Cardiac Modelling

markov-builder

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

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

BenNevis

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

hERGRapidCharacterisation

Rapid characterisation of hERG channel kinetics

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".

ionBench

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

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

appredict-docker

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"

ap-nimbus-deploy

BenNevisBenchmark

binding_model_OED

Code for optimal experimental design paper

ContinuationForOptimisation

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

empirical_quantification_of_model_discrepancy

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.

qc_viewer

Visualiser for quality control checks on automated patch-clamp machines

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"