Cardiac Modelling

BenNevis

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

fickleheart-method-tutorials

Code for the tutorials in the Fickle Heart model calibration with discrepancy 2020 paper.

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

markov-builder

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

pcpostprocess

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

RapidCharacterisationProtocols

Collection of experimental protocols in common patch clamp formats for rapid characterisation of ion channels

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

CardiacModelling/markov-builder

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

CardiacModelling/BenNevis

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

CardiacModelling/fitting-notebooks

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

CardiacModelling/FourWaysOfFitting

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

CardiacModelling/ionBench

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

CardiacModelling/VoltageClampModel

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

CardiacModelling/pcpostprocess

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

CardiacModelling/syncropatch_export

A Python package to export SynroPatch 384 data.

CardiacModelling/ap-nimbus-client

CardiacModelling/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".

CardiacModelling/space-filling-designs

Phase-voltage space filling optimal designs in Matlab

CardiacModelling/ap-nimbus

Cardiac modelling in containers

CardiacModelling/ap-nimbus-app-manager

API for cloudified AP Predict

CardiacModelling/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"

CardiacModelling/appredict-docker

CardiacModelling/ContinuationForOptimisation

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

CardiacModelling/ina-midpoints

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

CardiacModelling/L-type-Ca-rundown-experiments

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

CardiacModelling/nav-artefact-model

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

CardiacModelling/R56Q-modelling

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

CardiacModelling/BenNevisBenchmark

CardiacModelling/binding_model_OED

Code for optimal experimental design paper

CardiacModelling/empirical_quantification_of_model_discrepancy

CardiacModelling/L-type-Ca-rundown-modelling

CardiacModelling/MarkovModels

CardiacModelling/model-reduction-manifold-boundaries

Code for model reduction using manifold boundaries

CardiacModelling/multiprotocol_data_fitting

CardiacModelling/protocol-design-hERG

Voltage clamp protocol design for hERG.

CardiacModelling/relative-contributions

Relative contributions of transmembrane currents in human AP models

CardiacModelling/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"