{"id":"https://openalex.org/W2810797492","doi":"https://doi.org/10.1109/empdp.2019.8671623","title":"Reproducible Data Analysis Pipelines for Precision Medicine","display_name":"Reproducible Data Analysis Pipelines for Precision Medicine","publication_year":2019,"publication_date":"2019-02-01","ids":{"openalex":"https://openalex.org/W2810797492","doi":"https://doi.org/10.1109/empdp.2019.8671623","mag":"2810797492"},"language":"en","primary_location":{"id":"doi:10.1109/empdp.2019.8671623","is_oa":false,"landing_page_url":"https://doi.org/10.1109/empdp.2019.8671623","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5047783097","display_name":"Bj\u00f8rn Fjukstad","orcid":"https://orcid.org/0000-0001-8024-5881"},"institutions":[{"id":"https://openalex.org/I78037679","display_name":"UiT The Arctic University of Norway","ror":"https://ror.org/00wge5k78","country_code":"NO","type":"education","lineage":["https://openalex.org/I78037679"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Bjorn Fjukstad","raw_affiliation_strings":["Department of Computer Science, UiT The Arctic University of Norway, Troms\u00f8, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, UiT The Arctic University of Norway, Troms\u00f8, Norway","institution_ids":["https://openalex.org/I78037679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067257359","display_name":"Vanessa Dumeaux","orcid":"https://orcid.org/0000-0002-1280-6541"},"institutions":[{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Vanessa Dumeaux","raw_affiliation_strings":["PERFORM Centre, Concordia University, Montreal, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PERFORM Centre, Concordia University, Montreal, Canada","institution_ids":["https://openalex.org/I60158472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059804416","display_name":"Michael Hallett","orcid":"https://orcid.org/0000-0001-6738-6786"},"institutions":[{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Michael Hallett","raw_affiliation_strings":["Department of Biology, Concordia University, Montreal, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Concordia University, Montreal, Canada","institution_ids":["https://openalex.org/I60158472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013607592","display_name":"Lars Ailo Bongo","orcid":"https://orcid.org/0000-0002-7544-2482"},"institutions":[{"id":"https://openalex.org/I78037679","display_name":"UiT The Arctic University of Norway","ror":"https://ror.org/00wge5k78","country_code":"NO","type":"education","lineage":["https://openalex.org/I78037679"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Lars Ailo Bongo","raw_affiliation_strings":["Department of Computer Science, UiT The Arctic University of Norway, Troms\u00f8, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, UiT The Arctic University of Norway, Troms\u00f8, Norway","institution_ids":["https://openalex.org/I78037679"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.9683,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.87691269,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"299","last_page":"306"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994000196456909,"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":0.9994000196456909,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.986299991607666,"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":0.7402112483978271},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6599528193473816},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.6387019157409668},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.5381065607070923},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.47153812646865845},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4420836567878723},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4399428367614746},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.43175452947616577},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4167143702507019},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.411720335483551},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11979120969772339},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10448500514030457},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1035107672214508}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7402112483978271},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6599528193473816},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.6387019157409668},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.5381065607070923},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.47153812646865845},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4420836567878723},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4399428367614746