{"id":"https://openalex.org/W2123828642","doi":"https://doi.org/10.1093/bioinformatics/bts696","title":"nestly\u2014a framework for running software with nested parameter choices and aggregating results","display_name":"nestly\u2014a framework for running software with nested parameter choices and aggregating results","publication_year":2012,"publication_date":"2012-12-06","ids":{"openalex":"https://openalex.org/W2123828642","doi":"https://doi.org/10.1093/bioinformatics/bts696","mag":"2123828642","pmid":"https://pubmed.ncbi.nlm.nih.gov/23220574"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts696","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts696","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/387/48891926/bioinformatics_29_3_387.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/387/48891926/bioinformatics_29_3_387.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074561782","display_name":"Connor O. McCoy","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Connor O. McCoy","raw_affiliation_strings":["1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076585627","display_name":"Aaron Gallagher","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Gallagher","raw_affiliation_strings":["1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008533836","display_name":"Noah G. Hoffman","orcid":"https://orcid.org/0000-0001-6791-7727"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah G. Hoffman","raw_affiliation_strings":["1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084752404","display_name":"F. A. Matsen","orcid":"https://orcid.org/0000-0003-0607-6025"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederick A. Matsen","raw_affiliation_strings":["1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and 2Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074561782","https://openalex.org/A5084752404"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3685,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.59765037,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"29","issue":"3","first_page":"387","last_page":"388"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3391000032424927,"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":0.3391000032424927,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.3091000020503998,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.06710000336170197,"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/software","display_name":"Software","score":0.6728405356407166},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6619458794593811},{"id":"https://openalex.org/keywords/nested-set-model","display_name":"Nested set model","score":0.5342164635658264},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3400711417198181}],"concepts":[{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6728405356407166},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6619458794593811},{"id":"https://openalex.org/C103000020","wikidata":"https://www.wikidata.org/wiki/Q1978426","display_name":"Nested set model","level":3,"score":0.5342164635658264},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3400711417198181},{"id":"https://openalex.org/C510870499","wikidata":"https://www.wikidata.org/wiki/Q47607","display_name":"SQL","level":2,"score":0.0}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts696","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts696","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/387/48891926/bioinformatics_29_3_387.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23220574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23220574","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:europepmc.org:2892623","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3562064","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts696","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts696","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/387/48891926/bioinformatics_29_3_387.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1868398863","display_name":null,"funder_award_id":"R37 AI-038518","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3372332551","display_name":"Novel Computational Tools for Studying the Human Microbiome","funder_award_id":"5r01hg005966-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4290743894","display_name":null,"funder_award_id":"R01 HG005966","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5520316217","display_name":null,"funder_award_id":"NIH-R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5561463864","display_name":null,"funder_award_id":"R01 HG005966-01","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G6492140780","display_name":null,"funder_award_id":"R01 AI038518","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123828642.pdf","grobid_xml":"https://content.openalex.org/works/W2123828642.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1969042907","https://openalex.org/W1976394670","https://openalex.org/W2007091097","https://openalex.org/W2097438318","https://openalex.org/W2110417468","https://openalex.org/W2123100726","https://openalex.org/W2146509671","https://openalex.org/W6681564125"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"UNLABELLED:":[0],"The":[1],"execution":[2],"of":[3,12,25,59,78,92,102],"a":[4,17,26,49,68,86,107,121],"software":[5],"application":[6],"or":[7],"pipeline":[8],"using":[9,89],"various":[10],"combinations":[11,58],"parameters":[13,60],"and":[14,32,61,139],"inputs":[15],"is":[16,158],"common":[18],"task":[19],"in":[20],"bioinformatics.":[21],"In":[22],"the":[23,81,96,103,129,151],"absence":[24],"specialized":[27],"tool":[28],"to":[29,42,52,70,76,84,99],"organize,":[30],"streamline":[31],"formalize":[33],"this":[34],"process,":[35],"scientists":[36],"must":[37],"write":[38],"frequently":[39],"complex":[40,116],"scripts":[41],"perform":[43],"these":[44],"tasks.":[45],"We":[46,118],"present":[47],"nestly,":[48],"Python":[50,152],"package":[51],"facilitate":[53],"running":[54],"tools":[55],"with":[56],"nested":[57,72,126],"inputs.":[62],"nestly":[63,146],"provides":[64],"three":[65],"components.":[66],"First,":[67],"module":[69,122],"build":[71,131],"directory":[73],"structures":[74],"corresponding":[75],"choices":[77],"parameters.":[79],"Second,":[80],"nestrun":[82],"script":[83,98],"run":[85],"given":[87],"command":[88],"each":[90],"set":[91],"parameter":[93],"choices.":[94],"Third,":[95],"nestagg":[97],"aggregate":[100],"results":[101],"individual":[104],"runs":[105],"into":[106],"CSV":[108],"file,":[109],"as":[110,112],"well":[111],"support":[113],"for":[114,123,128],"more":[115],"aggregation.":[117],"also":[119],"include":[120],"easily":[124],"specifying":[125],"dependencies":[127],"SCons":[130],"tool,":[132],"enabling":[133],"incremental":[134],"builds.":[135],"AVAILABILITY:":[136],"Source,":[137],"documentation":[138],"tutorial":[140],"examples":[141],"are":[142],"available":[143],"at":[144],"http://github.com/fhcrc/nestly.":[145],"can":[147],"be":[148],"installed":[149],"from":[150],"Package":[153],"Index":[154],"via":[155],"pip;":[156],"it":[157],"open":[159],"source":[160],"(MIT":[161],"license).":[162]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
