openCARP examples

Basic single cell EP and limit cycle

This example introduces the basic steps of running electrophysiological simulations in an isolated myocyte using bench and limpetgui.

APD restitution

Action potenital duration (APD) restitution example in a single cell. As pacing frequency is increased, APD shortens.

Voltage clamp

This example explains the basic usage of bench for performing voltage clamp experiments.

EasyML to C code

This example explains the basics of using the code generation tool limpet_fe.py for generating ODE solver code for models of cellular dynamics. It also covers the creation of new models as a dynamic library.

EasyML basics

More information about the cell model math format EasyML.

Electromechanical coupling

Couple an electrophysiological cell model to a tension model.

Convert CellML to EasyML (.model)

Here you learn how to import CellML data into openCARP and what problems might occur during this process.

Convert EasyML (.model) to CellML

Learn how to convert your .model file (EasyML) to CellML.

Parallel single-cell simulations

See how to execute single-cell simulations in parallel and build populations of models.

Simple carputils example

This is not a real example but more of a template to base your own experiment on. It covers mesh generation, monodomain simulation and local activation time extraction during postprocessing.

Basic tissue EP: AP propagation

This example introduces to the basics of using the openCARP executable for simulating EP at the tissue and organ scale.

Extracellular stimulation

In this example you learn how to stimulate a tissue from the extracellular space.

Ionic model parameter adjustment to match APD

This example demonstrates how to adjust ionic model parameters to generate a specific action potential duration in your simulations.

Tuning conduction velocity

This example introduces the background for the relationship between conduction velocity and tissue conductivity.

Limit cycle initialization; cell to tissue state transfer

This example demonstrates how to initialize a cardiac tissue with state variables obtained from a single-cell stimulation.

Model parameter adjustment to match wavelength

This example demonstrates how to adjust parameters in tissue simulations to match experimental data for conduction velocity, APD, and wavelength.

Conduction velocity restitution

This example demonstrates how to compute conduction velocity (CV) restitution in cardiac tissue.

ERP restitution

This example shows how to calculate the effective refractory period (ERP) for a given combination of ionic conductances in a tissue slab using an S1S2 pacing protocol. An ERP restitution curve can also be plotted, if desired by the user.

Niederer et al. benchmark: numerical discretization

This example replicates the Niederer et al. benchmark and illustrates effects of some numerical settings including temporal and spatial discretization.

Region tagging

Regions are used to manage the assignment of heterogeneous tissue properties. This example explains the different approches of how regions can be defined.

Heterogeneity: conductivity regions

This example details how to assign different conductivities to different parts of a simulated tissue slice using region-wise tagging.

Heterogeneity: ionic model regions

This example details how to assign different single cell dynamics to different parts of a simulated tissue slice using region-wise tagging.

Heterogeneities: regions vs. gradiensts (nodal adjustment)

This example introduces the concepts of region-based and gradient-based heterogeneities for assigning spatially varying properties.

Heterogeneities: smooth gradients via nodal adjustments of ionic model parameters

This example details how to assign a gradient of single cell properties using the adjustments interface.

Output spatio-temporal state variable distributions

This example details how to output the values of state variables over time during a simulation.

Electrical mapping (LAT)

This example demonstrates how to compute local activation times (LATs) and action potential durations (APDs) of cells in a cardiac tissue during the simulation rather than during postprocessing.

Extracellular potentials and ECGs

This example explains the background of computing extracellular potentials and ECG using different techniques.

Periodic boundary conditions

Periodic boundary conditions connect the left edge of a sheet to the right, or the top to the bottom.

Local activation time

This example demonstrates how to compute local activation times (LATs) and action potential durations (APDs) of cells in a cardiac tissue

Laplace solutions

Computing Laplace-Dirichlet maps provide an elegant tool for describing the distance between defined boundaries.

Unequal anisotropy effects

Unequal anisotropy ratios in bidomain simulations can be responsible for the formation of unexpectedly complex polarization patterns.

Parameter sweeps

This example shows how to use polling files to sweep parameters.

Reentry induction protocols

This example shows the influence of different induction protocol on reentry initiation and maintenance.

ForCEPSS: VARP Protocol

This example demonstrates the usage of ForCEPSS implementation of the VARP (Virtual Arrhythmia Risk Predictor) protocols in the context of cardiac electrophysiology simulations.

Eikonal model

This example demonstrates how to set up and use the eikonal model.

Reaction-Eikonal Model

This example shows how to run reaction-eikonal simulations with (RE+) and without diffusion current (RE-).

Diffusion Reaction Eikonal Alternant Model - Pacing

This example demonstrates and explores pacing behavior while using the DREAM.

Diffusion Reaction Eikonal Alternant Model - Reentry

This example demonstrates how to set up and use the DREAM to simulate reentries.

Fitting CV restitution

This example shows how to find the parameters for CV restitution to use DREAM with other ionic models.

Fitting foot current parameters

This example shows how to find the parameters for Ifoot to run reaction-eikonal with other ionic models.

IGB utils

This example demonstrates several utilities to manipulate IGB files.