},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.43175452947616577},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4167143702507019},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.411720335483551},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11979120969772339},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10448500514030457},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1035107672214508},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/empdp.2019.8671623","is_oa":false,"landing_page_url":"https://doi.org/10.1109/empdp.2019.8671623","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)","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":29,"referenced_works":["https://openalex.org/W1574680346","https://openalex.org/W1818531208","https://openalex.org/W1921615383","https://openalex.org/W1978759257","https://openalex.org/W1984650538","https://openalex.org/W2016306999","https://openalex.org/W2110417468","https://openalex.org/W2136482257","https://openalex.org/W2138601221","https://openalex.org/W2146902212","https://openalex.org/W2158336776","https://openalex.org/W2169594074","https://openalex.org/W2408045830","https://openalex.org/W2521009248","https://openalex.org/W2526188806","https://openalex.org/W2605897695","https://openalex.org/W2607211817","https://openalex.org/W2613409207","https://openalex.org/W2762888391","https://openalex.org/W2765635284","https://openalex.org/W2765775596","https://openalex.org/W2769420359","https://openalex.org/W2797658776","https://openalex.org/W2950563407","https://openalex.org/W2982693266","https://openalex.org/W6713636576","https://openalex.org/W6726661869","https://openalex.org/W6744938664","https://openalex.org/W6750483270"],"related_works":["https://openalex.org/W2359178629","https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2375218795","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064"],"abstract_inverted_index":{"Precision":[0],"medicine":[1],"brings":[2],"the":[3,61,76,95,142,155],"promise":[4],"of":[5,60,177,208,226],"more":[6],"precise":[7],"diagnosis":[8],"and":[9,55,91,120,128,167,179,192],"individualized":[10],"therapeutic":[11],"strategies":[12],"from":[13,41],"analyzing":[14],"a":[15,49,100,188,214,224],"cancer's":[16],"genomic":[17],"signature.":[18],"Technologies":[19],"such":[20],"as":[21],"high-throughput":[22],"sequencing":[23,210],"enable":[24,80],"cheaper":[25],"data":[26,35,178,216],"collection":[27],"at":[28,75],"higher":[29],"speed,":[30],"but":[31],"rely":[32],"on":[33,116],"modern":[34,170],"analysis":[36,71,96,110,123,217],"platforms":[37],"to":[38,86,103,125,162,174,186],"extract":[39],"knowledge":[40],"these":[42,89],"high":[43],"dimensional":[44],"datasets.":[45],"Since":[46],"this":[47],"is":[48,84,114,213],"rapidly":[50],"advancing":[51],"field,":[52],"new":[53],"diagnoses":[54],"therapies":[56],"often":[57],"require":[58],"tailoring":[59],"analysis.":[62],"These":[63],"pipelines":[64,124],"are":[65],"therefore":[66],"developed":[67,109],"iteratively,":[68],"continuously":[69],"modifying":[70],"parameters":[72],"before":[73],"arriving":[74],"final":[77],"results.":[78],"To":[79],"reproducible":[81,105,164],"results":[82],"it":[83,212],"important":[85],"record":[87],"all":[88],"modifications":[90],"decisions":[92],"made":[93],"during":[94],"process.":[97],"We":[98,138,182],"built":[99],"system,":[101],"walrus,":[102],"support":[104],"analyses":[106,207],"for":[107,130,141,151,205],"iteratively":[108],"pipelines.":[111],"The":[112],"approach":[113],"based":[115],"our":[117],"experiences":[118],"developing":[119],"using":[121],"deep":[122],"provide":[126,163],"insights":[127],"recommendations":[129],"treatment":[131],"in":[132,154,223],"an":[133],"actual":[134],"breast":[135],"cancer":[136],"case.":[137],"designed":[139],"walrus":[140,158,185,204],"single":[143],"servers":[144],"or":[145],"small":[146],"compute":[147],"clusters":[148],"typically":[149],"available":[150],"novel":[152],"treatments":[153],"clinical":[156],"setting.":[157],"leverages":[159],"software":[160],"containers":[161],"execution":[165],"environments,":[166],"integrates":[168],"with":[169],"version":[171],"control":[172],"systems":[173],"capture":[175],"provenance":[176],"pipeline":[180],"parameters.":[181],"have":[183,202],"used":[184,203],"analyze":[187],"patient's":[189],"primary":[190],"tumor":[191],"adjacent":[193],"normal":[194],"tissue,":[195],"including":[196],"subsequent":[197],"metastatic":[198],"lesions.":[199],"Although":[200],"we":[201],"specialized":[206],"whole-exome":[209],"datasets,":[211],"general":[215],"tool":[218],"that":[219],"can":[220],"be":[221],"applied":[222],"variety":[225],"scientific":[227],"disciplines.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}