The aim of this course is to provide participants with an introduction to the Linux command line. This comprehensive course is primarily aimed at bench scientists that are taking their first steps in bioinformatics analysis.
Over the course of a single day, participants will learn the basics of the Linux terminal/command line, along with more advanced Linux concepts for automating bioinformatics alaysis tasks. A major focus of the course will be on practical skills with participants using real world datasets to automate bioinformatics analysis tasks.
The course will be delivered in a virtual format using a combination of video conferencing (Zoom) and text based messaging (Slack). All bioinformatics software and datasets required for the course will be provided through a virtual machine (VirtualBox) that is compatible with Mac, Windows and Linux. Instructions for installing and setting up Zoom, Slack and the virtual machine will be distributed to the participants before the course begins.
To participate in the course you will need:
A desktop computer or laptop with a speaker/headphones, mic and camera.
A minimum of 8 GB of memory and 30 GB of free disk space.
Ability to install Zoom, Slack and VirtualBox.
This course is aimed at research scientists who have little or no previous experience in bioinformatics and are making the transition to using bioinformatics in their research. Participants are expected to have some knowledge of or experience with life sciences, but no prior knowledge of computing or bioinformatics is expected.
Day 1 - Linux for bioinformatics
- Introduction to the Linux command line
- Overview of the Linux directory structure and how to navigate around this structure
- Manipulating (move, copy and delete) files using the command line
- Use of regular expressions to search for particular patterns in a file
- Use of the AWK programming language to extract and filter information from a file
- Introduction to For loops and bash scripts for automating analysis tasks
On completion of the course, participants can expect to have acquired:
A working knowledge of the Linux command line
Knowledge of advanced Linux commands for automating bioinformatics tasks