{"id":"https://openalex.org/W2951557916","doi":"https://doi.org/10.1093/jamia/ocx120","title":"Reproducible Bioconductor workflows using browser-based interactive notebooks and containers","display_name":"Reproducible Bioconductor workflows using browser-based interactive notebooks and containers","publication_year":2017,"publication_date":"2017-09-28","ids":{"openalex":"https://openalex.org/W2951557916","doi":"https://doi.org/10.1093/jamia/ocx120","mag":"2951557916","pmid":"https://pubmed.ncbi.nlm.nih.gov/29092073"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocx120","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocx120","pdf_url":"https://academic.oup.com/jamia/article-pdf/25/1/4/27901309/ocx120.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/jamia/article-pdf/25/1/4/27901309/ocx120.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074977361","display_name":"Reem Almugbel","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150356","display_name":"University of Washington Tacoma","ror":"https://ror.org/05n8t2628","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210150356"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reem Almugbel","raw_affiliation_strings":["Institute of Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012172477","display_name":"Ling\u2010Hong Hung","orcid":"https://orcid.org/0000-0002-5209-2248"},"institutions":[{"id":"https://openalex.org/I4210150356","display_name":"University of Washington Tacoma","ror":"https://ror.org/05n8t2628","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210150356"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ling-Hong Hung","raw_affiliation_strings":["Institute of Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021492309","display_name":"Jiaming Hu","orcid":"https://orcid.org/0009-0005-6489-7923"},"institutions":[{"id":"https://openalex.org/I4210150356","display_name":"University of Washington Tacoma","ror":"https://ror.org/05n8t2628","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210150356"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiaming Hu","raw_affiliation_strings":["Institute of Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069937659","display_name":"Abeer Almutairy","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150356","display_name":"University of Washington Tacoma","ror":"https://ror.org/05n8t2628","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210150356"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abeer Almutairy","raw_affiliation_strings":["Institute of Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020443649","display_name":"Nicole Ortogero","orcid":null},"institutions":[{"id":"https://openalex.org/I1330654748","display_name":"Madigan Army Medical Center","ror":"https://ror.org/01sfyq865","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330347796","https://openalex.org/I1330654748","https://openalex.org/I2800250139","https://openalex.org/I2800386880"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole Ortogero","raw_affiliation_strings":["Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA","institution_ids":["https://openalex.org/I1330654748"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007478420","display_name":"Yashaswi Tamta","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150356","display_name":"University of Washington Tacoma","ror":"https://ror.org/05n8t2628","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210150356"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yashaswi Tamta","raw_affiliation_strings":["Institute of Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021881439","display_name":"Ka Yee Yeung","orcid":"https://orcid.org/0000-0002-1754-7577"},"institutions":[{"id":"https://openalex.org/I4210150356","display_name":"University of Washington Tacoma","ror":"https://ror.org/05n8t2628","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210150356"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ka Yee Yeung","raw_affiliation_strings":["Institute of Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021881439"],"corresponding_institution_ids":["https://openalex.org/I4210150356"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":13.9866,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.98592873,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"4","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.8553000092506409,"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":0.8553000092506409,"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":0.06360000371932983,"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":0.013899999670684338,"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":0.7959799766540527},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7679761648178101},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.7096149325370789},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.630719780921936},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.5539594292640686},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.47585150599479675},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4573052227497101},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4566572904586792},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4471311569213867},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33707714080810547},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2528265714645386},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.21076631546020508}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7959799766540527},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7679761648178101},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.7096149325370789},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.630719780921936},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.5539594292640686},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.47585150599479675},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4573052227497101},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4566572904586792},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4471311569213867},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33707714080810547},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2528265714645386},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.21076631546020508},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","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":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","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":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/jamia/ocx120","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocx120","pdf_url":"https://academic.oup.com/jamia/article-pdf/25/1/4/27901309/ocx120.