Using argument notation to engineer biological simulations with increased confidence

Detalhes bibliográficos
Autor(a) principal: Alden, Kieran
Data de Publicação: 2015
Outros Autores: Andrews, Paul S., Polack, Fiona A. C., Veiga-Fernandes, Henrique, Coles, Mark C., Timmis, Jon
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/53201
Resumo: © 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
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spelling Using argument notation to engineer biological simulations with increased confidenceArtooArgumentationComputational modellingImmune system modellingSimulation© 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions.This work was part funded by the Wellcome Trust (ref: 097829) through the Centre for Chronic Diseases and Disorders (C2D2) at the University of York and the Medical Research Council (G0601156) to M.C. P.A. was funded by EPSRC grant no. EP/I005943/1 ‘Resilient Futures'. Part of F.A.C.P.'s contribution was supported by the CoSMoS project, EPSRC grant EP/E053505/1. J.T. is part funded by the Royal Society and the Royal Academy of Engineering. H.V.-F. was funded by the FCT Portugal (PTDC/SAU-MII/100016/2008), European Molecular Biology Organisation (Project 1648) and European Research Council (Project 207057).The Royal SocietyRepositório da Universidade de LisboaAlden, KieranAndrews, Paul S.Polack, Fiona A. C.Veiga-Fernandes, HenriqueColes, Mark C.Timmis, Jon2022-05-26T17:00:35Z20152015-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/53201engJ R Soc Interface. 2015 Mar 6;12(104):201410591742-568910.1098/rsif.2014.10591742-5662info: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:RCAAP2023-11-08T16:58:52Zoai:repositorio.ul.pt:10451/53201Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:04:09.849399Repositório 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 Using argument notation to engineer biological simulations with increased confidence
title Using argument notation to engineer biological simulations with increased confidence
spellingShingle Using argument notation to engineer biological simulations with increased confidence
Alden, Kieran
Artoo
Argumentation
Computational modelling
Immune system modelling
Simulation
title_short Using argument notation to engineer biological simulations with increased confidence
title_full Using argument notation to engineer biological simulations with increased confidence
title_fullStr Using argument notation to engineer biological simulations with increased confidence
title_full_unstemmed Using argument notation to engineer biological simulations with increased confidence
title_sort Using argument notation to engineer biological simulations with increased confidence
author Alden, Kieran
author_facet Alden, Kieran
Andrews, Paul S.
Polack, Fiona A. C.
Veiga-Fernandes, Henrique
Coles, Mark C.
Timmis, Jon
author_role author
author2 Andrews, Paul S.
Polack, Fiona A. C.
Veiga-Fernandes, Henrique
Coles, Mark C.
Timmis, Jon
author2_role author
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.
Polack, Fiona A. C.
Veiga-Fernandes, Henrique
Coles, Mark C.
Timmis, Jon
dc.subject.por.fl_str_mv Artoo
Argumentation
Computational modelling
Immune system modelling
Simulation
topic Artoo
Argumentation
Computational modelling
Immune system modelling
Simulation
description © 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015-01-01T00:00:00Z
2022-05-26T17:00:35Z
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/10451/53201
url http://hdl.handle.net/10451/53201
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv J R Soc Interface. 2015 Mar 6;12(104):20141059
1742-5689
10.1098/rsif.2014.1059
1742-5662
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 The Royal Society
publisher.none.fl_str_mv The Royal Society
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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