Hodgkin-Huxley Neuron with Ornstein-Uhlenbeck Synaptic Input

This project implements a Hodgkin-Huxley neuron model with synaptic input modeled as an Ornstein-Uhlenbeck (OU) process. It should be run as a marimo notebook.

Prerequisites

• Python 3.13+
• uv (recommended for dependency management)

Getting Started

Using Nix/devenv

If you have devenv installed, you can set up the environment automatically:

# Enter the development environment
devenv shell

# If you have envrc, the environment should automatically load
# every time you enter the project directory after you run direnv allow

# Run the notebook
marimo edit neuron.py

Using other environments

If you don't use Nix, you can use uv or pip to manage dependencies.

Using uv (recommended)

# Install dependencies and run the notebook
uv run marimo edit neuron.py

Using pip

# Install dependencies
pip install .

# Run the notebook
marimo edit neuron.py

Usage

The neuron.py file is a marimo notebook. You can interact with it in two ways:

1. Edit Mode (Interactive):

   marimo edit neuron.py

   This opens the notebook in your browser, allowing you to modify parameters and see real-time updates.

2. Run Mode (App):

   marimo run neuron.py

   This runs the notebook as a read-only web application.

3. Script Mode:

   python neuron.py

   Running it directly with Python will execute the notebook as a script.