Python implementation of hERG ion channel model

This repository contains scripts for solving a hERG ion channel model analytically and using an ODE solver.

Installation

It is recommended to install libraries and run scripts in a virtual environment to avoid version conflicts between different projects. In order to do this, follow these steps:

• virtualenv folder_name or if you have both python 2 and 3: virtualenv --python=python3 folder_name. Should virtualenv not be recognised you may need to call it as python -m virtualenv folder_name or (python -m virtualenv folder_name). If that doesn't work you may need to install virtualenv first pip install virtualenv.
• Activate the virtual environment using source folder_name/bin/activate. Simply type deactivate to exit the virtual environment at the end of a session.
• Install the required packages by typing pip install -r requirements.txt

Running

[Joseph to Do]

Tests

Tests are available to check whether the analytical solution of the ion channel model matches that obtained using an ODE solver. In order to run the tests, simply type pytest test_hh_markov_analytic.py.