cell-models 0.0.1

This package contains cell models and the ability to apply various protocols to them.

Cell Models Package

This package is meant to contain all Christini Lab models that are implemented in Python. As of writing this, there are 3 models: O'Hara Rudy, Paci, and Kernik.

Using and Installing this Project

This Python project is written in Python Packaging format. If you want to play around with the models quickly, you can cd into cell-models/ and edit the main.py file.

If you want to install these models locally, you can run python3 setup.py from the project root. This will make the files in cell-models/ globally available.

Tutorial

Much of the code below can be found in cell-models/main.py.

Instantiate and generate a response from models

The following will plot spontaneous Kernik and Paci models and a paced O'Hara Rudy model.

# Spontaneous / Stimulated
KERNIK_PROTOCOL = protocols.SpontaneousProtocol(2000)
kernik_baseline = KernikModel()
tr_b = kernik_baseline.generate_response(KERNIK_PROTOCOL)
plt.plot(tr_b.t, tr_b.y)
plt.show()

PACI_PROTOCOL = protocols.SpontaneousProtocol(2)
paci_baseline = PaciModel()
tr_bp = paci_baseline.generate_response(PACI_PROTOCOL)
plt.plot(tr_bp.t, tr_bp.y)
plt.show()

OHARA_RUDY = protocols.PacedProtocol(model_name="OR")
or_baseline = OharaRudyModel()
tr = or_baseline.generate_response(OHARA_RUDY)
plt.plot(tr.t, tr.y)
plt.show()

Update parameters for a model

The code below will plot the baseline Kernik model and an example model with new parameter values.

KERNIK_PROTOCOL = protocols.SpontaneousProtocol(2000)
kernik_baseline = KernikModel()
kernik_updated = KernikModel(
        updated_parameters={'G_K1': 1.2, 'G_Kr': 0.8, 'G_Na':2.2})
tr_baseline = kernik_baseline.generate_response(KERNIK_PROTOCOL)
tr_updated =  kernik_updated.generate_response(KERNIK_PROTOCOL)
plt.plot(tr_baseline.t, tr_baseline.y, label="Baseline")
plt.plot(tr_updated.t, tr_updated.y, label="Updated")
plt.legend()
plt.show()