Python for ecologists: Setup


Data for this lesson is from the Portal Project Teaching Database - available on FigShare.

For this lesson, we will use two files for the data. Download these files to your computer. Once you click on them they will be automatically downloaded to your default download directory.


Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

For this workshop we use Python version 3.x.

Required Python Packages for this workshop

Install the workshop packages

For installing these packages we will use Anaconda or Miniconda. They both use Conda, the main difference is that Anaconda comes with a lot of packages pre-installed. With Miniconda you will need to install the required packages.

Anaconda installation

Anaconda will install the workshop packages for you.

Download and install Anaconda

Download and install Anaconda. Remember to download and install the installer for Python 3.x.

Miniconda installation

Miniconda is a “light” version of Anaconda. If you install and use Miniconda you will also need to install the workshop packages.

Download and install Miniconda

Download and install Miniconda following the instructions. Remember to download and run the installer for Python 3.x.

Check the installation of Miniconda

From the terminal, type:

conda list

Install the required workshop packages with conda

From the terminal, type:

conda install -y numpy pandas matplotlib jupyter
conda install -c bokeh ggplot

Launch a Jupyter notebook

After installing either Anaconda or Miniconda and the workshop packages, launch a Jupyter notebook by typing this command from the terminal:

jupyter notebook

The notebook should open automatically in your browser. If it does not or you wish to use a different browser, open this link: http://localhost:8888.

Overview of the Jupyter notebook (Optional)

Example Jupyter Notebook
Screenshot of a Jupyter Notebook on quantum mechanics by Robert Johansson

How the Jupyter notebook works

After typing the command jupyter notebook, the following happens:

This workflow has several advantages:

How the notebook is stored

Notebook modes: Control and Edit

The notebook has two modes of operation: Control and Edit. Control mode lets you edit notebook level features; while, Edit mode lets you change the contents of a notebook cell. Remember a notebook is made up of a number of cells which can contain code, markdown, html, visualizations, and more.

Help and more information

Use the Help menu and its options when needed.