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:29092073","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29092073","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":"Journal of the American Medical Informatics Association : JAMIA","raw_type":null},{"id":"pmh:oai:digitalcommons.tacoma.uw.edu:tech_pub-1273","is_oa":false,"landing_page_url":"https://digitalcommons.tacoma.uw.edu/tech_pub/274","pdf_url":null,"source":{"id":"https://openalex.org/S4306400628","display_name":"University of Washington Tacoma Digital Commons (University of Washington Tacoma)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210150356","host_organization_name":"University of Washington Tacoma","host_organization_lineage":["https://openalex.org/I4210150356"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"School of Engineering and Technology Publications","raw_type":"text"},{"id":"pmh:oai:europepmc.org:5382458","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6381817","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6381817","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6381817","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":"J Am Med Inform Assoc","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/jamia/ocx120","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocx120","pdf_url":"https://academic.oup.com/jamia/article-pdf/25/1/4/27901309/ocx120.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5799999833106995}],"awards":[{"id":"https://openalex.org/G1128421816","display_name":null,"funder_award_id":"U54-HL127624","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7375544220","display_name":null,"funder_award_id":"U54 HL127624","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W69354671","https://openalex.org/W585341442","https://openalex.org/W1574680346","https://openalex.org/W1622128722","https://openalex.org/W1967717472","https://openalex.org/W1968320037","https://openalex.org/W1988593472","https://openalex.org/W1996275701","https://openalex.org/W2043398720","https://openalex.org/W2060797544","https://openalex.org/W2061939373","https://openalex.org/W2068153368","https://openalex.org/W2081098333","https://openalex.org/W2084843096","https://openalex.org/W2100596675","https://openalex.org/W2104279568","https://openalex.org/W2107301169","https://openalex.org/W2117388642","https://openalex.org/W2120700198","https://openalex.org/W2123735699","https://openalex.org/W2130410032","https://openalex.org/W2146646206","https://openalex.org/W2152239989","https://openalex.org/W2157795344","https://openalex.org/W2160697532","https://openalex.org/W2191679689","https://openalex.org/W2197241765","https://openalex.org/W2246750919","https://openalex.org/W2286935178","https://openalex.org/W2314821163","https://openalex.org/W2437571239","https://openalex.org/W2517352989","https://openalex.org/W2565191020","https://openalex.org/W2568779902","https://openalex.org/W2573716089","https://openalex.org/W2576419506","https://openalex.org/W2589427926","https://openalex.org/W2736977076","https://openalex.org/W2923409768","https://openalex.org/W2972810475","https://openalex.org/W3102150468","https://openalex.org/W3113043731","https://openalex.org/W4247513463","https://openalex.org/W4256315501","https://openalex.org/W4294107304","https://openalex.org/W6602776624","https://openalex.org/W6649317944","https://openalex.org/W6726071186","https://openalex.org/W6731771754","https://openalex.org/W6732085513","https://openalex.org/W6982728064"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2153583721","https://openalex.org/W2098339479","https://openalex.org/W2961215453","https://openalex.org/W2367815957","https://openalex.org/W2624709009"],"abstract_inverted_index":{"Objective:":[0],"Bioinformatics":[1],"publications":[2],"typically":[3],"include":[4],"complex":[5],"software":[6,24,108,125,134,180,186,226,234],"workflows":[7,74,155],"that":[8,38,163,223],"are":[9,92],"difficult":[10],"to":[11,26,41,51,75,131,169,182],"describe":[12,17],"in":[13,102],"a":[14,34,53,57,103,157,171],"manuscript.":[15],"We":[16,32,63,161],"and":[18,28,61,72,86,113,135,193,206,246],"demonstrate":[19,162],"the":[20,107,122,129,139,152,184,215],"use":[21,178],"of":[22,154,174,179,190,203,210,218],"interactive":[23,48,67,90,164,225],"notebooks":[25,49,69,91,140,165,227,239],"document":[27],"distribute":[29,43],"bioinformatics":[30,45,175,219],"research.":[31],"provide":[33],"user-friendly":[35],"tool,":[36],"BiocImageBuilder,":[37],"allows":[39],"users":[40],"easily":[42],"their":[44],"protocols":[46],"through":[47],"uploaded":[50],"either":[52],"GitHub":[54],"repository":[55],"or":[56],"private":[58],"server.":[59],"Materials":[60],"methods:":[62],"present":[64],"four":[65],"different":[66],"Jupyter":[68],"using":[70,118,143],"R":[71],"Bioconductor":[73],"infer":[76],"differential":[77],"gene":[78],"expression,":[79],"analyze":[80],"cross-platform":[81],"datasets,":[82],"process":[83],"RNA-seq":[84],"data":[85],"KinomeScan":[87],"data.":[88],"These":[89],"available":[93],"on":[94],"GitHub.":[95],"The":[96,177],"analytical":[97],"results":[98,205],"can":[99,110,166,195],"be":[100,111,167,196],"viewed":[101],"browser.":[104],"Most":[105],"importantly,":[106],"contents":[109],"executed":[112],"modified.":[114],"This":[115],"is":[116],"accomplished":[117],"Binder,":[119],"which":[120],"runs":[121],"notebook":[123],"inside":[124],"containers,":[126],"thus":[127],"avoiding":[128],"need":[130],"install":[132],"any":[133],"ensuring":[136],"reproducibility.":[137],"All":[138],"were":[141],"produced":[142],"custom":[144],"files":[145],"generated":[146],"by":[147],"BiocImageBuilder.":[148],"Results:":[149],"BiocImageBuilder":[150],"facilitates":[151],"publication":[153],"with":[156],"point-and-click":[158],"user":[159],"interface.":[160],"used":[168],"disseminate":[170],"wide":[172],"range":[173],"analyses.":[176],"containers":[181],"mirror":[183],"original":[185],"environment":[187],"ensures":[188],"reproducibility":[189],"results.":[191],"Parameters":[192],"code":[194],"dynamically":[197],"modified,":[198],"allowing":[199],"for":[200,232,242],"robust":[201],"verification":[202],"published":[204],"encouraging":[207],"rapid":[208],"adoption":[209],"new":[211],"methods.":[212],"Conclusion:":[213],"Given":[214],"increasing":[216],"complexity":[217],"workflows,":[220],"we":[221],"anticipate":[222],"these":[224],"will":[228],"become":[229],"as":[230,236,247],"necessary":[231],"documenting":[233,243],"methods":[235],"traditional":[237],"laboratory":[238],"have":[240],"been":[241],"bench":[244],"protocols,":[245],"ubiquitous.":[248]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
