{"id":"https://openalex.org/W2995675697","doi":"https://doi.org/10.1109/bibm47256.2019.8983263","title":"Using BioDepot-workflow-builder to Access Public Databases in a Containerized Environment","display_name":"Using BioDepot-workflow-builder to Access Public Databases in a Containerized Environment","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W2995675697","doi":"https://doi.org/10.1109/bibm47256.2019.8983263","mag":"2995675697"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983263","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983263","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034925075","display_name":"Christin Scott","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":"Christin Scott","raw_affiliation_strings":["School of Engineering and Technology, University of Washington,Tacoma,WA,USA","School of Engineering and Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology, University of Washington,Tacoma,WA,USA","institution_ids":["https://openalex.org/I4210150356"]},{"raw_affiliation_string":"School of Engineering and 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":["School of Engineering and Technology, University of Washington,Tacoma,WA,USA","School of Engineering and Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology, University of Washington,Tacoma,WA,USA","institution_ids":["https://openalex.org/I4210150356"]},{"raw_affiliation_string":"School of Engineering and Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021815916","display_name":"Wes Lloyd","orcid":"https://orcid.org/0000-0003-2021-8501"},"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":"Wes Lloyd","raw_affiliation_strings":["School of Engineering and Technology, University of Washington,Tacoma,WA,USA","School of Engineering and Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology, University of Washington,Tacoma,WA,USA","institution_ids":["https://openalex.org/I4210150356"]},{"raw_affiliation_string":"School of Engineering and 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":false,"raw_author_name":"Ka Yee Yeung","raw_affiliation_strings":["School of Engineering and Technology, University of Washington,Tacoma,WA,USA","School of Engineering and Technology, University of Washington, Tacoma, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering and Technology, University of Washington,Tacoma,WA,USA","institution_ids":["https://openalex.org/I4210150356"]},{"raw_affiliation_string":"School of Engineering and Technology, University of Washington, Tacoma, WA, USA","institution_ids":["https://openalex.org/I4210150356"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210150356"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1243","last_page":"1243"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9987999796867371,"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":0.9987999796867371,"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/T10885","display_name":"Gene expression and cancer classification","score":0.986299991607666,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8796396851539612},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7681643962860107},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5906597375869751},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5633457899093628},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5370755195617676},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5004277229309082},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3575230538845062},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.16091445088386536}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8796396851539612},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7681643962860107},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5906597375869751},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5633457899093628},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5370755195617676},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5004277229309082},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3575230538845062},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16091445088386536},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983263","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983263","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W2043398720","https://openalex.org/W2406493898","https://openalex.org/W2952768760","https://openalex.org/W2972810475"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520","https://openalex.org/W2547528905"],"abstract_inverted_index":{"Modern":[0],"day":[1],"analyses":[2,33,53,68],"of":[3,10,16,34,41],"biomedical":[4,35,87],"data":[5,36],"typically":[6],"involves":[7],"a":[8,38,55],"series":[9],"computational":[11],"tasks":[12],"called":[13],"workflows.":[14],"Each":[15],"these":[17,71],"modules":[18],"could":[19],"be":[20],"written":[21],"by":[22],"different":[23,29],"laboratories":[24],"and":[25],"thus,":[26],"potentially":[27],"requires":[28],"computing":[30],"environments.":[31],"Reproducible":[32],"is":[37],"growing":[39],"field":[40],"interest":[42],"[1].":[43],"This":[44],"makes":[45],"it":[46],"important":[47],"to":[48,51,63,85],"develop":[49],"tools":[50],"facilitate":[52],"in":[54,66],"reproducible":[56],"manner.":[57],"Software":[58],"containers":[59,73],"have":[60],"been":[61],"used":[62],"increase":[64],"reproducibility":[65],"bioinformatics":[67],"[2].":[69],"However,":[70],"software":[72],"often":[74],"use":[75],"command":[76],"line":[77],"tools,":[78],"requiring":[79],"expertise":[80],"that":[81],"make":[82],"them":[83],"inaccessible":[84],"many":[86],"scientists.":[88]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
