Journal article
Using argument notation to engineer biological simulations with increased confidence
- 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, pdf, 1.1MB, Terms of use)
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- Publisher copy:
- 10.1098/rsif.2014.1059
Authors
- Publisher:
- Royal Society
- Journal:
- Interface More from this journal
- Volume:
- 12
- Issue:
- 104
- Pages:
- ARTN 20141059
- Publication date:
- 2015-03-06
- Acceptance date:
- 2014-12-16
- DOI:
- EISSN:
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1742-5662
- ISSN:
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1742-5689
- Pmid:
-
25589574
- Language:
-
English
- Keywords:
- Pubs id:
-
pubs:821768
- UUID:
-
uuid:a9b786de-7ffd-4d0f-bd3d-15d8d1179f94
- Local pid:
-
pubs:821768
- Source identifiers:
-
821768
- Deposit date:
-
2019-10-31
Terms of use
- Copyright holder:
- Alden et al
- Copyright date:
- 2015
- Notes:
- & 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..
- Licence:
- CC Attribution (CC BY)
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