Utilising a simulation platform to understand the effect of domain model assumptions

Detalhes bibliográficos
Autor(a) principal: Alden, Kieran
Data de Publicação: 2014
Outros Autores: Andrews, Paul S., Veiga-Fernandes, Henrique, Timmis, Jon, Coles, Mark
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/51810
Resumo: © The Author(s) 2014. This article is published with open access at Springerlink.com. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
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spelling Utilising a simulation platform to understand the effect of domain model assumptionsModel compositionPeyer’s patchesSimulationStatistical analysis© The Author(s) 2014. This article is published with open access at Springerlink.com. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.Computational and mathematical modelling approaches are increasingly being adopted in attempts to further our understanding of complex biological systems. This approach can be subjected to strong criticism as substantial aspects of the biological system being captured are not currently known, meaning assumptions need to be made that could have a critical impact on simulation response. We have utilised the CoSMoS process in the development of an agent-based simulation of the formation of Peyer's patches (PP), gut-associated lymphoid organs that have a key role in the initiation of adaptive immune responses to infection. Although the use of genetic tools, imaging technologies and ex vivo culture systems has provided significant insight into the cellular components and associated pathways involved in PP development, interesting questions remain that cannot be addressed using these approaches, and as such well justified assumptions have been introduced into our model to counter this. Here we focus not on the development of the model itself, but instead demonstrate how the resultant simulation can be used to assess how these assumptions impact the simulation response. For example, we consider the impact of our assumption that the migration rate of lymphoid tissue cells into the gut remains constant throughout PP development. We demonstrate that an analysis of the assumptions made in the construction of the domain model may either increase confidence in the model as a representation of the biological system it captures, or may suggest areas where further biological experimentation is required.This work was funded by the Wellcome Trust [ref:097829] through the Centre for Chronic Diseases and Disorders (C2D2) at the University of York. Paul Andrews is funded by EPSRC grant EP/I005943/1 “Resilient Futures.” Henrique Veiga-Fernandes is funded by Fundação para a Ciência e Tecnologia (PTDC/SAU-MII/100016/2008), Portugal, European Molecular Biology Organisation (Project 1648) and European Research Council (Project 207057). Jon Timmis is part funded by the Royal Society and the Royal Academy of Engineering. Funding for Mark Coles comes from grants from the Human Frontiers Science Program (RGP0006/2009) and the Medical Research Council (G0601156).Springer NatureRepositório da Universidade de LisboaAlden, KieranAndrews, Paul S.Veiga-Fernandes, HenriqueTimmis, JonColes, Mark2022-03-17T17:19:35Z20142014-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/51810engNat Comput (2015) 14:99–1071567-781810.1007/s11047-014-9428-71572-9796info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T16:56:44Zoai:repositorio.ul.pt:10451/51810Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:03:02.094715Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Utilising a simulation platform to understand the effect of domain model assumptions
title Utilising a simulation platform to understand the effect of domain model assumptions
spellingShingle Utilising a simulation platform to understand the effect of domain model assumptions
Alden, Kieran
Model composition
Peyer’s patches
Simulation
Statistical analysis
title_short Utilising a simulation platform to understand the effect of domain model assumptions
title_full Utilising a simulation platform to understand the effect of domain model assumptions
title_fullStr Utilising a simulation platform to understand the effect of domain model assumptions
title_full_unstemmed Utilising a simulation platform to understand the effect of domain model assumptions
title_sort Utilising a simulation platform to understand the effect of domain model assumptions
author Alden, Kieran
author_facet Alden, Kieran
Andrews, Paul S.
Veiga-Fernandes, Henrique
Timmis, Jon
Coles, Mark
author_role author
author2 Andrews, Paul S.
Veiga-Fernandes, Henrique
Timmis, Jon
Coles, Mark
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Alden, Kieran
Andrews, Paul S.
Veiga-Fernandes, Henrique
Timmis, Jon
Coles, Mark
dc.subject.por.fl_str_mv Model composition
Peyer’s patches
Simulation
Statistical analysis
topic Model composition
Peyer’s patches
Simulation
Statistical analysis
description © The Author(s) 2014. This article is published with open access at Springerlink.com. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
publishDate 2014
dc.date.none.fl_str_mv 2014
2014-01-01T00:00:00Z
2022-03-17T17:19:35Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/51810
url http://hdl.handle.net/10451/51810
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Nat Comput (2015) 14:99–107
1567-7818
10.1007/s11047-014-9428-7
1572-9796
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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