Cardiac Modelling

markov-builder

Tool for building and manipulating Markov models of ion-channel kinetics

BenNevis

"Where is Ben Nevis" presents the landscape of Great Britain as a testbed for optimisation and sampling methods.

fitting-notebooks

Examples of parameter estimation in cardiac cell electrophysiology using Myokit and PINTS.

FourWaysOfFitting

Code to compare four different ways to fit an ion current model

ionBench

A benchmarking tool for comparing different parameter optimization algorithms for ion channel models

pcpostprocess

A Python package to run Lei et al. (2019) quality control on patch-clamp time-series data.

syncropatch_export

A Python package to export SynroPatch 384 data.

VoltageClampModel

Code to add a mathematical model of voltage-clamp artefacts to your ion channel simulations

ap-nimbus-client

hERG-binding-mechanisms

Source code and data for reproducing "The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk".

space-filling-designs

Phase-voltage space filling optimal designs in Matlab

ap-nimbus

Cardiac modelling in containers

ap-nimbus-app-manager

API for cloudified AP Predict

APD90_ex_vivo_vs_in_silico

Code to reproduce the figures and results from "Comparison of in silico predictions of action potential duration in response to inhibition of IKr and ICaL with new human ex-vivo recordings"

appredict-docker

ContinuationForOptimisation

Using limit cycle continuation methods to speed up evaluation of ion channel cell models

L-type-Ca-rundown-experiments

An investigation of rundown in automated patch clamp L-type calcium current

nav-artefact-model

Code for reproducing "Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings"

R56Q-modelling

A repository to reproduce modelling results for the R56Q-hERG project

BenNevisBenchmark

binding_model_OED

Code for optimal experimental design paper

empirical_quantification_of_model_discrepancy

ina-midpoints

Data and figures for "Variability in reported midpoints of (in)activation for cardiac INa"

L-type-Ca-rundown-modelling

MarkovModels

model-reduction-manifold-boundaries

Code for model reduction using manifold boundaries

multiprotocol_data_fitting

protocol-design-hERG

Voltage clamp protocol design for hERG.

relative-contributions

Relative contributions of transmembrane currents in human AP models

stochastic-gating

Code to replicate the analyses from the article "Parameter inference for stochastic reaction models of ion channel gating from whole-cell voltage-clamp data"