Introduction

Container-based technologies are designed to make it easier to create, deploy, and run applications by isolating them in self-contained software units (hence their name). The idea is to package software and/or code together with everything it needs (other packages it depends, various environment settings, etc.) into one unit, i.e. a container. This way we can ensure that the software or code functions in exactly the same way regardless of where it's executed. Containers are in many ways similar to virtual machines but more lightweight. Rather than starting up a whole new operating system, containers can use the same kernel (usually Linux) as the system that they're running on. This makes them much faster and smaller compared to virtual machines. While this might sound a bit technical, actually using containers is quite smooth and very powerful.

Containers have also proven to be a very good solution for packaging, running and distributing scientific data analyses. Some applications of containers relevant for reproducible research are:

• When publishing, package your analyses in a container image and let it accompany the article. This way interested readers can reproduce your analysis at the push of a button.
• Packaging your analysis in a container enables you to develop on e.g. your laptop and seamlessly move to cluster or cloud to run the actual analysis.
• Say that you are collaborating on a project and you are using Mac while your collaborator is using Windows. You can then set up a container image specific for your project to ensure that you are working in an identical environment.

One of the largest and most widely used container-based technologies is Docker. Just as with Git, Docker was designed for software development but is rapidly becoming widely used in scientific research. Another container-based technology is Singularity, which was developed to work well in computer cluster environments. We will cover both Docker and Singularity in this course, but the focus will be on the former (since that is the most widely used and runs on all three operating systems).