{"id":"https://openalex.org/W2054307206","doi":"https://doi.org/10.1007/s11047-014-9428-7","title":"Utilising a simulation platform to understand the effect of domain model assumptions","display_name":"Utilising a simulation platform to understand the effect of domain model assumptions","publication_year":2014,"publication_date":"2014-06-03","ids":{"openalex":"https://openalex.org/W2054307206","doi":"https://doi.org/10.1007/s11047-014-9428-7","mag":"2054307206","pmid":"https://pubmed.ncbi.nlm.nih.gov/25722664"},"language":"en","primary_location":{"id":"doi:10.1007/s11047-014-9428-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-014-9428-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-014-9428-7.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s11047-014-9428-7.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024360871","display_name":"Kieran Alden","orcid":"https://orcid.org/0000-0003-4411-1776"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]},{"id":"https://openalex.org/I69768126","display_name":"Hull York Medical School","ror":"https://ror.org/0003e4m70","country_code":"GB","type":"education","lineage":["https://openalex.org/I69768126"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Kieran Alden","raw_affiliation_strings":["York Computational Immunology Lab, University of York, York, UK ; Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK","York Computational Immunology Lab, University of York, York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK ; Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK","institution_ids":["https://openalex.org/I69768126"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105835589","display_name":"Paul S. Andrews","orcid":null},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Paul S. Andrews","raw_affiliation_strings":["York Computational Immunology Lab, University of York, York, UK ; Department of Computer Science, University of York, York, UK","York Computational Immunology Lab, University of York, York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK ; Department of Computer Science, University of York, York, UK","institution_ids":["https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010960233","display_name":"Henrique Veiga\u2010Fernandes","orcid":"https://orcid.org/0000-0001-6216-1836"},"institutions":[{"id":"https://openalex.org/I4392738257","display_name":"Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes","ror":"https://ror.org/019g8w217","country_code":null,"type":"facility","lineage":["https://openalex.org/I141596103","https://openalex.org/I4392738257"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Henrique Veiga-Fernandes","raw_affiliation_strings":["Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I4392738257"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080582720","display_name":"Jon Timmis","orcid":"https://orcid.org/0000-0003-1055-0471"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jon Timmis","raw_affiliation_strings":["York Computational Immunology Lab, University of York, York, UK ; Department of Electronics, University of York, York, UK","York Computational Immunology Lab, University of York, York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK ; Department of Electronics, University of York, York, UK","institution_ids":["https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048352835","display_name":"Mark Coles","orcid":"https://orcid.org/0000-0001-8079-9358"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]},{"id":"https://openalex.org/I69768126","display_name":"Hull York Medical School","ror":"https://ror.org/0003e4m70","country_code":"GB","type":"education","lineage":["https://openalex.org/I69768126"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Coles","raw_affiliation_strings":["York Computational Immunology Lab, University of York, York, UK ; Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK","Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, UK ; Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK","institution_ids":["https://openalex.org/I69768126"]},{"raw_affiliation_string":"Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK","institution_ids":["https://openalex.org/I52099693","https://openalex.org/I69768126"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024360871"],"corresponding_institution_ids":["https://openalex.org/I52099693","https://openalex.org/I69768126"],"apc_list":{"value":2890,"currency":"USD","value_usd":2890},"apc_paid":{"value":2581,"currency":"EUR","value_usd":2783},"fwci":0.6335,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.75012002,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"14","issue":"1","first_page":"99","last_page":"107"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.8324000239372253,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.8324000239372253,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.8112000226974487,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8105000257492065,"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":0.6740898489952087},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5618903636932373},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.520343005657196},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5081813335418701},{"id":"https://openalex.org/keywords/constant","display_name":"Constant (computer programming)","score":0.4703614413738251},{"id":"https://openalex.org/keywords/risk-analysis","display_name":"Risk analysis (engineering)","score":0.37946709990501404},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.35720571875572205},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14834502339363098},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09754714369773865}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6740898489952087},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5618903636932373},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.520343005657196},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5081813335418701},{"id":"https://openalex.org/C2777027219","wikidata":"https://www.wikidata.org/wiki/Q1284190","display_name":"Constant (computer programming)","level":2,"score":0.4703614413738251},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.37946709990501404},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.35720571875572205},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14834502339363098},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09754714369773865},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1007/s11047-014-9428-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-014-9428-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-014-9428-7.