openCARP examples

These examples are intended to transfer basic user know-how regarding most openCARP features in an efficient way. The scripts are designed as mini-experiments, which can also serve as basic building blocks for more complex experiments.

There is a number of examples dedicated to teaching openCARP fundamental know-how for those who are interested in building more complex experiments from scratch themselves or in extending pre-existing experiments. All executable examples are coded up in carputils to facilitate an easy execution of all experiments without significant additional effort and complex command line interactions.

Intended use

Most examples can be run by simply copying the command from the corresponding example web page. It is recommended to inspect the generated command lines to understand what the simulation looks like in the plain command line by adding the option --dry to the run script command line. You can download the examples from our repository.

Electrophysiology in single cell

The following examples illustrate how single cell modeling is performed using the tool bench. Additionally you learn how to integrate a single cell model from CellML into our library limpet using the math language EasyML

Electrophysiology tissue

These examples should inform you about the most basic steps in developing simple tissue simulations using openCARP

Basic tissue EP

Basic tissue EP

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

Extracellular stimulation

Extracellular stimulation

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

Tuning Conduction Velocity

Tuning Conduction Velocity

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

Init tissue from cell

Init tissue from cell

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

Adjust parameters

Adjust parameters

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

CV restitution

This example demonstrates how to compute conduction velocity restitution in cardiac tissue

APD adjustment

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

Tissue regions

Tissue regions

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

Region vs. gradient heterogeneities

Region vs. gradient heterogeneities

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

Regions & conductivities

Regions & conductivities

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

EP heterogeneity

EP heterogeneity

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

Region reunification

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

Smooth gradient

Smooth gradient

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

Periodic boundary conditions

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

Local activation time

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

Boundary conditions

Boundary conditions

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

Anisotropy effects

Anisotropy effects

Unequal anisotropy ratios can be responsible for the formation of unexpectedly complex polarization patterns

Parameter sweeps

This example shows how to use polling files to sweep parameters

Visualization

Here you will learn how to use the visualization tools LimpetGUI for single cell results and Meshalizer for tissue results

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