Simulation and Inference for Neuroscience

This repository contains the code for the Simulation and Inference for Neuroscience course taught at AIMS.

Download

You can download the repository by running:

git clone https://github.com/aims-neuroscience/simulation-and-inference-for-neuroscience.git

or by clicking the "Code" button above and clicking "Download ZIP".

Installation

There is two different ways to install the dependencies:

Option 1: Using uv

We recommend using uv to manage the dependencies. If you're on macOS or Linux you can install uv by running:

curl -LsSf https://astral.sh/uv/install.sh | sh

If you're on Windows you can install uv by running:

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Once you have uv installed, you can install the dependencies, create a python virtual environment and activate it by running:

uv sync
source .venv/bin/activate

Then you can run the notebooks by running:

jupyter-notebook notebooks/

If you are using an IDE, it should be able to detect the python environment and use it automatically. I recommend using vscode.

Option 2: Using conda

Alternatively, you can use conda to manage the dependencies. If you don't have conda installed, you can install it here.

Once you have conda installed, you can create a python environment and install the dependencies by running:

conda create -n sim-inf-neuro python=3.12
conda activate sim-inf-neuro
pip install -e .

Then you can run the notebooks by running:

jupyter-notebook notebooks/