{"id":"https://openalex.org/W2808867322","doi":"https://doi.org/10.2298/csis170510009v","title":"Solving the DNA fragment assembly problem with a parallel discrete firefly algorithm implemented on GPU","display_name":"Solving the DNA fragment assembly problem with a parallel discrete firefly algorithm implemented on GPU","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2808867322","doi":"https://doi.org/10.2298/csis170510009v","mag":"2808867322"},"language":"en","primary_location":{"id":"doi:10.2298/csis170510009v","is_oa":true,"landing_page_url":"https://doi.org/10.2298/csis170510009v","pdf_url":"http://www.doiserbia.nb.rs/ft.aspx?id=1820-02141800009V","source":{"id":"https://openalex.org/S206939107","display_name":"Computer Science and Information Systems","issn_l":"1820-0214","issn":["1820-0214","2406-1018"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310321031","host_organization_name":"ComSIS Consortium","host_organization_lineage":["https://openalex.org/P4310321031"],"host_organization_lineage_names":["ComSIS Consortium"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Science and Information Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"http://www.doiserbia.nb.rs/ft.aspx?id=1820-02141800009V","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085782739","display_name":"Pablo Javier Vidal","orcid":"https://orcid.org/0000-0001-6502-8010"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I3131880250","display_name":"National University of Austral Patagonia","ror":"https://ror.org/023f76417","country_code":"AR","type":"education","lineage":["https://openalex.org/I3131880250"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Pablo Vidal","raw_affiliation_strings":["CIT GSJ, CONICET Universidad Nacional de la Patagonia, Caleta Olivia, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIT GSJ, CONICET Universidad Nacional de la Patagonia, Caleta Olivia, Argentina","institution_ids":["https://openalex.org/I3131880250","https://openalex.org/I151201029"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065962628","display_name":"Ana Carolina Olivera","orcid":"https://orcid.org/0000-0001-7825-1959"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I3131880250","display_name":"National University of Austral Patagonia","ror":"https://ror.org/023f76417","country_code":"AR","type":"education","lineage":["https://openalex.org/I3131880250"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Ana Olivera","raw_affiliation_strings":["CIT GSJ, CONICET Universidad Nacional de la Patagonia, Caleta Olivia, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIT GSJ, CONICET Universidad Nacional de la Patagonia, Caleta Olivia, Argentina","institution_ids":["https://openalex.org/I3131880250","https://openalex.org/I151201029"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4639,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.63195844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"15","issue":"2","first_page":"273","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9976000189781189,"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/T12029","display_name":"DNA and Biological Computing","score":0.9976000189781189,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9939000010490417,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9936000108718872,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8165547847747803},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.6821675300598145},{"id":"https://openalex.org/keywords/firefly-algorithm","display_name":"Firefly algorithm","score":0.6371815800666809},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5883630514144897},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5722060203552246},{"id":"https://openalex.org/keywords/dna-computing","display_name":"DNA computing","score":0.564174473285675},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5100834965705872},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4942329227924347},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.4187277853488922},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3388804793357849},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.09062811732292175}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8165547847747803},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.6821675300598145},{"id":"https://openalex.org/C154982244","wikidata":"https://www.wikidata.org/wiki/Q5451844","display_name":"Firefly algorithm","level":3,"score":0.6371815800666809},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5883630514144897},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5722060203552246},{"id":"https://openalex.org/C82047324","wikidata":"https://www.wikidata.org/wiki/Q177126","display_name":"DNA computing","level":3,"score":0.564174473285675},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5100834965705872},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4942329227924347},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.4187277853488922},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3388804793357849},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.09062811732292175},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.2298/csis170510009v","is_oa":true,"landing_page_url":"https://doi.org/10.2298/csis170510009v","pdf_url":"http://www.doiserbia.nb.rs/ft.aspx?id=1820-02141800009V","source":{"id":"https://openalex.org/S206939107","display_name":"Computer Science and Information Systems","issn_l":"1820-0214","issn":["1820-0214","2406-1018"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310321031","host_organization_name":"ComSIS Consortium","host_organization_lineage":["https://openalex.org/P4310321031"],"host_organization_lineage_names":["ComSIS Consortium"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Science and Information Systems","raw_type":"journal-article"},{"id":"pmh:oai:americanae.aecid.es:3919442","is_oa":true,"landing_page_url":"http://hdl.handle.net/11336/102302","pdf_url":null,"source":{"id":"https://openalex.org/S4306400786","display_name":"Americanae (AECID Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"reponame:CONICET Digital (CONICET)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.2298/csis170510009v","is_oa":true,"landing_page_url":"https://doi.org/10.2298/csis170510009v","pdf_url":"http://www.doiserbia.nb.rs/ft.aspx?id=1820-02141800009V","source":{"id":"https://openalex.org/S206939107","display_name":"Computer Science and Information Systems","issn_l":"1820-0214","issn":["1820-0214","2406-1018"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310321031","host_organization_name":"ComSIS Consortium","host_organization_lineage":["https://openalex.org/P4310321031"],"host_organization_lineage_names":["ComSIS Consortium"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Science and Information Systems","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2941795740","display_name":null,"funder_award_id":"PIP 2015-2017","funder_id":"https://openalex.org/F4320321594","funder_display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas"},{"id":"https://openalex.org/G5266274040","display_name":null,"funder_award_id":"PIP 2015","funder_id":"https://openalex.org/F4320321594","funder_display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas"},{"id":"https://openalex.org/G6102413473","display_name":null,"funder_award_id":"PICT 2014-0430","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G6612484519","display_name":null,"funder_award_id":"2015-2017","funder_id":"https://openalex.org/F4320321594","funder_display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas"},{"id":"https://openalex.org/G7003424106","display_name":null,"funder_award_id":"PICT 2014","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G7378882120","display_name":null,"funder_award_id":"CONICET","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G849230359","display_name":null,"funder_award_id":"PICT 2014","funder_id":"https://openalex.org/F4320321594","funder_display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas"}],"funders":[{"id":"https://openalex.org/F4320321594","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59"},{"id":"https://openalex.org/F4320325381","display_name":"Universidad Nacional de la Patagonia Austral","ror":"https://ror.org/023f76417"},{"id":"https://openalex.org/F4320334832","display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","ror":"https://ror.org/03stxzb56"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2808867322.pdf","grobid_xml":"https://content.openalex.org/works/W2808867322.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W138900359","https://openalex.org/W210801244","https://openalex.org/W1527507758","https://openalex.org/W1543636183","https://openalex.org/W1596914020","https://openalex.org/W1612624539","https://openalex.org/W1766577897","https://openalex.org/W1797634622","https://openalex.org/W1965434026","https://openalex.org/W1987069789","https://openalex.org/W1998073824","https://openalex.org/W1999095989","https://openalex.org/W2006529263","https://openalex.org/W2010502318","https://openalex.org/W2042510074","https://openalex.org/W2044587647","https://openalex.org/W2046681803","https://openalex.org/W2046832190","https://openalex.org/W2050883661","https://openalex.org/W2058283730","https://openalex.org/W2093357099","https://openalex.org/W2098809090","https://openalex.org/W2153889777","https://openalex.org/W2154943049","https://openalex.org/W2159497035","https://openalex.org/W2166220592","https://openalex.org/W2166265186","https://openalex.org/W2170525931","https://openalex.org/W2182150153","https://openalex.org/W2257081743","https://openalex.org/W2398736067","https://openalex.org/W2752061190","https://openalex.org/W3098924781","https://openalex.org/W3106441463","https://openalex.org/W6636070404"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2027972911","https://openalex.org/W2146343568","https://openalex.org/W2013643406","https://openalex.org/W2157978810","https://openalex.org/W2111089054","https://openalex.org/W2597809628"],"abstract_inverted_index":{"The":[0,62],"Deoxyribonucleic":[1],"Acid":[2],"Fragment":[3,165],"Assembly":[4,166],"Problem":[5],"(DNA-FAP)":[6],"consists":[7],"in":[8,26,154],"reconstructing":[9],"a":[10,14,108,112,131,145,151],"DNA":[11,164],"chain":[12],"from":[13],"set":[15],"of":[16,82,96,117,123,173,179,194],"fragments":[17],"taken":[18],"randomly.":[19],"This":[20],"problem":[21],"represents":[22],"an":[23],"important":[24],"step":[25],"the":[27,38,75,83,92,99,121,136,158,163,171,174,177,180,185],"genome":[28],"project.":[29],"Several":[30],"authors":[31],"are":[32,65,105,182],"proposed":[33],"different":[34],"approaches":[35],"to":[36,134,156,187],"solve":[37],"DNA-FAP.":[39],"In":[40,138],"particular,":[41],"nature-inspired":[42],"algorithms":[43,64],"have":[44],"been":[45],"used":[46],"for":[47,111,161,189],"its":[48,56],"resolution.":[49],"Even":[50],"they":[51],"were":[52],"obtaining":[53],"good":[54],"results;":[55],"computational":[57],"time":[58],"associated":[59],"is":[60,80,89,128],"high.":[61],"bio-inspired":[63,118],"iterative":[66],"search":[67,159],"processes":[68],"that":[69],"can":[70],"explore":[71],"and":[72,115,143,176],"exploit":[73],"efficiently":[74],"solution":[76],"space.":[77],"Firefly":[78,147],"Algorithm":[79,148],"one":[81],"recent":[84],"evolutionary":[85],"computing":[86,126],"models":[87],"which":[88],"inspired":[90],"by":[91],"flashing":[93],"light":[94],"behaviour":[95],"fireflies.":[97],"Recently,":[98],"Graphics":[100],"Processing":[101],"Units":[102],"(GPUs)":[103],"technology":[104],"emerge":[106],"as":[107,130,197],"novel":[109],"environment":[110],"parallel":[113,125],"implementation":[114],"execution":[116],"algorithms.":[119],"Therefore,":[120],"use":[122],"GPU-based":[124],"it":[127],"possible":[129],"complementary":[132],"tool":[133],"speed-up":[135,157],"search.":[137],"this":[139],"work,":[140],"we":[141],"design":[142],"implement":[144],"Discrete":[146],"(DFA)":[149],"on":[150],"GPU":[152],"architecture":[153],"order":[155],"process":[160],"solving":[162],"Problem.":[167],"Through":[168],"several":[169],"experiments,":[170],"efficiency":[172],"algorithm":[175],"quality":[178],"results":[181],"demonstrated":[183],"with":[184],"potential":[186],"applied":[188],"longer":[190],"sequences":[191,193],"or":[192],"unknown":[195],"length":[196],"well.":[198]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}