Model calibration with discrepancy

This repo contains the code for reproducing the results in the examples in the paper "Considering discrepancy when calibrating a mechanistic electrophysiology model" by Lei, Ghosh, Whittaker, Aboelkassem, Beattie, Cantwell, Delhaas, Houston, Novaes, Panfilov, Pathmanathan, Riabiz, dos Santos, Walmsley, Worden, Mirams, and Wilkinson. doi:10.1098/rsta.2019.0349.

Requirements

The code requires Python (3.5+) and the following dependencies: PINTS, Myokit, Theano, StatsModels, Joblib.

In addition, Myokit requires a working compiler (e.g. gcc) and Sundials (CVODE) to be installed. For instructions, see http://myokit.org/install.

To setup, either run (for Linux/macOS users):

$ bash setup.sh

or navigate to the path where you downloaded this repo and run:

$ pip install --upgrade pip
$ pip install .

Action potential model example

See action-potential-models.

Ion channel model example

See ion-channel-models.

Acknowledging this work

If you publish any work based on the contents of this repository please cite (CITATION file):

Lei, C.L. et al. (2020). Considering discrepancy when calibrating a mechanistic electrophysiology model. Philosophical Transactions of the Royal Society A, 378: 20190349.