Setting-up your environment

March 10, 2026 · View on GitHub

Please install Python and the different packages needed for the course before the start of the course.

Several options exist to install Python, we give 3 of them in this document.


Setup using Anaconda 🐍

Anaconda and Jupyter notebook

Anaconda is an open-source python distribution that bundles python 3 along with a large number of useful python modules such as SciPy, NumPy, or Pandas.

  • It also bundles other useful software such as the conda package manager (which allows easy installation of bioinformatics software) and Jupyter Notebook.
  • Anaconda is cross-platform and available for Windows, Linux, and MacOS operating systems.

Jupyter Notebook is an open-source application that runs locally in your web-browser and allows you to create documents that contain both code and text annotations (in Markdown).


Installing Anaconda

To test whether your installation is working, try to launch Jupyter Notebook:

  • Linux/MacOS: open a terminal and type jupyter-notebook.
  • Windows: in the start menu, search for "Jupyter Notebook (Anaconda)" and start the application.

Launching the application should open a new tab in your default web-browser with the Jupyter Notebook launch page. From there you can browse your computer for existing notebooks (.ipynb files), or you can click on new > Python3 to open a new empty notebook.

An introduction to Jupyter Notebook will be given at the start of the lecture, so installing Anaconda and checking that Jupyter Notebook is running is all you need to do for now.



Setup using Python and pip 🌱

  1. Download and install Python from its official source.

  2. In principle, you should now also have a command named pip installed (it comes together with Python). You can test it by running:

    python -m pip --version
python3 -m pip --version   # On some systems, python installs as "python3".

    ✨ Note: on some systems, Python installs as an executable named python3, while on others it installs as python.

  3. Install the packages needed for the course with pip

    pip install -r requirements.txt

    🔥 Important: you must be located at the root of the course material directory for the commands to work (in the directory where the requirements.txt file is found).



Setup using uv ⚡

uv is a modern Python version and package manager. To install uv, please refer to the official documentation.

✨ Note: using uv implies that all your Python package installations and command executions will run a so-called "virtual environment". Using virtual environments is a good practice, but also adds a (small) extra layer of complexity.


After uv is installed, proceed as follow:

  1. Install Python, Jupyter notebook and all other Python packages needed the course.

    uv sync

    🔥 Important: you must be located at the root of the course material directory for the commands to work (in the directory where the pyproject.toml file is found).

  2. Start a Jupyter Notebook session in the virtual environment.

    uv run jupyter-notebook

If at some later point in time you want to update the virtual environment to the latest version of its Python packages:

uv sync --upgrade

To update uv itself, or clean its local cache. These commands can be executed from anywhere.

uv self update   # Upgrade uv to its latest version.
uv cache clean   # Clear local cache where downloaded python packages are stored.