Bioinformatic Analysis with 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. Containerized 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. This course will introduce the basic concepts of containers and their deployment at CSC.

BioMonth 2022

In March-April 2022 we offer you a nice opportunity to learning how to use supercomputer Puhti to do your data processing or simulations effectively, and how to handle your data not only while doing the analysis, but also before and after that! Join the BioMonth 2022 classes and make sure you get the most out of our services* and your data management in shape!

* The CSC services discussed in this course are free-of-charge for academic research, education and training purposes in Finnish higher education institutions and in state research institutes (subsidized by the Ministry of Education and Culture, Finland).  

With 1 registration you get 3 half-days (9:00-12:00) of interesting topics:

Wed 30.3. - Fri 1.4.

  • Using CSC services efficiently from biousers point-of-view
  • SDS services
  • Data management

Note also:

23.3.-25.3. Using CSC environment efficiently 

Wed 6.4.- Fri 8.4. RNA-seq data analysis with Chipster -separate registration!



Containers and Workflows in Bioinformatics

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. This course will focus on the deployment of containerised applications in HPC environment. The course will also introduce a modern workflows manager (i.e., nextflow ) to perform complex analysis in bioinformatics..

Biocontainers (101):Containerised Applications in Bioinformatics

This is a basic level course on containers which are a modern way of deploying complex applications. In this course, the basics of docker container and its containnerised applications in bioinformatics will be discussed. Emphasis will be given to the deployment of different pre-existing dockerised bio-applications. Selected examples from different omics’ disciplines such as genomics, proteomics and metabolomics will be covered. We will introduce HPC-compliant containers in CSC environment.

Single-cell RNA-seq data analysis with Chipster

This introductory course covers single-cell RNA-seq data analysis methods, tools and file formats. The free* and user-friendly Chipster software is used in the exercises, and the course is thus suitable for everybody.
* See: https://chipster.csc.fi/access.shtml