433","display_name":"Derrick W. Crook","orcid":"https://orcid.org/0000-0002-0590-2850"},"institutions":[{"id":"https://openalex.org/I348769827","display_name":"Public Health England","ror":"https://ror.org/00vbvha87","country_code":"GB","type":"government","lineage":["https://openalex.org/I1311074006","https://openalex.org/I348769827"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Derrick Crook","raw_affiliation_strings":["NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom","institution_ids":["https://openalex.org/I348769827","https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5082592955"],"corresponding_institution_ids":["https://openalex.org/I2802742124"],"apc_list":null,"apc_paid":null,"fwci":0.0859,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.47784861,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"9","issue":null,"first_page":"478","last_page":"480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9965000152587891,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.698112428188324},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6480462551116943},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6313974261283875},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5909090042114258},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5214421153068542},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34940481185913086},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2645004689693451},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2144966423511505},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20471754670143127}],"concepts":[{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.698112428188324},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6480462551116943},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6313974261283875},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5909090042114258},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5214421153068542},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34940481185913086},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2645004689693451},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2144966423511505},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20471754670143127}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/cloud.2019.00083","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cloud.2019.00083","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE 12th International Conference on Cloud Computing (CLOUD)","raw_type":"proceedings-article"},{"id":"pmh:oai:https://orca.cardiff.ac.uk:125841","is_oa":false,"landing_page_url":"https://orca.cardiff.ac.uk/125841/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401195","display_name":"ORCA Online Research @Cardiff (Cardiff University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79510175","host_organization_name":"Cardiff University","host_organization_lineage":["https://openalex.org/I79510175"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference or Workshop Item"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:d581fd3c-d772-4556-a281-aa91f70942cb","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:d581fd3c-d772-4556-a281-aa91f70942cb","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference item"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5199999809265137}],"awards":[{"id":"https://openalex.org/G6358829866","display_name":null,"funder_award_id":"BBS/E/F/000PR10348","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8005818532","display_name":null,"funder_award_id":"BBS/E/F/000PR10352","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8173229303","display_name":null,"funder_award_id":"MR/L015080/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1921615383","https://openalex.org/W2013469333","https://openalex.org/W2110041134","https://openalex.org/W2110417468","https://openalex.org/W2146902212","https://openalex.org/W2158485828","https://openalex.org/W2166022874","https://openalex.org/W2281036777","https://openalex.org/W2296335794","https://openalex.org/W2310259903","https://openalex.org/W2346143774","https://openalex.org/W2576576365","https://openalex.org/W2605897695","https://openalex.org/W2613409207","https://openalex.org/W2835610065","https://openalex.org/W2898347103","https://openalex.org/W4232188079","https://openalex.org/W6695237428","https://openalex.org/W6697144307"],"related_works":["https://openalex.org/W4244478748","https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W4223488648","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2134969820","https://openalex.org/W2251605416","https://openalex.org/W2560439919","https://openalex.org/W4389340727"],"abstract_inverted_index":{"Pathogen":[0,21],"genomic":[1,40,98,125,146],"data":[2,41,100,126,128,131,147],"analysis":[3,42,108],"can":[4],"be":[5],"extremely":[6],"bespoke":[7],"and":[8,15,32,38,66,72,87,106,130,140,149],"diverse.":[9],"This":[10],"paper":[11],"presents":[12],"our":[13],"plan":[14],"progress":[16],"towards":[17],"creating":[18],"a":[19,142],"Scalable":[20],"Pipeline":[22],"Platform":[23,83],"(SP":[24],"<sup":[25,51,75,91,116],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[26,52,76,92,117],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">3</sup>":[27,53,77,93,118],")":[28],"providing":[29],"an":[30],"efficient":[31],"unified":[33],"process":[34],"of":[35,46,137,144],"collecting,":[36],"analysing":[37],"comparing":[39],"with":[43,109],"the":[44,135],"benefit":[45],"elastic":[47],"cloud":[48,67,150],"computing.":[49],"SP":[50,74,90,115],"enables":[54],"container-centric":[55],"bioinformatic":[56,111],"workflows":[57],"run":[58],"on":[59,78],"personal":[60],"computers,":[61],"High-performance":[62],"computing":[63],"(HPC)":[64],"clusters":[65],"platforms.":[68],"We":[69,113],"have":[70],"deployed":[71],"tested":[73],"local":[79],"HPC,":[80],"Google":[81],"Cloud":[82],"(GCP),":[84],"Microsoft":[85],"Azure":[86],"OpenStack":[88],"Platforms.":[89],"allows":[94],"users":[95],"to":[96],"fetch":[97],"sequencing":[99],"from":[101],"European":[102],"Nucleotide":[103],"Archive":[104],"(ENA)":[105],"conduct":[107],"open-source":[110],"pipelines.":[112],"believe":[114],"will":[119],"promote":[120],"common":[121],"standards":[122],"around":[123],"pathogen":[124],"quality,":[127],"processing":[129],"analysis,":[132],"helping":[133],"answer":[134],"challenges":[136],"tools":[138],"divergence":[139],"leveraging":[141],"pool":[143],"public":[145],"repository":[148],"resources.":[151]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
