DTP: Computational Physiology

Note

This is release 2016.08 of the DTP Computational Physiology module documentation. Some previous releases are available at: http://readthedocs.org/projects/dtp-compphys/versions/

Anonymous feedback on any part of this module can be left at: http://goo.gl/forms/0OOhzkwnFo

Welcome to the Computational Physiology module of the Doctoral Training Programme from the MedTech CoRE. In this series of tutorials, you will be exposed to a selection of the methods used by scientists in the MedTech CoRE working in the field of computational physiology - the application of engineering and mathematical sciences to the study of physiology.

This series of tutorials will first guide you through the main steps in a “standard” clinical workflow that takes advantage of computational physiology: image processing, geometric model building, simulation, and visualisation. You will then be led through the development and implementation of a complete clinically focused workflow which will take advantage of the skills you have developed in the earlier modules. In demonstrating each of these steps we make use of examples for various organ systems being investigated under the MedTech CoRE. Each session will begin with a introductory lecture from a scientist working on the example organ system for that session who will present current research relevant to the MedTech CoRE. We hope to make recordings of these lectures available to those following the module remotely.

Finally, the course ends with an introduction to some of the key tools that are used in this field locally.

Contents

• 1. Clinical Workflows
  • 1.1. Computational Physiology - Segmentation
  • 1.2. Computational Physiology - Model Construction
  • 1.3. Computational Physiology - Simulation
  • 1.4. Computational Physiology - Visualisation
  • 1.5. Computational Physiology - Complete Workflow
• 2. Projects
  • 2.1. Project: Parameter Estimation
  • 2.2. Project: Femur Fitting
• 3. Introduction to (ODE) Modelling Best Practices
  • 3.1. Tutorial on CellML, OpenCOR & the Physiome Model Repository
• 4. Software Tools
  • 4.1. MAP Client
  • 4.2. OpenCOR
  • 4.3. OpenCMISS-Neon
  • 4.4. OpenCMISS-Iron & OpenCMISS-Zinc
• 5. DTP Computational Physiology to do list
  • 5.1. General
  • 5.2. Within sections