Mastering the Terminal with Bash and Unix (September 2024)

A 2-day workshop on the Bash shell and terminal command line tools, scripts, and pipelines for data analysis

Knowledge on how to use a terminal command line is an essential skill, not just for data scientists, but for any biomedical researcher who needs to work with large datasets, including registry data, clinical datasets and high-throughput biological data. 

In combination with the basics of bash, mastering the command line will allow you to wrangle large datasets and run command line softwares for data analysis, including  those for sequence alignment, gene annotation, SNP & CNV calling, web-scraping, protein structure analysis, and much much more.

Additionally, you will build the skill set you need to work on high performance computer (HPC) systems and external servers, when the power of your local machine does not suffice.

This is a 2-day introductory workshop to the Bash shell and command line interpreter.
In the workshop, we will take you though:

1. Understanding what a terminal is, how to use it, how to get help and handle errors
2. Setting up a good directory structure for computational projects
3. Performing basic unix operations on files
4. Automating workflow through scripts and workflow language
5. Navigating on unix-based HPC environments (servers) such as computerome 2.0