{"id":"https://openalex.org/W2630275926","doi":"https://doi.org/10.1093/bioinformatics/btx403","title":"BioQueue: a novel pipeline framework to accelerate bioinformatics analysis","display_name":"BioQueue: a novel pipeline framework to accelerate bioinformatics analysis","publication_year":2017,"publication_date":"2017-06-16","ids":{"openalex":"https://openalex.org/W2630275926","doi":"https://doi.org/10.1093/bioinformatics/btx403","mag":"2630275926","pmid":"https://pubmed.ncbi.nlm.nih.gov/28633441"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx403","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3286/25165596/btx403.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/33/20/3286/25165596/btx403.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100411267","display_name":"Yao Li","orcid":"https://orcid.org/0000-0003-2827-8824"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Li Yao","raw_affiliation_strings":["College of Life Science, Northeast Forestry University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089385206","display_name":"Heming Wang","orcid":"https://orcid.org/0009-0003-9124-8238"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Heming Wang","raw_affiliation_strings":["School of Life Science and Technology, Shanghai Tech University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Science and Technology, Shanghai Tech University, Shanghai, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102905596","display_name":"Yuanyuan Song","orcid":"https://orcid.org/0000-0002-9183-5884"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Song","raw_affiliation_strings":["College of Life Science, Northeast Forestry University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000593102","display_name":"Guangchao Sui","orcid":"https://orcid.org/0000-0002-8164-5585"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guangchao Sui","raw_affiliation_strings":["College of Life Science, Northeast Forestry University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5000593102","https://openalex.org/A5100411267"],"corresponding_institution_ids":["https://openalex.org/I47689461"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4054,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.59502152,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"20","first_page":"3286","last_page":"3288"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4041999876499176,"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":0.4041999876499176,"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":0.35350000858306885,"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":0.07050000131130219,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8885908722877502},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6865513324737549},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.5502533912658691},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5500999689102173},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.5217862129211426},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.49331703782081604},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4847942888736725},{"id":"https://openalex.org/keywords/message-queue","display_name":"Message queue","score":0.4373123347759247},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4099465608596802},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3888380825519562},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.0955224335193634}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8885908722877502},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6865513324737549},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.5502533912658691},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5500999689102173},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.5217862129211426},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.49331703782081604},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4847942888736725},{"id":"https://openalex.org/C26324664","wikidata":"https://www.wikidata.org/wiki/Q1065525","display_name":"Message queue","level":2,"score":0.4373123347759247},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4099465608596802},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3888380825519562},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0955224335193634},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx403","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3286/25165596/btx403.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:28633441","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28633441","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx403","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/20/3286/25165596/btx403.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":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1609721597","display_name":null,"funder_award_id":"81472635","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G205680441","display_name":null,"funder_award_id":"81472635","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"},{"id":"https://openalex.org/G3092426913","display_name":null,"funder_award_id":"81672795","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4985502510","display_name":null,"funder_award_id":"81672795","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W2123100726","https://openalex.org/W2136207878","https://openalex.org/W2136482257","https://openalex.org/W2310259903","https://openalex.org/W2510875395"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W3131163342","https://openalex.org/W2166271660","https://openalex.org/W2142369114","https://openalex.org/W2002770077","https://openalex.org/W2361728394","https://openalex.org/W2352631095","https://openalex.org/W2408577762","https://openalex.org/W2092256833","https://openalex.org/W3038222916"],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"the":[2,20,52,56,76,110,119,149],"rapid":[3],"development":[4],"of":[5,11,22,58,78,133],"Next-Generation":[6],"Sequencing,":[7],"a":[8,59,63,66,97,102,128,135],"large":[9],"amount":[10],"data":[12,179],"is":[13,69,159],"now":[14],"available":[15,161,181],"for":[16,71],"bioinformatics":[17],"research.":[18],"Meanwhile,":[19],"presence":[21],"many":[23],"pipeline":[24],"frameworks":[25],"makes":[26],"it":[27,68],"possible":[28],"to":[29,74,107],"analyse":[30],"these":[31,34,72],"data.":[32],"However,":[33],"tools":[35,73],"concentrate":[36],"mainly":[37],"on":[38,48],"their":[39],"syntax":[40,131],"and":[41,44,81,115,121],"design":[42],"paradigms,":[43],"dispatch":[45,123],"jobs":[46,124],"based":[47],"users'":[49],"experience":[50],"about":[51],"resources":[53,112],"needed":[54,117],"by":[55,85,118],"execution":[57],"certain":[60],"step":[61,106,120],"in":[62],"protocol.":[64],"As":[65],"result,":[67],"difficult":[70],"maximize":[75],"potential":[77],"computing":[79],"resources,":[80],"avoid":[82],"errors":[83],"caused":[84],"overload,":[86],"such":[87],"as":[88],"memory":[89,114],"overflow.":[90],"RESULTS:":[91],"Here,":[92],"we":[93],"have":[94],"developed":[95],"BioQueue,":[96],"web-based":[98],"framework":[99],"that":[100],"contains":[101],"checkpoint":[103],"before":[104],"each":[105],"automatically":[108],"estimate":[109],"system":[111,152],"(CPU,":[113],"disk)":[116],"then":[122],"accordingly.":[125],"BioQueue":[126,158],"possesses":[127],"shell":[129],"command-like":[130],"instead":[132],"implementing":[134],"new":[136],"script":[137],"language,":[138],"which":[139],"means":[140],"most":[141],"biologists":[142],"without":[143],"computer":[144],"programming":[145],"background":[146],"can":[147,167],"access":[148],"efficient":[150],"queue":[151],"with":[153],"ease.":[154],"AVAILABILITY":[155],"AND":[156],"IMPLEMENTATION:":[157],"freely":[160],"at":[162,170,182],"https://github.com/liyao001/BioQueue.":[163],"The":[164],"extensive":[165],"documentation":[166],"be":[168],"found":[169],"http://bioqueue.readthedocs.io.":[171],"CONTACT:":[172],"li_yao@outlook.com":[173],"or":[174],"gcsui@nefu.edu.cn.":[175],"SUPPLEMENTARY":[176],"INFORMATION:":[177],"Supplementary":[178],"are":[180],"Bioinformatics":[183],"online.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
