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Docker Basics

Welcome to another episode of Bite-Sized! In this video, we will introduce you to Docker, one of the most powerful tools for reproducible research.

What is Docker?​

Docker is a tool that allows you to package your application together with everything it needs to run. A typical docker container includes:

  • The programming language version
  • All required packages and libraries
  • System libraries
  • Operating system settings

Think of it as a lightweight, isolated setup for running an application that ensures your code runs exactly the same way on your machine, on your supervisor's machine, or anywhere else. Unlike a full virtual machine, containers are fast and efficient, they share your computer's operating system kernel while keeping everything else isolated.

Reproducibility

If your code runs inside a Docker container on your machine, it will run exactly the same way on someone else's machine. This is the core promise of Docker for reproducible research.

The "Works on My Machine" Problem

Without a standardized environment, code that works perfectly on your laptop might suddenly break when sent to a supervisor or collaborator. This is often due to:

  • Mismatched package versions
  • Differing Python versions
  • Different operating systems

Docker solves this problem by packaging everything your code needs into a single, portable container.

Why Docker for Open Science?​

In Open Science, ensuring reproducible results, transparent workflows, and long-term usability of research code is essential. Instead of just sharing your code and hoping collaborators can get it to work, Docker allows you to share the exact research environment you used — code, dependencies, and all.

Installation & Testing​

For Mac and Windows:

  1. Download Docker Desktop from docker.com
  2. For Mac, make sure to pick the right version for your processor:
    • Apple Silicon (M1/M2/M3): ARM64 version
    • Intel: Intel version

For Linux:

  1. Go to docs.docker.com/engine/install
  2. Select your distribution and follow the provided steps

To test your installation:

docker run hello-world

If you see the message "Hello from Docker!", everything is working correctly!

What's Next?​

In the next video, we'll create our first Docker container and show you how to containerize a simple Python research project. Get ready to put Docker into action!