{"id":"https://openalex.org/W2310259903","doi":"https://doi.org/10.1093/bib/bbw020","title":"A review of bioinformatic pipeline frameworks","display_name":"A review of bioinformatic pipeline frameworks","publication_year":2016,"publication_date":"2016-03-24","ids":{"openalex":"https://openalex.org/W2310259903","doi":"https://doi.org/10.1093/bib/bbw020","mag":"2310259903","pmid":"https://pubmed.ncbi.nlm.nih.gov/27013646"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbw020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbw020","pdf_url":"https://academic.oup.com/bib/article-pdf/18/3/530/25408774/bbw020.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/18/3/530/25408774/bbw020.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064934412","display_name":"Jeremy Leipzig","orcid":"https://orcid.org/0000-0001-7224-9620"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeremy Leipzig","raw_affiliation_strings":["Department of Biomedical and Health Informatics, The Children\u2019s Hospital of Philadelphia, 3535 Market Street, Room 1063, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical and Health Informatics, The Children\u2019s Hospital of Philadelphia, 3535 Market Street, Room 1063, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064934412"],"corresponding_institution_ids":["https://openalex.org/I1335321130"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":133.6686,"has_fulltext":false,"cited_by_count":271,"citation_normalized_percentile":{"value":0.99966655,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"18","issue":"3","first_page":"bbw020","last_page":"bbw020"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9919000267982483,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9824000000953674,"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":0.810232400894165},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7971742153167725},{"id":"https://openalex.org/keywords/workbench","display_name":"Workbench","score":0.6760460138320923},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.6695277690887451},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.622193455696106},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4985487461090088},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4879435896873474},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.46225589513778687},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.45909175276756287},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.43579694628715515},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4105566442012787},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.24533051252365112},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2099677324295044},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1522495150566101},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.0848977267742157}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.810232400894165},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7971742153167725},{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.6760460138320923},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.6695277690887451},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.622193455696106},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4985487461090088},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4879435896873474},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.46225589513778687},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.45909175276756287},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.43579694628715515},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4105566442012787},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.24533051252365112},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2099677324295044},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1522495150566101},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0848977267742157},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbw020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbw020","pdf_url":"https://academic.oup.com/bib/article-pdf/18/3/530/25408774/bbw020.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27013646","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27013646","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:4283564","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5429012","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbw020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbw020","pdf_url":"https://academic.oup.com/bib/article-pdf/18/3/530/25408774/bbw020.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5400000214576721,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2310259903.pdf","grobid_xml":"https://content.openalex.org/works/W2310259903.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2013434113","https://openalex.org/W2051643755","https://openalex.org/W2095680943","https://openalex.org/W2097058024","https://openalex.org/W2097438318","https://openalex.org/W2110417468","https://openalex.org/W2123100726","https://openalex.org/W2124796057","https://openalex.org/W2129666400","https://openalex.org/W2136207878","https://openalex.org/W2136482257","https://openalex.org/W2146437022","https://openalex.org/W2168133698","https://openalex.org/W2169594074","https://openalex.org/W6674561533","https://openalex.org/W6679517723","https://openalex.org/W6684698009"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W2109648960","https://openalex.org/W2166015079","https://openalex.org/W2388480422","https://openalex.org/W2050384624","https://openalex.org/W2321287347","https://openalex.org/W2776888796","https://openalex.org/W2951120646","https://openalex.org/W2356913294","https://openalex.org/W2903672016"],"abstract_inverted_index":{"High-throughput":[0],"bioinformatic":[1],"analyses":[2],"increasingly":[3],"rely":[4],"on":[5,19,63],"pipeline":[6,56],"frameworks":[7,17],"to":[8],"process":[9],"sequence":[10],"and":[11,37,48,66],"metadata.":[12],"Modern":[13],"implementations":[14],"of":[15,53],"these":[16],"differ":[18],"three":[20],"key":[21],"dimensions:":[22],"using":[23,29],"an":[24],"implicit":[25],"or":[26,33,42],"explicit":[27],"syntax,":[28],"a":[30,39],"configuration,":[31],"convention":[32],"class-based":[34],"design":[35,51],"paradigm":[36],"offering":[38],"command":[40],"line":[41],"workbench":[43],"interface.":[44],"Here":[45],"I":[46,58],"survey":[47],"compare":[49],"the":[50,67],"philosophies":[52],"several":[54],"current":[55],"frameworks.":[57],"provide":[59],"practical":[60],"recommendations":[61],"based":[62],"analysis":[64],"requirements":[65],"user":[68],"base.":[69]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":41},{"year":2020,"cited_by_count":37},{"year":2019,"cited_by_count":53},{"year":2018,"cited_by_count":43},{"year":2017,"cited_by_count":35},{"year":2016,"cited_by_count":10},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
