.. DTP Computational Physiology - Simulation documentation master file, created by
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.. _dtp_cp_simulation:

Computational Physiology - Simulation
=====================================

This tutorial was created as part of the Computational Physiology module in the `MedTech CoRE <http://cmdt.org.nz>`_ 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:

.. toctree::
   :maxdepth: 2

   odeintegration
   biologicalcomplexity
   multiscale
   
.. _dtp_cp_sim_overview:

TL;DR
-----

The quick highlights in this tutorial.

#. Introduce the concept of numerical integration of systems of differential equations. 

   #. Two specific algorithms presented: :ref:`Euler's method <dtp_cp_sim_ode_euler>` and :ref:`CVODE <dtp_cp_sim_ode_cvode>`.
   #. Investigate the impact of choosing the correct algorithm control parameters (:ref:`dtp_cp_sim_ode_task1`).
   #. Observe the limitations and the computational cost associated with numerical method choices (:ref:`dtp_cp_sim_ode_task2`) and algorithm parameterisation (:ref:`dtp_cp_sim_ode_task3`). 

#. How much biological detial is too much?
#. Integrating cellular models into organ models.

   
..   Indices and tables
   ==================
   
   * :ref:`genindex`
   * :ref:`modindex`
   * :ref:`search`