{"id":"https://openalex.org/W2564557214","doi":"https://doi.org/10.1109/iccabs.2016.7802784","title":"Poster: Diagnosing and treating code-duplication problems in bioinformatics libraries","display_name":"Poster: Diagnosing and treating code-duplication problems in bioinformatics libraries","publication_year":2016,"publication_date":"2016-10-01","ids":{"openalex":"https://openalex.org/W2564557214","doi":"https://doi.org/10.1109/iccabs.2016.7802784","mag":"2564557214"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2016.7802784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2016.7802784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","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/A5028731027","display_name":"Mohammad Shabbir Hasan","orcid":"https://orcid.org/0000-0001-6263-631X"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mohammad Shabbir Hasan","raw_affiliation_strings":["Dept. of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063912603","display_name":"Saima Sultana Tithi","orcid":"https://orcid.org/0000-0001-5087-0125"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saima Sultana Tithi","raw_affiliation_strings":["Dept. of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013168771","display_name":"Eli Tilevich","orcid":"https://orcid.org/0000-0003-2415-6926"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eli Tilevich","raw_affiliation_strings":["Eli Tilevich, Software Innovations Lab, Virginia Tech, Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"Eli Tilevich, Software Innovations Lab, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061868278","display_name":"Liqing Zhang","orcid":"https://orcid.org/0000-0003-4660-9199"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liqing Zhang","raw_affiliation_strings":["Dept. of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5028731027"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18322903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9947999715805054,"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":0.9947999715805054,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9869999885559082,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.9858999848365784,"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/maintainability","display_name":"Maintainability","score":0.7400631904602051},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7236713767051697},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.6227739453315735},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.5707406997680664},{"id":"https://openalex.org/keywords/software-quality","display_name":"Software quality","score":0.5313563942909241},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5096986293792725},{"id":"https://openalex.org/keywords/software-maintenance","display_name":"Software maintenance","score":0.495230108499527},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4651634991168976},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.42075857520103455},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.41866326332092285},{"id":"https://openalex.org/keywords/code-refactoring","display_name":"Code refactoring","score":0.41690051555633545},{"id":"https://openalex.org/keywords/code-review","display_name":"Code review","score":0.4153473675251007},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.3392414450645447},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3232690989971161}],"concepts":[{"id":"https://openalex.org/C160713754","wikidata":"https://www.wikidata.org/wiki/Q1389965","display_name":"Maintainability","level":2,"score":0.7400631904602051},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7236713767051697},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.6227739453315735},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5707406997680664},{"id":"https://openalex.org/C117447612","wikidata":"https://www.wikidata.org/wiki/Q1412670","display_name":"Software quality","level":4,"score":0.5313563942909241},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5096986293792725},{"id":"https://openalex.org/C101317890","wikidata":"https://www.wikidata.org/wiki/Q940053","display_name":"Software maintenance","level":4,"score":0.495230108499527},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4651634991168976},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.42075857520103455},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.41866326332092285},{"id":"https://openalex.org/C152752567","wikidata":"https://www.wikidata.org/wiki/Q116877","display_name":"Code refactoring","level":3,"score":0.41690051555633545},{"id":"https://openalex.org/C150292731","wikidata":"https://www.wikidata.org/wiki/Q1342704","display_name":"Code review","level":5,"score":0.4153473675251007},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.3392414450645447},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3232690989971161},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2016.7802784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2016.7802784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W2075996757","https://openalex.org/W2102619694","https://openalex.org/W2113354821","https://openalex.org/W2167200667"],"related_works":["https://openalex.org/W2146134503","https://openalex.org/W2512989791","https://openalex.org/W2186150085","https://openalex.org/W2219145617","https://openalex.org/W2026866620","https://openalex.org/W4236840126","https://openalex.org/W1648987790","https://openalex.org/W1514851312","https://openalex.org/W4233305372","https://openalex.org/W2010680342"],"abstract_inverted_index":{"As":[0,29],"computing":[1],"is":[2],"an":[3,119],"enabling":[4],"tool":[5,121,176],"of":[6,16,24,68,71,79,94,106,114,141,148],"bioinformatics,":[7],"software":[8,62],"quality":[9,105,147],"can":[10,177],"influence":[11],"not":[12],"only":[13],"the":[14,17,22,55,72,77,92,103,112,139,146],"efficiency":[15],"research":[18],"process,":[19],"but":[20],"also":[21],"degree":[23],"confidence":[25],"in":[26],"scientific":[27],"findings.":[28],"we":[30,90,98,117,131],"discovered,":[31],"popular":[32,107],"bioinformatics":[33,108],"C++":[34,152,159],"libraries":[35,166],"suffer":[36,168],"from":[37,169],"problems":[38],"that":[39,122,164,173],"make":[40],"their":[41,180],"code":[42,51,74,104,128],"hard":[43],"to":[44,82,101,144],"maintain,":[45],"finetune,":[46],"and":[47,64,125,157,172],"extend.":[48],"In":[49,87],"particular,":[50],"duplication":[52],"caused":[53],"by":[54],"ubiquitous":[56],"copy-and-paste":[57],"development":[58],"practice,":[59],"substantially":[60],"complicates":[61],"maintenance":[63],"evolution.":[65],"The":[66],"presence":[67],"multiple":[69],"clones":[70],"same":[73],"snippet":[75],"multiples":[76],"amount":[78],"effort":[80],"required":[81],"modify":[83],"or":[84],"extend":[85],"it.":[86],"this":[88],"paper,":[89],"present":[91],"results":[93,113,140,162],"a":[95],"systematic":[96],"study":[97],"have":[99],"conducted":[100],"understand":[102],"libraries.":[109],"Based":[110],"on":[111],"our":[115,133,174],"study,":[116],"developed":[118],"automated":[120,175],"systematically":[123],"identifies":[124],"consolidates":[126],"duplicated":[127],"blocks.":[129],"Here":[130],"describe":[132],"tool\u2014ReBio":[134],"<sup":[135],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[136],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">1</sup>":[137],"\u2014and":[138],"applying":[142],"it":[143],"improve":[145,179],"several":[149],"commonly":[150],"used":[151],"libraries,":[153],"including":[154],"SeqAn,":[155],"BEDtools,":[156],"NCBI":[158],"Toolkit.":[160],"Our":[161],"reveal":[163],"these":[165],"indeed":[167],"poor":[170],"maintainability,":[171],"effectively":[178],"quality.":[181]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
