Ecology Workshop Overview: Setup for Python workshop

Overview

This workshop is designed to be run on your laptop. First, you will need to download the data we use in the workshop. Then, you need to install some software. After following the instructions on this page, you should have everything you need to participate fully in the workshop!

Data

You can download all of the data used in this workshop by clicking this download link. The file is 38.4 MB.

Clicking the download link will automatically download all of the files to your default download directory as a single compressed (.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder application).

For a full description of the data used in this workshop see the data page.

Software

Software Install Manual Available for Description
Spreadsheet program Link Link Linux, MacOS, Windows Spreadsheet program for organizing tabular data.
OpenRefine Link Link Linux, MacOS, Windows Program for reproducibly cleaning data.
Python See install instructions below.   Linux, MacOS, Windows Programming language for data analysis and visualisation.
SQLite Browser Link Link Linux, MacOS, Windows Tool for creating, designing, and editing database files.

Spreadsheet program

OpenRefine

Python and Jupyter Notebooks

Anaconda installation

Download and install Anaconda. Remember to choose the installer for Python 3.x. Anaconda does not include the plotting package plotnine. To install this package, open your terminal application and type:

conda install -c conda-forge plotnine

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 following the instructions. Remember to choose the installer for Python 3.x.

From your terminal application, type:

conda list

To install the packages we’ll be using in the workshop, type:

conda install -y numpy pandas matplotlib jupyter
conda install -c conda-forge plotnine

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.

For a brief introduction to Jupyter Notebooks, please consult our Introduction to Jupyter Notebooks page.

SQL

Congratulations! You are now ready for the workshop!