Initial Setup

MacOS

Most servers in the world run on Linux and when it comes to software engineering, machine learning and bioinformatics, Linux is the preferred operating system.

I have developed this course with a focus on MacOS as that is my main machine. I find for coding on MacOS is much easier as MacOS was originally based on UNIX and the terminal is similar to modern Linux distros.

If you are using Windows, we will use the built-in Command Prompt (cmd.exe) throughout this course — no extra setup needed. Open it with Win + R, type cmd, and press Enter. Where commands differ between MacOS/Linux and Windows, this course shows both side by side.

When I first got into coding, I was predominantly using Windows so am familiar with it. I no longer have a Windows machine and cannot test this material on Windows at the moment — please raise an issue if a Windows command does not work for you.

Before we get started we need to get your machine set up with the necessary tools. We will be using Python 3.12, VSCode, and GitHub to start with. Later in the course we will use Microsoft Azure for cloud servers.

Prerequisites

• Install Python 3.12 https://www.python.org/ (we stay one version behind the latest to avoid package compatibility issues — latest is 3.13 as of writing, so we use 3.12)
• Install VSCode https://code.visualstudio.com/
• Set up a GitHub account http://github.com
• Check Git is installed by running git --version, if not install it https://git-scm.com/
• Cloud (later): a Microsoft Azure account. We will use Azure for servers in the Cloud section.