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Using argument notation to engineer biological simulations with increased confidence

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dc.contributor.authorAlden, Kieran
dc.contributor.authorAndrews, Paul S.
dc.contributor.authorPolack, Fiona A. C.
dc.contributor.authorVeiga-Fernandes, Henrique
dc.contributor.authorColes, Mark C.
dc.contributor.authorTimmis, Jon
dc.date.accessioned2022-05-26T17:00:35Z
dc.date.available2022-05-26T17:00:35Z
dc.date.issued2015
dc.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.pt_PT
dc.description.abstractThe 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.pt_PT
dc.description.sponsorshipThis 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).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationJ R Soc Interface. 2015 Mar 6;12(104):20141059pt_PT
dc.identifier.doi10.1098/rsif.2014.1059pt_PT
dc.identifier.eissn1742-5662
dc.identifier.issn1742-5689
dc.identifier.urihttp://hdl.handle.net/10451/53201
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherThe Royal Societypt_PT
dc.relationInstitutional Strategic Support Fund 2011/12.
dc.relationRole of haematopoietic cell subsets during lymphoid organogenesis
dc.relationRole of the proto-oncogene Ret during lymphocyte development and function
dc.relation.publisherversionhttps://royalsocietypublishing.org/journal/rsifpt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectArtoopt_PT
dc.subjectArgumentationpt_PT
dc.subjectComputational modellingpt_PT
dc.subjectImmune system modellingpt_PT
dc.subjectSimulationpt_PT
dc.titleUsing argument notation to engineer biological simulations with increased confidencept_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardNumber097829
oaire.awardNumberPTDC/SAU-MII/100016/2008
oaire.awardNumber207057
oaire.awardTitleInstitutional Strategic Support Fund 2011/12.
oaire.awardTitleRole of haematopoietic cell subsets during lymphoid organogenesis
oaire.awardTitleRole of the proto-oncogene Ret during lymphocyte development and function
oaire.awardURIinfo:eu-repo/grantAgreement/WT/Cross-Remit/097829
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FSAU-MII%2F100016%2F2008/PT
oaire.awardURIinfo:eu-repo/grantAgreement/EC/FP7/207057/EU
oaire.citation.issue104pt_PT
oaire.citation.titleJournal of The Royal Society Interfacept_PT
oaire.citation.volume12pt_PT
oaire.fundingStreamCross-Remit
oaire.fundingStream3599-PPCDT
oaire.fundingStreamFP7
person.familyNameVeiga-Fernandes
person.givenNameHenrique
person.identifier.ciencia-idC919-1B92-794F
person.identifier.orcid0000-0001-6216-1836
person.identifier.scopus-author-id6508113770
project.funder.identifierhttp://doi.org/10.13039/100010269
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.nameWellcome Trust
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameEuropean Commission
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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relation.isAuthorOfPublication.latestForDiscoverye33cff40-943e-4de1-b0e3-af20b294c0cf
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