Models for the OpenCOR and PMR tutorial by Peter Hunter

Models for the Tutorial on CellML, OpenCOR & the Physiome Model Repository

In this workspace we have the model and simulation experiment descriptions for the examples used in the tutorial on CellML, OpenCOR & the Physiome Model Repository created by Peter Hunter. The latest version of the tutorial itself is available at: http://tutorial-on-cellml-opencor-and-pmr.readthedocs.org/. This tutorial is also utilised as part of the Computational Physiology module of the MedTech CoRE Doctoral Training Program.

While the tutorial often leads the reader through creating these models from the beginning, here we provide the complete models and associated simulation experiments. As expected from the title of the tutorial, the models themselves are encoded in the CellML format. The simulation experiments are encoded in the SED-ML format and where possible we link directly to them to enable the user to simply launch them directly in OpenCOR from the repository (and also from within the tutorial documentation).

Van der Pol oscillator

Used in the Create and run a simple CellML model: editing and simulation section of the tutorial, the classical Van der Pol oscillator is the first model described in the tutorial. The simulation experiment for this model described in the tutorial can be obtained by loading the corresponding SED-ML document into OpenCOR and executing the simulation. The results of which are shown below.

Screenshot illustrating the results of executing the Van der Pol simulation experiment in OpenCOR.

Exponential decay: A simple first order ODE

Used as the simplest example of a first order differential equation, this model consists of a single equation. One of the simulation experiments for this model described in the tutorial can be obtained by loading the corresponding SED-ML document into OpenCOR and executing the simulation.

The Lorenz attractor

The Lorenz attractor model is used in the tutorial as both an example of interesting dynamics and an illustration of the encoding of a third order differential equation as three first order equations in CellML. The figure below illustrates the results obtain by loading the corresponding SED-ML document into OpenCOR and executing the simulation.

Screenshot illustrating the results of executing the Lorenz attractor simulation experiment in OpenCOR.

Gating kinetics explained

The A model of ion channel gating and current: Introducing CellML units section in the tutorial introduces the concept of units in CellML models, and along the way provides an explanation of gating kinetics that are common when investigating ion channel behaviour (at least those channels which are voltage senstitive). As such, this model provides a neat little toy for investigating the formulation of traditional ion channel models. Once again, the corresponding SED-ML document is available to help get the reader started.

The Hodgkin & Huxley potassium and sodium channels

In the tutorial, the Hodgkin & Huxley potassium channel and sodium channel are used as the examples illustrating core CellML concepts. As these models get more complex, they are also a great example demonstrating the utility of providing SED-ML alongside the model, as shown with the results presented in the figure below.

Screenshot illustrating the results of executing this potassium simulation experiment in OpenCOR.
Source
Derived from workspace Models for the OpenCOR and PMR tutorial by Peter Hunter at changeset 1368c1579b75.
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