{"id":"https://openalex.org/W3185911499","doi":"https://doi.org/10.5220/0010546302880294","title":"VDNA-Lab: A Computational Simulation Platform for DNA Multi-strand Dynamics","display_name":"VDNA-Lab: A Computational Simulation Platform for DNA Multi-strand Dynamics","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3185911499","doi":"https://doi.org/10.5220/0010546302880294","mag":"3185911499"},"language":"en","primary_location":{"id":"doi:10.5220/0010546302880294","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0010546302880294","pdf_url":null,"source":null,"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":"Proceedings of the 11th International Conference on Simulation and Modeling Methodologies, Technologies and Applications","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5220/0010546302880294","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048439161","display_name":"Frankie Spencer","orcid":null},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Frankie Spencer","raw_affiliation_strings":["Department of Information Technologies, \u00c5bo Akademi University, Turku, Finland, --- Select a Country ---"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technologies, \u00c5bo Akademi University, Turku, Finland, --- Select a Country ---","institution_ids":["https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054005888","display_name":"Usman Sanwal","orcid":null},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Usman Sanwal","raw_affiliation_strings":["Department of Information Technologies, \u00c5bo Akademi University, Turku, Finland, --- Select a Country ---"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technologies, \u00c5bo Akademi University, Turku, Finland, --- Select a Country ---","institution_ids":["https://openalex.org/I130217899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081215602","display_name":"Eugen Czeizler","orcid":"https://orcid.org/0000-0002-1607-1554"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I4210115638","display_name":"National Institute of Research and Development for Biological Sciences","ror":"https://ror.org/028wkbm97","country_code":"RO","type":"facility","lineage":["https://openalex.org/I4210115638"]}],"countries":["FI","RO"],"is_corresponding":false,"raw_author_name":"Eugen Czeizler","raw_affiliation_strings":["Department of Information Technologies, \u00c5bo Akademi University, Turku, Finland, --- Select a Country ---","National Institute for Research and Development of Biological Sciences, Bucharest, Romania, --- Select a Country ---"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technologies, \u00c5bo Akademi University, Turku, Finland, --- Select a Country ---","institution_ids":["https://openalex.org/I130217899"]},{"raw_affiliation_string":"National Institute for Research and Development of Biological Sciences, Bucharest, Romania, --- Select a Country ---","institution_ids":["https://openalex.org/I4210115638"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1333632,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"288","last_page":"294"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9865000247955322,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9865000247955322,"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/T12029","display_name":"DNA and Biological Computing","score":0.9488999843597412,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.946399986743927,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental 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":0.6195699572563171},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.4895726144313812},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4690186381340027},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4665037989616394},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.37585747241973877},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2680462896823883},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13070181012153625},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10711303353309631}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6195699572563171},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4895726144313812},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4690186381340027},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4665037989616394},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.37585747241973877},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2680462896823883},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13070181012153625},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10711303353309631},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5220/0010546302880294","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0010546302880294","pdf_url":null,"source":null,"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":"Proceedings of the 11th International Conference on Simulation and Modeling Methodologies, Technologies and Applications","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.atira.dk:publications/f3873df9-1100-449e-808d-6fa35a8f9bbb","is_oa":false,"landing_page_url":"https://research.abo.fi/en/publications/f3873df9-1100-449e-808d-6fa35a8f9bbb","pdf_url":null,"source":{"id":"https://openalex.org/S4406923060","display_name":"\u00c5bo Akademi University Research Portal","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"doi:10.5220/0010546302880294","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0010546302880294","pdf_url":null,"source":null,"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":"Proceedings of the 11th International Conference on Simulation and Modeling Methodologies, Technologies and Applications","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"The":[0,12,158],"dynamics":[1],"of":[2,18,97],"nucleic-acids":[3],"dynamical":[4],"systems":[5,43],"is":[6,38,160],"intrinsically":[7],"based":[8,52],"on":[9,21,29,53],"local":[10,54],"interaction.":[11],"major":[13],"acting":[14],"mechanisms":[15],"are":[16],"that":[17,41],"Watson-Crick":[19],"complementarity":[20],"one-hand,":[22],"generating":[23,32],"binding":[24],"events,":[25],"and":[26,35,86,136,156],"thermal":[27],"energy":[28],"the":[30,58,67,115,122,128,145],"other,":[31],"random":[33],"motion":[34],"un-binding.":[36],"It":[37,107],"thus":[39],"predictable":[40],"such":[42,56,94],"can":[44,141],"be":[45,142],"successfully":[46],"captured":[47],"by":[48],"computational":[49,130],"modeling":[50,60,131],"paradigms":[51],"interactions,":[55],"as":[57,95,125,127],"rule-based":[59],"methodology.":[61],"In":[62],"this":[63],"research":[64],"we":[65],"introduce":[66],"Virtual":[68],"DNA":[69,91,98,123],"Lab":[70],"(VDNA-Lab)":[71],"a":[72,109],"simulation":[73],"tool":[74],"which":[75,150],"provides":[76],"an":[77],"easy":[78],"to":[79,120,133],"use":[80],"graphical":[81],"interface":[82],"for":[83,90,153],"creating,":[84],"running":[85],"visualizing":[87],"synthetic":[88],"simulations":[89,135],"assembly":[92,96,105],"systems,":[93,103],"nanostructures,":[99],"strand":[100],"displacement":[101],"cascades":[102],"DNA-tile":[104],"etc.":[106],"employs":[108],"custom":[110],"designed":[111],"model,":[112],"implemented":[113],"in":[114],"BioNetGen":[116],"Language":[117],"(BNGL)":[118],"formalism,":[119],"capture":[121],"dynamics,":[124],"well":[126],"NFsim":[129],"engine":[132],"run":[134],"generate":[137],"outputs.":[138],"These":[139],"outputs":[140],"visualized":[143],"using":[144],"VDNA-Lab\u2019s":[146],"own":[147],"visualization":[148],"tool,":[149],"allows":[151],"also":[152],"further":[154],"analysis":[155],"filtering.":[157],"software":[159],"freely":[161],"available":[162],"at":[163],"https://github.com/Frankie-Spencer/virtual":[164],"dna":[165],"lab.":[166]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
