{"id":"https://openalex.org/W7169549222","doi":"https://doi.org/10.1145/3803437.3805577","title":"Bio-Aware Software Engineering for Reproducible Research","display_name":"Bio-Aware Software Engineering for Reproducible Research","publication_year":2026,"publication_date":"2026-07-05","ids":{"openalex":"https://openalex.org/W7169549222","doi":"https://doi.org/10.1145/3803437.3805577"},"language":null,"primary_location":{"id":"doi:10.1145/3803437.3805577","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3803437.3805577","pdf_url":null,"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 34th ACM International Conference on the Foundations of Software Engineering","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3803437.3805577","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5141055436","display_name":"Yiming Zeng","orcid":"https://orcid.org/0009-0006-5842-0130"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yiming Zeng","raw_affiliation_strings":["University of Connecticut, Storrs, Connecticut, USA"],"raw_orcid":"https://orcid.org/0009-0006-5842-0130","affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, Connecticut, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056404982","display_name":"Dingbang Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dingbang Wang","raw_affiliation_strings":["University of Connecticut, Storrs, USA"],"raw_orcid":"https://orcid.org/0009-0002-9675-6824","affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5141098237","display_name":"Ryan Green","orcid":"https://orcid.org/0009-0006-6114-486X"},"institutions":[{"id":"https://openalex.org/I1325886976","display_name":"Siemens (Germany)","ror":"https://ror.org/059mq0909","country_code":"DE","type":"company","lineage":["https://openalex.org/I1325886976"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ryan Green","raw_affiliation_strings":["Siemens Digital Industries Software, Cincinnati, Ohio, USA"],"raw_orcid":"https://orcid.org/0009-0006-6114-486X","affiliations":[{"raw_affiliation_string":"Siemens Digital Industries Software, Cincinnati, Ohio, USA","institution_ids":["https://openalex.org/I1325886976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103160577","display_name":"Sandeep Kaur Kuttal","orcid":"https://orcid.org/0000-0003-0172-7087"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandeep Kaur Kuttal","raw_affiliation_strings":["North Carolina State University, Raleigh, USA"],"raw_orcid":"https://orcid.org/0000-0003-0172-7087","affiliations":[{"raw_affiliation_string":"North Carolina State University, Raleigh, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102842945","display_name":"Jinze Liu","orcid":"https://orcid.org/0000-0003-0555-9412"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinze Liu","raw_affiliation_strings":["Virginia Commonwealth University, Richmond, Virginia, USA"],"raw_orcid":"https://orcid.org/0000-0003-0555-9412","affiliations":[{"raw_affiliation_string":"Virginia Commonwealth University, Richmond, Virginia, USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072070511","display_name":"Tingting Yu","orcid":"https://orcid.org/0000-0002-9461-4251"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tingting Yu","raw_affiliation_strings":["University of Connecticut, Storrs, Connecticut, USA"],"raw_orcid":"https://orcid.org/0000-0002-9461-4251","affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, Connecticut, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":"1307","last_page":"1311"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/bridge","display_name":"Bridge (graph theory)","score":0.5098999738693237},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49549999833106995},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.36419999599456787},{"id":"https://openalex.org/keywords/software-system","display_name":"Software system","score":0.34040001034736633},{"id":"https://openalex.org/keywords/social-software-engineering","display_name":"Social software engineering","score":0.31529998779296875},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.31029999256134033},{"id":"https://openalex.org/keywords/software-analytics","display_name":"Software analytics","score":0.3102000057697296},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.3061999976634979}],"concepts":[{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.6572999954223633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5938000082969666},{"id":"https://openalex.org/C100776233","wikidata":"https://www.wikidata.org/wiki/Q2532492","display_name":"Bridge (graph theory)","level":2,"score":0.5098999738693237},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49549999833106995},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4481000006198883},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.36419999599456787},{"id":"https://openalex.org/C149091818","wikidata":"https://www.wikidata.org/wiki/Q2429814","display_name":"Software system","level":3,"score":0.34040001034736633},{"id":"https://openalex.org/C182500959","wikidata":"https://www.wikidata.org/wiki/Q7551380","display_name":"Social software