Introduction to software containerization in bioinformatics

ISCB RSG Italy

This course will introduce attendants on how to make reproducible, portable and reusable bioinformatics software&pipelines

M﻿OTIVATIONReproducibility is a major principle underpinning the scientific method, and it is of pivotal importance for bioinformatics studies.Bioinformatics analyses are typically the results of pipelines of software packages, each one having multiple running options and frequent updates that often changes their default behaviors. Moreover, bioinformatics softwares extensively rely on external libraries/packages, thus limiting the portability and reusability of the software, requiring to properly install and configur a large amount of dependencies, and building/compiling of the application on different target systems.Containers are the solutions to most of the above issues. Containers use lightweight virtualization strategies to encapsulate an entire execution environment that can be easily shared, deployed and executed in a variety of computing systems in an efficient and fully reproducible way.Overall, containers are the solution to many of the issues related to reproducibility of bioinformatics analyses, and they also provide a very efficient way to ensure reusability and portability of bioinformatics software&amp;pipelines.L﻿EARNING OUTCOMES- Understand software containerization and its impact in terms of reproducibility, portability and reusability of software and results in all the fields of science and research, with practical application to the bioinformatics field.- Understand the different virtualization strategies (e.g. containers vs virtual machines) from both users’ and developers’ points of view.- Ability to develop, build, run and share simple containers based on Singularity container engine in variety of computing systems (desktop/workstation, HPC infrastructures, etc.)P﻿REREQUISITESBasic knowledge of Linux-based operating systems (e.g. Ubuntu) and Linux terminals is required.

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Introduction to software containerization in bioinformatics

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