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},{"id":"pmid:25722664","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25722664","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":"Natural computing","raw_type":null},{"id":"pmh:oai:europepmc.org:3303410","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4333240","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:repositorio.ul.pt:10451/51810","is_oa":true,"landing_page_url":"http://hdl.handle.net/10451/51810","pdf_url":null,"source":{"id":"https://openalex.org/S4306401074","display_name":"Reposit\u00f3rio da Universidade de Lisboa (University of Lisbon)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I141596103","host_organization_name":"University of Lisbon","host_organization_lineage":["https://openalex.org/I141596103"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1007/s11047-014-9428-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-014-9428-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-014-9428-7.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1768913244","display_name":null,"funder_award_id":"G0601156","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1933809232","display_name":null,"funder_award_id":"RGP0006","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G5378717371","display_name":"IDEAS Factory - Resilient Futures","funder_award_id":"EP/I005943/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5515747171","display_name":null,"funder_award_id":"313089","funder_id":"https://openalex.org/F4320312926","funder_display_name":"Crohn's and Colitis Foundation"},{"id":"https://openalex.org/G606666009","display_name":null,"funder_award_id":"EP/I005943/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312926","display_name":"Crohn's and Colitis Foundation","ror":"https://ror.org/05f2xbq60"},{"id":"https://openalex.org/F4320320005","display_name":"Royal Academy of Engineering","ror":"https://ror.org/0526snb40"},{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320332773","display_name":"Centre for Chronic Diseases and Disorders","ror":"https://ror.org/04m01e293"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2054307206.pdf","grobid_xml":"https://content.openalex.org/works/W2054307206.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W575496914","https://openalex.org/W1577650155","https://openalex.org/W1871004530","https://openalex.org/W1897184448","https://openalex.org/W1965335252","https://openalex.org/W1979034309","https://openalex.org/W1993321999","https://openalex.org/W2009917832","https://openalex.org/W2023566060","https://openalex.org/W2040580015","https://openalex.org/W2043116521","https://openalex.org/W2077157308","https://openalex.org/W2086829762","https://openalex.org/W2125413784","https://openalex.org/W2132635773","https://openalex.org/W2145703742","https://openalex.org/W2148655474","https://openalex.org/W2152803686","https://openalex.org/W2154328223","https://openalex.org/W2162742070","https://openalex.org/W2168574777","https://openalex.org/W2185516849","https://openalex.org/W2397852341"],"related_works":["https://openalex.org/W2062195135","https://openalex.org/W2795079307","https://openalex.org/W2793058541","https://openalex.org/W2378491141","https://openalex.org/W3118638206","https://openalex.org/W1983629434","https://openalex.org/W4324271173","https://openalex.org/W1967645776","https://openalex.org/W2352227742","https://openalex.org/W4390679071"],"abstract_inverted_index":{"Computational":[0],"and":[1,100,113,130],"mathematical":[2],"modelling":[3],"approaches":[4],"are":[5,36],"increasingly":[6],"being":[7,34],"adopted":[8],"in":[9,61,83,117,209,220],"attempts":[10],"to":[11,24,43,90,142,166],"further":[12,237],"our":[13,140,182],"understanding":[14],"of":[15,30,64,68,71,86,95,152,181,188,205,212,226],"complex":[16],"biological":[17,32,228,238],"systems.":[18],"This":[19],"approach":[20],"can":[21,163],"be":[22,44,125,164],"subjected":[23],"strong":[25],"criticism":[26],"as":[27,131,223],"substantial":[28],"aspects":[29],"the":[31,58,62,69,84,93,110,150,153,160,172,179,185,193,206,210,213,221,227],"system":[33,229],"captured":[35],"not":[37,148],"currently":[38],"known,":[39],"meaning":[40],"assumptions":[41,135,170,207],"need":[42],"made":[45,208],"that":[46,78,123,184,202],"could":[47],"have":[48,56,79,136],"a":[49,80,224],"critical":[50],"impact":[51,171,180],"on":[52,149],"simulation":[53,67,162,173],"response.":[54,174],"We":[55,200],"utilised":[57],"CoSMoS":[59],"process":[60],"development":[63,151],"an":[65,203],"agent-based":[66],"formation":[70],"Peyer's":[72],"patches":[73],"(PP),":[74],"gut-associated":[75],"lymphoid":[76,189],"organs":[77],"key":[81],"role":[82],"initiation":[85],"adaptive":[87],"immune":[88],"responses":[89],"infection.":[91],"Although":[92],"use":[94],"genetic":[96],"tools,":[97],"imaging":[98],"technologies":[99],"ex":[101],"vivo":[102],"culture":[103],"systems":[104],"has":[105],"provided":[106],"significant":[107],"insight":[108],"into":[109,139,192],"cellular":[111],"components":[112],"associated":[114],"pathways":[115],"involved":[116],"PP":[118,198],"development,":[119],"interesting":[120],"questions":[121],"remain":[122],"cannot":[124],"addressed":[126],"using":[127],"these":[128,169],"approaches,":[129],"such":[132],"well":[133],"justified":[134],"been":[137],"introduced":[138],"model":[141,154,215,222],"counter":[143],"this.":[144],"Here":[145],"we":[146,177],"focus":[147],"itself,":[155],"but":[156],"instead":[157],"demonstrate":[158,201],"how":[159,168],"resultant":[161],"used":[165],"assess":[167],"For":[175],"example,":[176],"consider":[178],"assumption":[183],"migration":[186],"rate":[187],"tissue":[190],"cells":[191],"gut":[194],"remains":[195],"constant":[196],"throughout":[197],"development.":[199],"analysis":[204],"construction":[211],"domain":[214],"may":[216,233],"either":[217],"increase":[218],"confidence":[219],"representation":[225],"it":[230],"captures,":[231],"or":[232],"suggest":[234],"areas":[235],"where":[236],"experimentation":[239],"is":[240],"required.":[241]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
