{"id":"https://openalex.org/W7126019418","doi":"https://doi.org/10.1109/bibm66473.2025.11356995","title":"Toward Autonomous Biofilm Engineering: A Vision for a Digital Twin-Based Lab Automation","display_name":"Toward Autonomous Biofilm Engineering: A Vision for a Digital Twin-Based Lab Automation","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126019418","doi":"https://doi.org/10.1109/bibm66473.2025.11356995"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356995","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356995","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","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/A5091622645","display_name":"Bichar Dip Shrestha Gurung","orcid":"https://orcid.org/0000-0002-9818-5108"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bichar Dip Shrestha Gurung","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005279080","display_name":"Timothy W. Hartman","orcid":"https://orcid.org/0000-0002-4127-9672"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy W. Hartman","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085659215","display_name":"D. Tuyen","orcid":"https://orcid.org/0000-0003-0256-6414"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tuyen Do","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061731299","display_name":"V. Gadhamshetty","orcid":null},"institutions":[{"id":"https://openalex.org/I184647316","display_name":"South Dakota School of Mines and Technology","ror":"https://ror.org/00ch7yk27","country_code":"US","type":"education","lineage":["https://openalex.org/I184647316"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Venkataramana Gadhamshetty","raw_affiliation_strings":["South Dakota School of Mines and Technology,Dept. of Civil and Environmental Engineering,Rapid City,USA"],"affiliations":[{"raw_affiliation_string":"South Dakota School of Mines and Technology,Dept. of Civil and Environmental Engineering,Rapid City,USA","institution_ids":["https://openalex.org/I184647316"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003549657","display_name":"Etienne Z. Gnimpi\u00e9ba","orcid":"https://orcid.org/0000-0002-5338-084X"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Etienne Z. Gnimpieba","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5091622645"],"corresponding_institution_ids":["https://openalex.org/I189957204"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.67277334,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"7566","last_page":"7573"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10593","display_name":"Bacterial biofilms and quorum sensing","score":0.4185999929904938,"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"}},"topics":[{"id":"https://openalex.org/T10593","display_name":"Bacterial biofilms and quorum sensing","score":0.4185999929904938,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.11270000040531158,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T13052","display_name":"Molecular Communication and Nanonetworks","score":0.03720000013709068,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.6585999727249146},{"id":"https://openalex.org/keywords/blueprint","display_name":"Blueprint","score":0.6241000294685364},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6189000010490417},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.5340999960899353},{"id":"https://openalex.org/keywords/biofilm","display_name":"Biofilm","score":0.5292999744415283},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.41600000858306885},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3402999937534332}],"concepts":[{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.6585999727249146},{"id":"https://openalex.org/C155911762","wikidata":"https://www.wikidata.org/wiki/Q422321","display_name":"Blueprint","level":2,"score":0.6241000294685364},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6189000010490417},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.5340999960899353},{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.5292999744415283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5259000062942505},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.41600000858306885},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3695000112056732},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.35010001063346863},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.3328999876976013},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.322299987077713},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.3043999969959259},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3012000024318695},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2921999990940094},{"id":"https://openalex.org/C5339829","wikidata":"https://www.wikidata.org/wiki/Q1425977","display_name":"Machine vision","level":2,"score":0.2671000063419342},{"id":"https://openalex.org/C136085584","wikidata":"https://www.wikidata.org/wiki/Q910289","display_name":"Overlay","level":2,"score":0.2605000138282776},{"id":"https://openalex.org/C85135244","wikidata":"https://www.wikidata.org/wiki/Q1799487","display_name":"Laboratory automation","level":3,"score":0.25949999690055847},{"id":"https://openalex.org/C81860439","wikidata":"https://www.wikidata.org/wiki/Q251212","display_name":"Internet of Things","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.25440001487731934},{"id":"https://openalex.org/C98025372","wikidata":"https://www.wikidata.org/wiki/Q477538","display_name":"Systems architecture","level":3,"score":0.25429999828338623},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2538999915122986}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356995","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356995","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2480010979","https://openalex.org/W2553095014","https://openalex.org/W2950734534","https://openalex.org/W3015034412","https://openalex.org/W4293434832","https://openalex.org/W4311281428","https://openalex.org/W4313525413","https://openalex.org/W4390970055","https://openalex.org/W4390971125","https://openalex.org/W4401535000"],"related_works":[],"abstract_inverted_index":{"Biofilm":[0],"research":[1],"is":[2,126],"undergoing":[3],"a":[4,9,44,47,67,129,197],"significant":[5],"transformation":[6],"due":[7],"to":[8,12,127,156],"growing":[10,22],"need":[11],"address":[13],"biological":[14,173],"complexity,":[15],"temporal":[16],"dynamics,":[17],"and":[18,33,63,90,101,111,175,187],"environmental":[19],"sensitivity.":[20],"These":[21],"needs":[23],"demand":[24],"experimental":[25],"platforms":[26],"that":[27,52],"are":[28],"far":[29],"more":[30],"autonomous,":[31,185],"scalable,":[32],"computationally":[34,188],"integrated":[35],"than":[36],"current":[37],"microbiology":[38],"lab":[39,109,150],"workflows.":[40],"This":[41,93],"paper":[42,125],"presents":[43],"vision":[45,199],"for":[46,70,82,132,184,200],"digital":[48,137],"twin-driven":[49],"\u201ccyber-physical":[50],"laboratory\u201d":[51],"combines":[53],"modular":[54],"robotics,":[55],"automated":[56,177],"imaging,":[57],"an":[58,77],"Internet":[59],"of":[60,106,123,203],"Things":[61],"network,":[62],"AI-based":[64],"phenotyping":[65],"into":[66],"cohesive":[68],"system":[69],"next-generation":[71],"computational":[72,204],"biofilm":[73,142,190,205],"engineering.":[74,206],"We":[75,192],"outline":[76],"eight-component":[78],"architecture":[79,94,180],"comprising":[80],"twins":[81],"physical,":[83],"environmental,":[84],"biological,":[85],"protocol,":[86],"data,":[87],"AI/ML,":[88],"control,":[89,178],"safety":[91],"constraints.":[92],"will":[95],"enable":[96],"virtual":[97],"experimentation,":[98],"predictive":[99,172],"simulation,":[100],"self-correction,":[102],"with":[103,136,154,171],"the":[104,112,120,152,182,201],"goal":[105],"interactive":[107],"total":[108],"automation":[110],"\u201crobot":[113],"scientist\u201d.":[114],"Although":[115],"we":[116],"demonstrate":[117],"early":[118],"prototypes,":[119],"main":[121],"objective":[122],"this":[124,179,194],"articulate":[128],"forward-looking":[130],"blueprint":[131],"how":[133],"cyber-physical":[134],"labs":[135],"twinning":[138],"can":[139],"fundamentally":[140],"reshape":[141],"research.":[143],"Two":[144],"use":[145],"cases":[146],"implementation":[147],"in":[148],"our":[149],"shows":[151],"feasibility":[153],"up":[155],"500":[157],"samples":[158,163],"run":[159],"per":[160,164],"day":[161],"(10,000":[162],"week).":[165],"By":[166],"integrating":[167],"real-time":[168],"data":[169],"streams":[170],"models":[174],"closed-loop":[176],"sets":[181],"stage":[183],"reproducible,":[186],"guided":[189],"experimentation.":[191],"propose":[193],"platform":[195],"as":[196],"foundational":[198],"future":[202]},"counts_by_year":[],"updated_date":"2026-02-01T03:34:12.195049","created_date":"2026-01-30T00:00:00"}