Biocontainers (101) 

Biocontainers (101) is a basic level course to learn skills required for running bioinformatics applications in a containerised environment. This is a remote course and includes both lectures and hands-on exercises.

Why this bio-course on containers

Bioinformatics tools often require installing different dependencies in a controlled environment. Containers allow you to logically package your application (e.g., a bioinformatics tool) together with libraries and other dependencies, providing isolated environments for running your software services. Containerised applications can be run in an isolated runtime environment independent of the actual environment (e.g., private data center, the public cloud, or even a developer’s personal laptop) in which the applications are running in. These are recently gaining popularity as a standard way to distribute, deploy, and run services by developers and system administrators.

Expected learning in this course

In this basic course, you will be introduced to the fundamentals of container technology (mainly, docker) in addition to the selected examples of containerised bioinformatics applications. This basic understanding of containers is necessary to be able to work with bio applications in a containerised environment with different options and requirements.

More specifically, you will learn:

– The essential concepts of running docker containers

– How to use docker volumes to manage persistent data

– The basics of docker networks

– The containerised applications in Bioinformatics

– The basic Singularity concepts for running in HPC environment

After this course, one will be able to launch and work with pre-existing containerised applications in his or her work-life as a bioinformatician.

Pre-requisites:

One should be comfortable working with the command line environment in Linux and able to use any common editors (e.g., vi, nano, or emacs, etc.) in order to get the maximum benefit from this course. 

So, ideal candidates for this course are:

–       Bioinformaticians or computer scientists with some bio-background

–       Biologists with Linux skills

Expected way of learning

–       Lectures

–       Tutorials

–       Hands-on assignments

Practicalities (More information will be updated here)

Biocontainers course uses VirtualBox environment for hands-on sessions. Course participants have to make sure that VirtualBox will be working on your computer.

Instructions on downloading the image and working with VirtualBox.

Your own Linux environment may be fine as long as you take care of it by yourself. 

e-Lena e-learning platform will be used in the course.  

Lecturers

Laxman Yetukuri and Ari-Matti Saren