{"id":"https://openalex.org/W2768735173","doi":"https://doi.org/10.1093/bioinformatics/btx759","title":"PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool","display_name":"PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool","publication_year":2017,"publication_date":"2017-11-22","ids":{"openalex":"https://openalex.org/W2768735173","doi":"https://doi.org/10.1093/bioinformatics/btx759","mag":"2768735173","pmid":"https://pubmed.ncbi.nlm.nih.gov/29186378"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx759","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1603/25120783/btx759.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/34/9/1603/25120783/btx759.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081719581","display_name":"Anbo Zhou","orcid":"https://orcid.org/0000-0001-9264-7458"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anbo Zhou","raw_affiliation_strings":["Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086109470","display_name":"Yeting Zhang","orcid":"https://orcid.org/0000-0002-9611-9051"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yeting Zhang","raw_affiliation_strings":["Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063862193","display_name":"Yazhou Sun","orcid":"https://orcid.org/0000-0003-4401-1011"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I47449453","display_name":"Kean University","ror":"https://ror.org/04wzzqn13","country_code":"US","type":"education","lineage":["https://openalex.org/I47449453"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Yazhou Sun","raw_affiliation_strings":["New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ, USA","Shenzhen Diagnoa Genomics Tech Co. Ltd, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ, USA","institution_ids":["https://openalex.org/I47449453"]},{"raw_affiliation_string":"Shenzhen Diagnoa Genomics Tech Co. Ltd, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024706936","display_name":"Jinchuan Xing","orcid":"https://orcid.org/0000-0001-6469-8733"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jinchuan Xing","raw_affiliation_strings":["Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024706936","https://openalex.org/A5063862193"],"corresponding_institution_ids":["https://openalex.org/I100135526","https://openalex.org/I102322142","https://openalex.org/I47449453"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3321,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.89275753,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"34","issue":"9","first_page":"1603","last_page":"1605"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.3589000105857849,"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":0.3589000105857849,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.14880000054836273,"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":0.1476999968290329,"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/simple","display_name":"Simple (philosophy)","score":0.8183560371398926},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7860702276229858},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6971816420555115},{"id":"https://openalex.org/keywords/engineering-drawing","display_name":"Engineering drawing","score":0.38350194692611694},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3625437617301941},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3589361310005188},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.17074808478355408}],"concepts":[{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.8183560371398926},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7860702276229858},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6971816420555115},{"id":"https://openalex.org/C199639397","wikidata":"https://www.wikidata.org/wiki/Q1788588","display_name":"Engineering drawing","level":1,"score":0.38350194692611694},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3625437617301941},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3589361310005188},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17074808478355408},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx759","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1603/25120783/btx759.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:29186378","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29186378","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/btx759","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx759","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1603/25120783/btx759.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":0.6299999952316284,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2768735173.pdf","grobid_xml":"https://content.openalex.org/works/W2768735173.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1919257374","https://openalex.org/W2078962046","https://openalex.org/W2110417468","https://openalex.org/W2123100726","https://openalex.org/W2136482257","https://openalex.org/W2143051000","https://openalex.org/W2168103533"],"related_works":["https://openalex.org/W1585007175","https://openalex.org/W2382521049","https://openalex.org/W2144385241","https://openalex.org/W2165950148","https://openalex.org/W4253593777","https://openalex.org/W2951497643","https://openalex.org/W4300101996","https://openalex.org/W3101625811","https://openalex.org/W3037187668","https://openalex.org/W2338854850"],"abstract_inverted_index":{"Summary:":[0],"Analysis":[1],"pipelines":[2,13],"are":[3,14,33,179],"an":[4,94,99],"essential":[5],"part":[6],"of":[7,115],"bioinformatics":[8],"research,":[9],"and":[10,21,47,62,89,93,121,141,146,164],"ad":[11],"hoc":[12],"frequently":[15],"created":[16],"by":[17],"researchers":[18],"for":[19,36],"prototyping":[20,38],"proof-of-concept":[22],"purposes.":[23],"However,":[24],"most":[25,124],"existing":[26],"pipeline":[27,42,60],"management":[28,85],"system":[29,102],"or":[30,39,171,173],"workflow":[31],"engines":[32],"too":[34],"complex":[35],"rapid":[37],"learning":[40],"the":[41,108],"concept.":[43],"A":[44],"lightweight,":[45],"user-friendly":[46],"flexible":[48],"solution":[49],"is":[50,67,151,160],"thus":[51],"desirable.":[52],"In":[53],"this":[54,132],"study,":[55],"we":[56],"developed":[57],"a":[58,68,74,136],"new":[59],"construction":[61],"maintenance":[63],"tool,":[64],"PipelineDog.":[65],"This":[66],"web-based":[69],"integrated":[70],"development":[71],"environment":[72],"with":[73],"modern":[75],"web":[76,133,149],"graphical":[77],"user":[78],"interface.":[79],"It":[80,97],"offers":[81],"cross-platform":[82],"compatibility,":[83],"project":[84],"capabilities,":[86],"code":[87,105],"formatting":[88],"error":[90],"checking":[91],"functions":[92],"online":[95,109,165],"repository.":[96],"uses":[98],"easy-to-read/write":[100],"script":[101],"that":[103],"encourages":[104,113],"reuse.":[106],"With":[107],"repository,":[110],"it":[111],"also":[112],"sharing":[114],"pipelines,":[116],"which":[117],"enhances":[118],"analysis":[119],"reproducibility":[120],"accountability.":[122],"For":[123],"users,":[125],"PipelineDog":[126,148],"requires":[127],"no":[128],"software":[129],"installation.":[130],"Overall,":[131],"application":[134],"provides":[135],"way":[137],"to":[138],"rapidly":[139],"create":[140],"easily":[142],"manage":[143],"pipelines.":[144],"Availability":[145],"implementation:":[147],"app":[150],"freely":[152],"available":[153,161,180],"at":[154,162,167,181],"http://web.pipeline.dog.":[155],"The":[156],"command":[157],"line":[158],"version":[159],"http://www.npmjs.com/package/pipelinedog":[163],"repository":[166],"http://repo.pipeline.dog.":[168],"Contact:":[169],"ysun@kean.edu":[170],"xing@biology.rutgers.edu":[172],"ysun@diagnoa.com.":[174],"Supplementary":[175,177],"information:":[176],"data":[178],"Bioinformatics":[182],"online.":[183]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
