{"id":"https://openalex.org/W3090642000","doi":"https://doi.org/10.1109/tcbb.2020.3028776","title":"In Silico Laboratory Experiments Using Statistical Model Checking: A New Model of the Palytoxin-Induced Pump Channel as Case Study","display_name":"In Silico Laboratory Experiments Using Statistical Model Checking: A New Model of the Palytoxin-Induced Pump Channel as Case Study","publication_year":2020,"publication_date":"2020-10-05","ids":{"openalex":"https://openalex.org/W3090642000","doi":"https://doi.org/10.1109/tcbb.2020.3028776","mag":"3090642000","pmid":"https://pubmed.ncbi.nlm.nih.gov/33017286"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3028776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3028776","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5090196027","display_name":"Gabriel Domingo Vilallonga","orcid":"https://orcid.org/0000-0002-5590-9807"},"institutions":[{"id":"https://openalex.org/I73822459","display_name":"National University of San Luis","ror":"https://ror.org/00mczdx43","country_code":"AR","type":"education","lineage":["https://openalex.org/I73822459"]}],"countries":["AR"],"is_corresponding":true,"raw_author_name":"Gabriel Vilallonga","raw_affiliation_strings":["Computer Department, National University of San Luis, San Luis, Argentina"],"affiliations":[{"raw_affiliation_string":"Computer Department, National University of San Luis, San Luis, Argentina","institution_ids":["https://openalex.org/I73822459"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065679148","display_name":"Daniel Eduardo Riesco","orcid":"https://orcid.org/0000-0001-7335-7471"},"institutions":[{"id":"https://openalex.org/I73822459","display_name":"National University of San Luis","ror":"https://ror.org/00mczdx43","country_code":"AR","type":"education","lineage":["https://openalex.org/I73822459"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Daniel Riesco","raw_affiliation_strings":["Computer Department, National University of San Luis, San Luis, Argentina"],"affiliations":[{"raw_affiliation_string":"Computer Department, National University of San Luis, San Luis, Argentina","institution_ids":["https://openalex.org/I73822459"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024529604","display_name":"Ant\u00f4nio-Carlos G. de Almeida","orcid":"https://orcid.org/0000-0003-4893-338X"},"institutions":[{"id":"https://openalex.org/I166595947","display_name":"Federal University of S\u00e3o Jo\u00e3o del-Rei","ror":"https://ror.org/03vrj4p82","country_code":"BR","type":"education","lineage":["https://openalex.org/I166595947"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Antonio-Carlos G. de Almeida","raw_affiliation_strings":["Department of Biosystems Engineering, Federal University of S\u00e3o Jo\u00e3o del Rei, S\u00e3o Jo\u00e3o del Rei, MG, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Biosystems Engineering, Federal University of S\u00e3o Jo\u00e3o del Rei, S\u00e3o Jo\u00e3o del Rei, MG, Brazil","institution_ids":["https://openalex.org/I166595947"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038533104","display_name":"Ant\u00f4nio M\u00e1rcio Rodrigues","orcid":"https://orcid.org/0000-0002-2678-9180"},"institutions":[{"id":"https://openalex.org/I166595947","display_name":"Federal University of S\u00e3o Jo\u00e3o del-Rei","ror":"https://ror.org/03vrj4p82","country_code":"BR","type":"education","lineage":["https://openalex.org/I166595947"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Antonio M. Rodrigues","raw_affiliation_strings":["Department of Biosystems Engineering, Federal University of S\u00e3o Jo\u00e3o del Rei, S\u00e3o Jo\u00e3o del Rei, MG, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Biosystems Engineering, Federal University of S\u00e3o Jo\u00e3o del Rei, S\u00e3o Jo\u00e3o del Rei, MG, Brazil","institution_ids":["https://openalex.org/I166595947"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020200827","display_name":"S\u00e9rgio Campos","orcid":"https://orcid.org/0000-0002-0377-3143"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]},{"id":"https://openalex.org/I4210156583","display_name":"Laboratoire d'Informatique de Paris-Nord","ror":"https://ror.org/05g1zjw44","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210091279","https://openalex.org/I4210156583","https://openalex.org/I4210159245"]}],"countries":["BR","FR"],"is_corresponding":false,"raw_author_name":"Sergio V. A. Campos","raw_affiliation_strings":["Computer Science Department, Minas Gerais Federal University, Belo Horizonte, Brasil"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Minas Gerais Federal University, Belo Horizonte, Brasil","institution_ids":["https://openalex.org/I110200422","https://openalex.org/I4210156583"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5090196027"],"corresponding_institution_ids":["https://openalex.org/I73822459"],"apc_list":null,"apc_paid":null,"fwci":0.1669,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.50743426,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"6","first_page":"2816","last_page":"2822"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9937999844551086,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9937999844551086,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9904000163078308,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9861000180244446,"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":0.7788782119750977},{"id":"https://openalex.org/keywords/palytoxin","display_name":"Palytoxin","score":0.7564547061920166},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.588587760925293},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5622290372848511},{"id":"https://openalex.org/keywords/channel","display_name":"Channel (broadcasting)","score":0.46804141998291016},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.4575771987438202},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3023494482040405},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.18356189131736755},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10540485382080078},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.0871993899345398}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7788782119750977},{"id":"https://openalex.org/C2776506862","wikidata":"https://www.wikidata.org/wiki/Q425134","display_name":"Palytoxin","level":3,"score":0.7564547061920166},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.588587760925293},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5622290372848511},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.46804141998291016},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.4575771987438202},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3023494482040405},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.18356189131736755},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10540485382080078},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0871993899345398},{"id":"https://openalex.org/C2777367657","wikidata":"https://www.wikidata.org/wiki/Q184651","display_name":"Toxin","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000095702","descriptor_name":"Polyether Toxins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000178","descriptor_name":"Acrylamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000178","descriptor_name":"Acrylamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000178","descriptor_name":"Acrylamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000254","descriptor_name":"Sodium-Potassium-Exchanging ATPase","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000254","descriptor_name":"Sodium-Potassium-Exchanging ATPase","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D000254","descriptor_name":"Sodium-Potassium-Exchanging ATPase","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D003064","descriptor_name":"Cnidarian Venoms","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003064","descriptor_name":"Cnidarian Venoms","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D003064","descriptor_name":"Cnidarian Venoms","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.3028776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3028776","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33017286","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33017286","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.47999998927116394}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322980","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","ror":"https://ror.org/00nc55f03"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W180513329","https://openalex.org/W187227677","https://openalex.org/W1500442791","https://openalex.org/W1569248486","https://openalex.org/W1761383617","https://openalex.org/W1874944649","https://openalex.org/W1981170859","https://openalex.org/W1987535580","https://openalex.org/W2000947342","https://openalex.org/W2039181814","https://openalex.org/W2042321087","https://openalex.org/W2074807783","https://openalex.org/W2078149040","https://openalex.org/W2079045633","https://openalex.org/W2093033248","https://openalex.org/W2093179886","https://openalex.org/W2103822775","https://openalex.org/W2108777506","https://openalex.org/W2110903336","https://openalex.org/W2125930621","https://openalex.org/W2134073447","https://openalex.org/W2139696544","https://openalex.org/W2147556100","https://openalex.org/W2147748964","https://openalex.org/W2155418451","https://openalex.org/W2166423024","https://openalex.org/W2167154952","https://openalex.org/W2178254916","https://openalex.org/W2219609441","https://openalex.org/W2271042972","https://openalex.org/W2576480798","https://openalex.org/W2787596386","https://openalex.org/W2793007069","https://openalex.org/W2963108031","https://openalex.org/W3101168669","https://openalex.org/W3140384403","https://openalex.org/W6848561989"],"related_works":["https://openalex.org/W1985354493","https://openalex.org/W2041645350","https://openalex.org/W2003776343","https://openalex.org/W2126342724","https://openalex.org/W1967004579","https://openalex.org/W1567980165","https://openalex.org/W2177141550","https://openalex.org/W2012187838","https://openalex.org/W2026060074","https://openalex.org/W2395285286"],"abstract_inverted_index":{"Studying":[0],"biological":[1,51,196],"systems":[2],"is":[3],"a":[4,38,44,113,148,156],"difficult":[5],"but":[6,24],"important":[7,23],"task.":[8],"Traditional":[9],"methods":[10],"include":[11],"laboratory":[12,78],"experimentation":[13],"and":[14,55,62,96,134,164,180,192],"computer":[15],"simulations.":[16,69],"However,":[17],"often":[18],"researchers":[19],"need":[20],"to":[21,42,49,60,63,76,88,92,111,154,176,182,190],"explore":[22,64,93],"potentially":[25,198],"rare":[26],"events":[27,54,95],"that":[28,46,57],"are":[29,86],"not":[30,141],"easily":[31],"observed":[32],"or":[33],"simulated.":[34],"We":[35,70,106],"use":[36,169],"UPPAAL-SMC,":[37],"formal":[39],"verification":[40],"tool":[41],"support":[43],"methodology":[45,110,172],"allows":[47],"us":[48,175],"model":[50,116,159,191],"systems,":[52,197],"specify":[53],"conditions":[56,97,101],"we":[58,85,129,150],"want":[59],"analyze,":[61],"system":[65],"executions":[66],"using":[67],"controlled":[68],"also":[71],"describe":[72],"an":[73],"efficient":[74],"way":[75],"reproduce":[77],"experiments":[79],"in":[80,102,144],"silico.":[81],"Unlike":[82],"traditional":[83],"simulations,":[84],"able":[87,153],"guide":[89],"the":[90,161,178,200],"experiment":[91],"special":[94],"by":[98],"expressing":[99],"these":[100],"temporal":[103],"logic":[104],"formulas.":[105],"have":[107,130,151],"applied":[108],"this":[109,184],"create":[112],"more":[114],"detailed":[115],"of":[117,170,202],"Palytoxin-induced":[118],"Na":[119],"<sup>+</sup>/K":[120],"<sup>+</sup>":[121],"pump":[122],"channels":[123],"than":[124],"was":[125],"previously":[126],"possible.":[127],"Moreover,":[128],"reproduced":[131],"experimental":[132],"protocols":[133],"their":[135],"associated":[136],"electrophysiological":[137],"recordings,":[138],"which":[139],"has":[140,173],"been":[142,152],"done":[143],"previous":[145],"works.":[146],"As":[147],"consequence,":[149],"propose":[155],"new":[157],"diprotomeric":[158],"for":[160],"PTX-pump":[162],"complex":[163,195],"study":[165],"its":[166],"behaviour.":[167],"The":[168],"our":[171],"enabled":[174],"reduce":[177],"effort":[179],"time":[181],"perform":[183],"research.":[185],"It":[186],"can":[187],"be":[188],"used":[189],"analyze":[193],"other":[194],"increasing":[199],"productivity":[201],"such":[203],"studies.":[204]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
