Using argument notation to engineer biological simulations with increased confidence

Kieran Alden*, Paul S. Andrews, Fiona A.C. Polack, Henrique Veiga-Fernandes, Mark C. Coles, Jon Timmis

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Citations (SciVal)

Abstract

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.

Original languageEnglish
Article number20141059
JournalJournal of the Royal Society Interface
Volume12
Issue number104
DOIs
Publication statusPublished - 06 Mar 2015
Externally publishedYes

Keywords

  • Argumentation
  • ARTOO
  • Computational modelling
  • Immune system modelling
  • Simulation
  • Humans
  • Peyer's Patches/physiology
  • Algorithms
  • Animals
  • Models, Biological
  • Computer Simulation
  • Lymphoid Tissue/pathology
  • Software
  • Internet
  • Cell Movement

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