Understanding tissue morphology: model repurposing using the CoSMoS process

Adam T. Sampson, James L. Bown, Hilal S. Khalil, Yusuf Y. Deeni

    Research output: Contribution to journalArticle

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    Abstract

    We present CoSMoS as a way of structuring thinking on how to reuse parts of an existing model and simulation in a new model and its implementation. CoSMoS provides a lens through which to consider, post-implementation, the assumptions made during the design and implementation of a software simulation of physical interactions in the formation of vascular structures from endothelial cells. We show how the abstract physical model and its software implementation can be adapted for a different problem: the growth of cancer cells under varying environmental perturbations. We identify the changes that must be made to adapt the model to its new context, along with the gaps in our knowledge of the domain that must be filled by wet-lab experimentation when recalibrating the model. Through parameter exploration, we identify the parameters that are critical to the dynamic physical structure of the modelled tissue, and we calibrate these parameters using a series of in vitro experiments. Drawing inspiration from the CoSMoS project structure, we maintain confidence in the repurposed model, and achieve a satisfactory degree of model reuse within our in silico experimental system.
    Original languageEnglish
    Pages (from-to)109–128
    Number of pages20
    JournalNatural Computing
    Volume14
    Issue number1
    Early online date7 Oct 2014
    DOIs
    Publication statusPublished - 1 Mar 2015

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    Sampson, Adam T. ; Bown, James L. ; Khalil, Hilal S. ; Deeni, Yusuf Y. / Understanding tissue morphology: model repurposing using the CoSMoS process. In: Natural Computing. 2015 ; Vol. 14, No. 1. pp. 109–128.
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    Understanding tissue morphology: model repurposing using the CoSMoS process. / Sampson, Adam T.; Bown, James L.; Khalil, Hilal S.; Deeni, Yusuf Y.

    In: Natural Computing, Vol. 14, No. 1, 01.03.2015, p. 109–128.

    Research output: Contribution to journalArticle

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