2.3. Computational Physiology - Simulation

This tutorial was created as part of the Computational Physiology module in the MedTech CoRE Doctoral Training Programme. The tasks presented in this tutorial are designed to make the reader aware of common key skills required for the application of mathematical models in computational simulation experiments in the context of computational physioloyg. We will demonstrate these skills across a range of spatial scales and numerical methods.

Contents:

• 2.3.1. Integrating systems of differential equations
  • 2.3.1.1. Numerical integrators
• 2.3.2. Biological Complexity
• 2.3.3. Multiscale simulation
  • 2.3.3.1. Task 4 - electrophysiological simulation
• 2.3.4. Where do these models come from?
  • 2.3.4.1. Task 5: explore CellML using OpenCOR
  • 2.3.4.2. Task 6: find the ICC model
  • 2.3.4.3. Task 7: the Simulation Experiment Description Markup Language
  • 2.3.4.4. Task 8: explore alternate ICC models

2.3.5. TL;DR

The quick highlights in this tutorial.

1. Introduce the concept of numerical integration of systems of differential equations.
   1. Two specific algorithms presented: Euler’s method and CVODE.
   2. Investigate the impact of choosing the correct algorithm control parameters (Task 1 - the effect of step size).
   3. Observe the limitations and the computational cost associated with numerical method choices (Task 2 - fixed vs adaptive stepping) and algorithm parameterisation (Task 3 - error control).
2. How much biological detial is too much?
3. Integrating cellular models into organ models.
4. Exploring models from the repository.