{"id":"https://openalex.org/W4387346475","doi":"https://doi.org/10.1145/3584371.3612948","title":"A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and Maintainability","display_name":"A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and Maintainability","publication_year":2023,"publication_date":"2023-09-03","ids":{"openalex":"https://openalex.org/W4387346475","doi":"https://doi.org/10.1145/3584371.3612948"},"language":"en","primary_location":{"id":"doi:10.1145/3584371.3612948","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612948","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612948","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612948","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058825907","display_name":"Justin Z. Tam","orcid":"https://orcid.org/0000-0003-3280-7397"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Justin Z Tam","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0000-0003-3280-7397","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069833605","display_name":"Alexandra Chua","orcid":"https://orcid.org/0009-0009-1352-5264"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexandra Chua","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0009-0009-1352-5264","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103059926","display_name":"Adyn Gallagher","orcid":"https://orcid.org/0009-0004-5509-2130"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adyn Gallagher","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0009-0004-5509-2130","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093003481","display_name":"Denice Omene","orcid":"https://orcid.org/0009-0006-1952-7269"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Denice Omene","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0009-0006-1952-7269","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102996707","display_name":"Danielle Okun","orcid":"https://orcid.org/0009-0005-3032-7076"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danielle Okun","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0009-0005-3032-7076","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028356812","display_name":"Dominic DiFranzo","orcid":"https://orcid.org/0000-0001-6039-1806"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dominic DiFranzo","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0000-0001-6039-1806","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062182398","display_name":"Brian Y. Chen","orcid":"https://orcid.org/0000-0001-9025-0107"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Y Chen","raw_affiliation_strings":["Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States"],"raw_orcid":"https://orcid.org/0000-0001-9025-0107","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Lehigh University, Bethlehem, PA, United States","institution_ids":["https://openalex.org/I186143895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5058825907"],"corresponding_institution_ids":["https://openalex.org/I186143895"],"apc_list":null,"apc_paid":null,"fwci":1.0785,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.87501424,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9988999962806702,"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":0.9988999962806702,"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.9947999715805054,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8023726344108582},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.6564042568206787},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5945360660552979},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5622076988220215},{"id":"https://openalex.org/keywords/maintainability","display_name":"Maintainability","score":0.5191525816917419},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.5163763761520386},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5018317699432373},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4845499098300934},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.47017306089401245},{"id":"https://openalex.org/keywords/software-framework","display_name":"Software framework","score":0.4592658281326294},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.44760602712631226},{"id":"https://openalex.org/keywords/resource-oriented-architecture","display_name":"Resource-oriented architecture","score":0.44096478819847107},{"id":"https://openalex.org/keywords/software-construction","display_name":"Software construction","score":0.3918222188949585},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3868376612663269},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3604809045791626},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.23145321011543274}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8023726344108582},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.6564042568206787},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5945360660552979},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5622076988220215},{"id":"https://openalex.org/C160713754","wikidata":"https://www.wikidata.org/wiki/Q1389965","display_name":"Maintainability","level":2,"score":0.5191525816917419},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.5163763761520386},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5018317699432373},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4845499098300934},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.47017306089401245},{"id":"https://openalex.org/C76518257","wikidata":"https://www.wikidata.org/wiki/Q271680","display_name":"Software framework","level":5,"score":0.4592658281326294},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.44760602712631226},{"id":"https://openalex.org/C97382630","wikidata":"https://www.wikidata.org/wiki/Q13501132","display_name":"Resource-oriented architecture","level":5,"score":0.44096478819847107},{"id":"https://openalex.org/C186846655","wikidata":"https://www.wikidata.org/wiki/Q3398377","display_name":"Software construction","level":4,"score":0.3918222188949585},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3868376612663269},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3604809045791626},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.23145321011543274}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3584371.3612948","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612948","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612948","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3584371.3612948","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612948","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612948","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G7675215327","display_name":null,"funder_award_id":"R01GM123131","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387346475.pdf","grobid_xml":"https://content.openalex.org/works/W4387346475.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2075128814","https://openalex.org/W2104594675","https://openalex.org/W2131646073","https://openalex.org/W2488156821","https://openalex.org/W2604622795","https://openalex.org/W2883843233"],"related_works":["https://openalex.org/W2370452582","https://openalex.org/W4229542741","https://openalex.org/W405938132","https://openalex.org/W2365277668","https://openalex.org/W2145298726","https://openalex.org/W1786307180","https://openalex.org/W7865839","https://openalex.org/W1589514039","https://openalex.org/W2057326075","https://openalex.org/W1480329237"],"abstract_inverted_index":{"Rapid":[0],"advancements":[1],"in":[2,6,80,180,192,198],"structural":[3,101],"bioinformatics":[4],"result":[5],"short":[7],"software":[8,26,124],"lifespans":[9],"due":[10],"to":[11,23,38,121,178],"issues":[12],"with":[13,64,103],"scalability,":[14],"portability":[15],"and":[16,52,59,66,88,108,141],"maintainability.":[17],"In":[18],"many":[19],"cases,":[20],"researchers":[21],"aim":[22],"distribute":[24],"scientific":[25],"as":[27,71,111,113],"part":[28],"of":[29,57,132,156,186],"a":[30,40,48,72,81,104,114,130,158,181,193],"research":[31],"project":[32],"but":[33],"lack":[34],"the":[35,60,76,86,92,133,136,143,146,149,154,173,187],"development":[36],"resources":[37],"maintain":[39],"robust":[41],"web":[42,49,78,159,166,188],"application":[43,50,70,79,95,189],"server.":[44],"Here,":[45],"we":[46,151],"introduce":[47,152],"framework":[51],"example":[53,69,185],"that":[54,117,163],"takes":[55],"advantage":[56],"containers":[58],"virtualization":[61],"capabilities":[62],"associated":[63],"them,":[65],"present":[67],"an":[68],"template.":[73],"We":[74],"contain":[75],"full":[77],"container,":[82,127],"which":[83,128],"packages":[84],"all":[85],"code":[87],"dependencies":[89],"required":[90,138],"for":[91,100,139,161,169],"software.":[93,144],"The":[94,126],"itself":[96],"is":[97,129],"built":[98,191],"specifically":[99],"bioinformatics,":[102],"front":[105],"end":[106,116],"GUI":[107],"molecular":[109],"viewer":[110],"well":[112],"back":[115],"can":[118,195],"be":[119,196],"altered":[120],"run":[122],"arbitrary":[123],"tools.":[125],"snapshot":[131],"software,":[134],"limits":[135],"effort":[137],"porting":[140],"maintaining":[142],"At":[145],"same":[147],"time,":[148],"architecture":[150],"streamlines":[153],"process":[155],"starting":[157],"server":[160],"programmers":[162],"are":[164],"not":[165],"developers.":[167],"Finally,":[168],"computationally":[170],"intensive":[171],"work,":[172],"container":[174,194],"transfers":[175],"computing":[176],"costs":[177],"users":[179],"pay-as-you-use":[182],"model.":[183],"An":[184],"implementation":[190],"found":[197],"section":[199],"5.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}