{"id":"https://openalex.org/W2056347060","doi":"https://doi.org/10.1109/embc.2013.6610802","title":"A versatile platform for multilevel modeling of physiological systems: Template/instance framework for large-scale modeling and simulation","display_name":"A versatile platform for multilevel modeling of physiological systems: Template/instance framework for large-scale modeling and simulation","publication_year":2013,"publication_date":"2013-07-01","ids":{"openalex":"https://openalex.org/W2056347060","doi":"https://doi.org/10.1109/embc.2013.6610802","mag":"2056347060","pmid":"https://pubmed.ncbi.nlm.nih.gov/24110989"},"language":"en","primary_location":{"id":"doi:10.1109/embc.2013.6610802","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2013.6610802","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-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/A5076163894","display_name":"Yoshiyuki Asai","orcid":"https://orcid.org/0000-0001-5519-4306"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yoshiyuki Asai","raw_affiliation_strings":["Okinawa Institute of Science and Technology, Graduate University, Japan","Okinawa Inst. of Sci. & Technol., Grad. Univ., Okinawa, Japan"],"affiliations":[{"raw_affiliation_string":"Okinawa Institute of Science and Technology, Graduate University, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Okinawa Inst. of Sci. & Technol., Grad. Univ., Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090276476","display_name":"Takeshi Ab\u00e9","orcid":"https://orcid.org/0000-0002-7074-4561"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takeshi Abe","raw_affiliation_strings":["Okinawa Institute of Science and Technology, Graduate University, Japan","Okinawa Inst. of Sci. & Technol., Grad. Univ., Okinawa, Japan"],"affiliations":[{"raw_affiliation_string":"Okinawa Institute of Science and Technology, Graduate University, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Okinawa Inst. of Sci. & Technol., Grad. Univ., Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112104695","display_name":"Hideki Oka","orcid":null},"institutions":[{"id":"https://openalex.org/I2800939219","display_name":"RIKEN Center for Brain Science","ror":"https://ror.org/04j1n1c04","country_code":"JP","type":"facility","lineage":["https://openalex.org/I2800939219","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hideki Oka","raw_affiliation_strings":["Neuroinformatics Japan Center, RIKEN Brain Science Institute, Wako, Saitama, Japan","Neuroinf. Japan Center, RIKEN Brain Sci. Inst., Wako, Japan"],"affiliations":[{"raw_affiliation_string":"Neuroinformatics Japan Center, RIKEN Brain Science Institute, Wako, Saitama, Japan","institution_ids":["https://openalex.org/I2800939219"]},{"raw_affiliation_string":"Neuroinf. Japan Center, RIKEN Brain Sci. Inst., Wako, Japan","institution_ids":["https://openalex.org/I2800939219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062323789","display_name":"Masao Okita","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masao Okita","raw_affiliation_strings":["Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","Grad. Sch. of Information Science and Technology, Osaka University, Suita, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Grad. Sch. of Information Science and Technology, Osaka University, Suita, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110979204","display_name":"T. OKUYAMA","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tomohiro Okuyama","raw_affiliation_strings":["Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","Grad. Sch. of Information Science and Technology, Osaka University, Suita, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Grad. Sch. of Information Science and Technology, Osaka University, Suita, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111729293","display_name":"Kenichi Hagihara","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ken-ichi Hagihara","raw_affiliation_strings":["Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","Grad. Sch. of Information Science and Technology, Osaka University, Suita, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Grad. Sch. of Information Science and Technology, Osaka University, Suita, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101748369","display_name":"Samik Ghosh","orcid":"https://orcid.org/0000-0002-0239-5400"},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Samik Ghosh","raw_affiliation_strings":["Systems Biology Institute, Tokyo, Japan","Syst. Biol. Inst., Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Systems Biology Institute, Tokyo, Japan","institution_ids":["https://openalex.org/I4210118579"]},{"raw_affiliation_string":"Syst. Biol. Inst., Tokyo, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108400380","display_name":"Yukiko Matsuoka","orcid":null},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yukiko Matsuoka","raw_affiliation_strings":["Systems Biology Institute, Tokyo, Japan","Syst. Biol. Inst., Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Systems Biology Institute, Tokyo, Japan","institution_ids":["https://openalex.org/I4210118579"]},{"raw_affiliation_string":"Syst. Biol. Inst., Tokyo, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108642574","display_name":"Yoshihisa Kurachi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshihisa Kurachi","raw_affiliation_strings":["Systems Biology Institute, Tokyo, Japan","Grad. School of Med., Osaka University Suita, Japan"],"affiliations":[{"raw_affiliation_string":"Systems Biology Institute, Tokyo, Japan","institution_ids":["https://openalex.org/I4210118579"]},{"raw_affiliation_string":"Grad. School of Med., Osaka University Suita, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041639990","display_name":"Hrioaki Kitano","orcid":null},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hrioaki Kitano","raw_affiliation_strings":["Systems Biology Institute, Tokyo, Japan","Syst. Biol. Inst., Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Systems