The aim of this virtual training is to introduce participants to working in Unix and creating Conda environments for running simple bioinformatics tasks. The training is divided into three sessions. In the first session, participants will be introduced to the Unix ecosystem and basic Unix commands useful for inspecting various files. In the second session, participants will focus on file manipulation and consolidate their understanding of the command line interface. The third session aims to enhance participants’ ability to perform bioinformatics tasks in the command line by setting up and using Conda environments.

Duration: Three half-days on 20, 21 and 22 August 2024 from 10:00 to 14:00 (CET)

Location: Online - Find the link after enrolment. 

Audience: Public health microbiologists, epidemiologist, or beginners in bioinformatics interested in learning about the power of the command line interface and setting up separate environments with bioinformatics tools.

Objectives:  

Upon completion of this workshop, participants will be able to:

• Understand and recognize Unix as an ecosystem
• Execute several basic commands in the terminal
• Navigate in Unix
• Run simple commands for inspecting files
• Manipulate file contents from command line
• Understand the differences between file locations and running commands in the terminal
• Understand principles behind package management in separate environments
• Have a basic understanding of the Conda ecosystem for handling environments and packages
• Download and install Mamba on Ubuntu
• Use Mamba - A Conda ecosystem package manager
• Create and activate environments
• Install a bioinformatics software
• Run a bioinformatics analysis

Participation: This course is open for public enrolment from 29 July 2024.