Drug effects demo

In this demo we show how to modulate the cell model with pharmacological effects

import pprint
from pathlib import Path

import simcardems

# Create configurations with custom output directory
here = Path(__file__).absolute().parent
outdir = here / "results_drug_demo"

# Specify paths to the geometry that we will use
geometry_path = here / "geometries/slab.h5"
geometry_schema_path = here / "geometries/slab.json"

Please see https://computationalphysiology.github.io/cardiac_geometries/ for more info about the geometries

# Specify path to the file containing drug scaling factors
drug_factors_path = here / "drug_factors/drug_factors.json"

The scaling factors in this file are applied to the corresponding ion currents as a modulator of the ion channel conductance. The example file reduces the sodium current to 10%.

config = simcardems.Config(
    outdir=outdir,
    geometry_path=geometry_path,
    geometry_schema_path=geometry_schema_path,
    T=1000,
    drug_factors_file=drug_factors_path,
)

# Print current configuration
pprint.pprint(config.as_dict())

runner = simcardems.Runner(config)
runner.solve(T=config.T, save_freq=config.save_freq, show_progress_bar=True)

This will create the output directory results_drug_demo with the following output

results_simple_demo
├── results.h5
├── state.h5

The file state.h5 contains the final state which can be used if you want use the final state as a starting point for the next simulation. The file results.h5 contains the Displacement (\(u\)), active tension (\(T_a\)), voltage (\(V\)) and calcium (\(Ca\)) for each time step. We can also plot the traces using the postprocess module

simcardems.postprocess.plot_state_traces(outdir.joinpath("results.h5"), "center")

Here we also specify that we want the trace from the center of the slab

This will create a figure in the output directory called state_traces.png which in this case is shown in Figure 5 we see the resulting state traces.

Fig. 5 Traces of the stretch (\(\lambda\)), the active tension (\(T_a\)), the membrane potential (\(V\)) and the intercellular calcium concentration (\(Ca\)) at the center of the geometry.

We can also save the output to xdmf-files that can be viewed in Paraview

simcardems.postprocess.make_xdmffiles(outdir.joinpath("results.h5"))

The xdmf files are can be opened in Paraview to visualize the different variables.