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.
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 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. They provide the means to start a light-weight virtualization environment, i.e., a container, based on Linux kernel namespaces and control groups (cgroups). Such virtualization environment is cheap to create, manage, and destroy, requires a negligible amount of time to set-up, and provides performance equatable with the one of the host. Docker offers an intuitive way to manage containers by abstracting and automating the low-level configuration of namespaces and cgroups, ultimately enabling the development of an entire ecosystem of tools and products around containers.
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:
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.
One will be able to launch and work with pre-existing containerised applications in their work life as bioinformaticians.
While we don’t discourage anybody from joining this course, one should be comfortable working with commandline environment e.g., in Linux terminal, editing files with common editors (e.g., vi, nano, emacs, etc.) in order to get maximum benefit from this course.
Bioinformatician Biologist with linux skills Biologists who are willing to get some feel of containers may join the course
Practice ! practice ! and practice !!!
Lectures as HTML slides. Use cursor keys or click left/right side of the slide to change it. You can print the slides to PDF with Chrome, just tweak the print settings a bit.