Setting-up your environment

Please install the following software on your personal laptop before the start of the course.

Anaconda and Jupyter notebook

Anaconda is an open-source python distribution that bundles python3 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-plateform and available for both Windows and UNIX (Linux, 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 install anaconda:

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

  • UNIX: 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.

Last modified: Friday, 12 March 2021, 11:21 AM