{"id":"https://openalex.org/W2998652703","doi":"https://doi.org/10.1093/bioinformatics/btz956","title":"Bioinformatics pipeline using JUDI: <i>Just Do It!</i>","display_name":"Bioinformatics pipeline using JUDI: <i>Just Do It!</i>","publication_year":2019,"publication_date":"2019-12-24","ids":{"openalex":"https://openalex.org/W2998652703","doi":"https://doi.org/10.1093/bioinformatics/btz956","mag":"2998652703","pmid":"https://pubmed.ncbi.nlm.nih.gov/31882996"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz956","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz956","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2572/36209081/btz956.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2572/36209081/btz956.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086885083","display_name":"Soumitra Pal","orcid":"https://orcid.org/0000-0003-4840-3944"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Soumitra Pal","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA"],"raw_orcid":"https://orcid.org/0000-0003-4840-3944","affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089548776","display_name":"Teresa M. Przytycka","orcid":"https://orcid.org/0000-0002-6261-277X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Teresa M Przytycka","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA"],"raw_orcid":"https://orcid.org/0000-0002-6261-277X","affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5086885083"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.5957,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.91942399,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"36","issue":"8","first_page":"2572","last_page":"2574"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.7552000284194946,"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":0.7552000284194946,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0763000026345253,"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":0.04749999940395355,"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/scripting-language","display_name":"Scripting language","score":0.7989776730537415},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7783429622650146},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7645086050033569},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7086992859840393},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6764140725135803},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5521709322929382},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.46300628781318665},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3613024950027466},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32604068517684937},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.31100574135780334},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23595324158668518}],"concepts":[{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7989776730537415},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7783429622650146},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7645086050033569},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7086992859840393},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6764140725135803},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5521709322929382},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.46300628781318665},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3613024950027466},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32604068517684937},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.31100574135780334},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23595324158668518}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz956","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz956","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2572/36209081/btz956.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31882996","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31882996","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7868055","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7868055","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz956","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz956","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2572/36209081/btz956.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1529006120","https://openalex.org/W1596936080","https://openalex.org/W2013434113","https://openalex.org/W2097464861","https://openalex.org/W2110417468","https://openalex.org/W2116096983","https://openalex.org/W2122000245","https://openalex.org/W2128374023","https://openalex.org/W2129666400","https://openalex.org/W2136207878","https://openalex.org/W2310259903","https://openalex.org/W2572857085","https://openalex.org/W2605897695","https://openalex.org/W2951189885","https://openalex.org/W2954441188","https://openalex.org/W3123082630","https://openalex.org/W6697974936"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2375304607"],"abstract_inverted_index":{"SUMMARY:":[0],"Large-scale":[1],"data":[2,185],"analysis":[3],"in":[4,15,114],"bioinformatics":[5],"requires":[6],"pipelined":[7],"execution":[8,42],"of":[9,43,49,63,85,100,127,142,144,150,166],"multiple":[10],"software.":[11],"Generally":[12],"each":[13,115],"stage":[14],"a":[16,87,105,111,121,132,148],"pipeline":[17,55,122,129,134],"takes":[18],"considerable":[19],"computing":[20],"resources":[21],"and":[22,117],"several":[23],"workflow":[24],"management":[25,102],"systems":[26],"(WMS),":[27],"e.g.":[28,65],"Snakemake,":[29],"Nextflow,":[30],"Common":[31],"Workflow":[32],"Language,":[33],"Galaxy,":[34],"etc.":[35,69],"have":[36],"been":[37],"developed":[38,81],"to":[39,57,75,91],"ensure":[40,76],"optimum":[41],"the":[44,50,54,98,128,140],"stages":[45],"across":[46],"two":[47],"invocations":[48],"pipeline.":[51],"However,":[52],"when":[53],"needs":[56],"be":[58],"executed":[59],"with":[60,120,135],"different":[61],"settings":[62,95],"parameters,":[64,137],"thresholds,":[66],"underlying":[67],"algorithms,":[68],"these":[70],"WMS":[71],"require":[72],"significant":[73],"scripting":[74,145],"an":[77],"optimal":[78],"execution.":[79],"We":[80],"JUDI":[82,124,138,157],"on":[83,97],"top":[84],"DoIt,":[86],"Python":[88],"based":[89,96],"WMS,":[90],"systematically":[92],"handle":[93],"parameter":[94,112,155,176],"principles":[99],"database":[101,113],"systems.":[103],"Using":[104],"novel":[106,175],"modular":[107],"approach":[108],"that":[109],"encapsulates":[110],"task":[116],"file":[118],"associated":[119],"stage,":[123],"simplifies":[125],"plug-and-play":[126],"stages.":[130],"For":[131],"typical":[133],"n":[136],"reduces":[139],"number":[141],"lines":[143],"required":[146],"by":[147],"factor":[149],"O(n).":[151],"With":[152],"properly":[153],"designed":[154],"databases,":[156],"not":[158],"only":[159],"enables":[160],"reproducing":[161],"research":[162],"under":[163,174],"published":[164],"values":[165],"parameters":[167],"but":[168],"also":[169],"facilitates":[170],"exploring":[171],"newer":[172],"results":[173],"settings.":[177],"AVAILABILITY":[178],"AND":[179],"IMPLEMENTATION:":[180],"https://github.com/ncbi/JUDI.":[181],"SUPPLEMENTARY":[182],"INFORMATION:":[183],"Supplementary":[184],"are":[186],"available":[187],"at":[188],"Bioinformatics":[189],"online.":[190]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2020-01-10T00:00:00"}