engineering","level":5,"score":0.31529998779296875},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.31029999256134033},{"id":"https://openalex.org/C171981572","wikidata":"https://www.wikidata.org/wiki/Q7554239","display_name":"Software analytics","level":5,"score":0.3102000057697296},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3061999976634979},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3003000020980835},{"id":"https://openalex.org/C58328972","wikidata":"https://www.wikidata.org/wiki/Q184609","display_name":"Expert system","level":2,"score":0.3001999855041504},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.2924000024795532},{"id":"https://openalex.org/C85973986","wikidata":"https://www.wikidata.org/wiki/Q1091731","display_name":"Exploratory research","level":2,"score":0.26820001006126404},{"id":"https://openalex.org/C44416564","wikidata":"https://www.wikidata.org/wiki/Q7554199","display_name":"Software Engineering Process Group","level":5,"score":0.2680000066757202},{"id":"https://openalex.org/C186846655","wikidata":"https://www.wikidata.org/wiki/Q3398377","display_name":"Software construction","level":4,"score":0.26260000467300415},{"id":"https://openalex.org/C202105479","wikidata":"https://www.wikidata.org/wiki/Q265013","display_name":"Software evolution","level":5,"score":0.2547999918460846},{"id":"https://openalex.org/C161821725","wikidata":"https://www.wikidata.org/wiki/Q917415","display_name":"Regression testing","level":5,"score":0.25270000100135803}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3803437.3805577","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3803437.3805577","pdf_url":null,"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 34th ACM International Conference on the Foundations of Software Engineering","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3803437.3805577","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3803437.3805577","pdf_url":null,"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 34th ACM International Conference on the Foundations of Software Engineering","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3027614770","display_name":null,"funder_award_id":"CCF 2403747","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G798987815","display_name":null,"funder_award_id":"IIS-2313890","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1574680346","https://openalex.org/W2054628911","https://openalex.org/W2110417468","https://openalex.org/W2148906281","https://openalex.org/W2160697532","https://openalex.org/W2613409207","https://openalex.org/W2793993424","https://openalex.org/W2954370766","https://openalex.org/W3020759564","https://openalex.org/W3089207120","https://openalex.org/W3184026316","https://openalex.org/W4235074396","https://openalex.org/W4410454004","https://openalex.org/W4411005431","https://openalex.org/W4413337859","https://openalex.org/W7103754783"],"related_works":[],"abstract_inverted_index":{"Bioinformatics":[0],"stands":[1],"at":[2],"a":[3,35,44,114],"precarious":[4],"intersection:":[5],"while":[6,59,77],"biological":[7,56],"questions":[8],"are":[9,64,80],"cutting-edge,":[10],"the":[11,29,32,55,101,133],"software":[12,135],"infrastructure":[13,136],"supporting":[14],"them":[15],"is":[16],"often":[17],"fragile,":[18],"\"ad":[19],"hoc\",":[20],"and":[21,70,130,140,153],"ephemeral.":[22],"In":[23],"this":[24],"paper,":[25],"we":[26,74],"reflect":[27],"on":[28],"state":[30],"of":[31,38,116],"practice":[33],"through":[34],"qualitative":[36],"study":[37],"bioinformatics":[39,155],"researchers.":[40],"Our":[41],"findings":[42],"reveal":[43],"systemic":[45],"failure:":[46],"researchers":[47],"with":[48,61],"Computer":[49],"Science":[50],"backgrounds":[51,63],"struggle":[52],"to":[53,87,105],"bridge":[54],"\"knowledge":[57],"gap\",":[58],"those":[60],"Biology":[62],"bogged":[65],"down":[66],"by":[67,142],"\"installation":[68],"hell\"":[69],"fragmented":[71],"documentation.":[72],"Furthermore,":[73],"observe":[75,127],"that":[76,100],"AI":[78],"tools":[79],"increasingly":[81],"adopted,":[82],"their":[83],"usage":[84],"remains":[85],"superficial\u2014restricted":[86],"generating":[88],"isolated":[89],"code":[90],"snippets":[91],"rather":[92],"than":[93],"addressing":[94],"structural":[95],"engineering":[96],"debt.":[97],"We":[98,112],"argue":[99],"current":[102],"solution\u2014expecting":[103],"scientists":[104],"act":[106],"as":[107],"expert":[108],"systems":[109],"engineers\u2014is":[110],"unscalable.":[111],"propose":[113],"vision":[115,148],"Bio-Aware":[117],"Software":[118],"Engineering":[119],"(BASE):":[120],"an":[121],"AI-driven":[122],"paradigm":[123],"where":[124],"\"invisible\"":[125],"agents":[126],"exploratory":[128],"analysis":[129],"automatically":[131],"synthesize":[132],"necessary":[134],"(containers,":[137],"regression":[138],"tests,":[139],"documentation)":[141],"leveraging":[143],"domain-specific":[144],"knowledge":[145],"graphs.":[146],"This":[147],"points":[149],"toward":[150],"more":[151],"reproducible":[152],"maintainable":[154],"workflows.":[156]},"counts_by_year":[],"updated_date":"2026-07-18T05:58:53.570196","created_date":"2026-07-18T00:00:00"}