Biology Institute, Tokyo, Japan","institution_ids":["https://openalex.org/I4210118579"]},{"raw_affiliation_string":"Syst. Biol. Inst., Tokyo, Japan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5076163894"],"corresponding_institution_ids":["https://openalex.org/I142637625"],"apc_list":null,"apc_paid":null,"fwci":1.0235,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.75823379,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2013","issue":null,"first_page":"5529","last_page":"5532"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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":0.9991000294685364,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9825999736785889,"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/T13286","display_name":"Modeling and Simulation Systems","score":0.973800003528595,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/computer-science","display_name":"Computer science","score":0.8224669694900513},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.6526681184768677},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.577745258808136},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5537197589874268},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4853779077529907},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4692637324333191},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.4534674882888794},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4091905951499939},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.34529173374176025},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16425642371177673},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.09531116485595703}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8224669694900513},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.6526681184768677},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.577745258808136},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5537197589874268},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4853779077529907},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4692637324333191},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.4534674882888794},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4091905951499939},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.34529173374176025},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16425642371177673},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09531116485595703},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001479","descriptor_name":"Basal Ganglia","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001479","descriptor_name":"Basal Ganglia","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001479","descriptor_name":"Basal Ganglia","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010829","descriptor_name":"Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010829","descriptor_name":"Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010829","descriptor_name":"Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc.2013.6610802","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2013.6610802","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:24110989","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24110989","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1975493056","https://openalex.org/W1982174804","https://openalex.org/W2028146834","https://openalex.org/W2029754211","https://openalex.org/W2042880070","https://openalex.org/W2046993276","https://openalex.org/W2071869593","https://openalex.org/W2098584633","https://openalex.org/W2110728169","https://openalex.org/W2126628133","https://openalex.org/W2143784594","https://openalex.org/W2147990117","https://openalex.org/W2150908245","https://openalex.org/W4247347321"],"related_works":["https://openalex.org/W1994468522","https://openalex.org/W2379971018","https://openalex.org/W2370942061","https://openalex.org/W2386975346","https://openalex.org/W2099682047","https://openalex.org/W2057537409","https://openalex.org/W1494152264","https://openalex.org/W1513606646","https://openalex.org/W2385120298","https://openalex.org/W2386058939"],"abstract_inverted_index":{"Building":[0],"multilevel":[1,63],"models":[2,30,141],"of":[3,17,61,95,100,102,135],"physiological":[4,78],"systems":[5],"is":[6,83,106,108,111,152],"a":[7,14,81,86,90,143],"significant":[8],"and":[9,20,26,37,88,118,146],"effective":[10],"method":[11],"for":[12,44,138],"integrating":[13],"huge":[15],"amount":[16],"bio-physiological":[18],"data":[19],"knowledge":[21],"obtained":[22],"by":[23],"earlier":[24],"experiments":[25],"simulations.":[27],"Since":[28],"such":[29],"tend":[31],"to":[32,113],"be":[33],"large":[34],"in":[35,39,71,80],"size":[36],"complicated":[38],"structure,":[40],"appropriate":[41],"software":[42,51],"frameworks":[43],"supporting":[45],"modeling":[46],"activities":[47],"are":[48,69,123],"required.":[49],"A":[50],"platform,":[52],"PhysioDesigner,":[53],"has":[54],"been":[55],"developed,":[56],"which":[57,103,128],"supports":[58],"the":[59,98,104,115,136,149],"process":[60],"creating":[62],"models.":[64],"Models":[65],"developed":[66,133],"on":[67,131],"PhysioDesigner":[68,150],"established":[70],"an":[72,93],"XML":[73],"format":[74],"called":[75],"PHML.":[76],"Every":[77],"entity":[79],"model":[82,91,105],"represented":[84],"as":[85],"module,":[87],"hence":[89],"constitutes":[92],"aggregation":[94],"modules.":[96],"When":[97],"number":[99],"entities":[101,116],"comprised":[107],"large,":[109],"it":[110],"difficult":[112],"manage":[114],"manually,":[117],"some":[119],"semiautomatic":[120],"assistive":[121],"functions":[122],"necessary.":[124],"In":[125],"this":[126],"article,":[127],"focuses":[129],"particularly":[130],"recently":[132],"features":[134],"platform":[137,151],"building":[139],"large-scale":[140],"utilizing":[142],"template/instance":[144],"framework":[145],"morphological":[147],"information,":[148],"introduced.":[153]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
