Using argument notation to engineer biological simulations with increased confidence

Alden, Kieran James, Andrews, Paul Simon, Polack, Fiona, Veiga-Fernandes, Henrique, Coles, Mark Christopher and Timmis, Jonathan (2015) Using argument notation to engineer biological simulations with increased confidence. Journal of the Royal Society Interface, 12 (104). ISSN 1742-5689

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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 (, 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.

Item Type: Article
Subjects: Computing
Divisions: Services > University Executive
Depositing User: Klaire Purvis-Shepherd
Date Deposited: 07 Jun 2019 13:56
Last Modified: 27 Jan 2021 16:30
ORCID for Jonathan Timmis: ORCID iD

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