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Natural Computing

, Volume 14, Issue 1, pp 109–128 | Cite as

Understanding tissue morphology: model repurposing using the CoSMoS process

  • Ye Li
  • Adam T. Sampson
  • James Bown
  • Hilal S. Khalil
  • Yusuf Deeni
Article
  • 118 Downloads

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.

Keywords

Calibration CoSMoS Model reuse Simulation 

Notes

Acknowledgments

The authors would like to thank their colleagues who kindly provided resources for this paper. David Harrison and Peter Mullen (University of St. Andrews) provided the HCT-116 cells used for the experiments in Sect. 4. Figure 10 appears courtesy of Simon Langdon (University of Edinburgh). Figure 15 appears courtesy of Peter Caie (University of Edinburgh). James Bown acknowledges support from the Northwood Trust.

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Ye Li
    • 1
  • Adam T. Sampson
    • 1
  • James Bown
    • 1
  • Hilal S. Khalil
    • 1
  • Yusuf Deeni
    • 1
  1. 1.SIMBIOSAbertay UniversityDundeeUK

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