Course Intro
Practical Computing Skills for Omics Data (PLNTPTH 6193)
2024-02-27
The Unix shell & shell scripts (Wk 1 & 4)
Being able to work in the Unix shell is a fundamental skill in computational biology.
- You’ll spend a lot of time with the Unix shell, starting this week
- We’ll also write shell scripts, and will use VS Code for this and other purposes.
Bash (shell language)
VS Code
Project organization and Markdown (Wk 2)
Good project organization & documentation is a necessary starting point for reproducible research.
You’ll learn best practices for project organization, file naming, etc.
To document and report what you are doing, you’ll use Markdown files.
Markdown
Version control with Git and GitHub (Wk 3)
Using version control, you can more effectively keep track of project progress, collaborate, share code, revisit earlier versions, and undo.
Git is the version control software we will use,
and GitHub is the website that hosts Git projects (repositories).You’ll also use Git+GitHub to hand in your final project assignments.
High-performance computing with OSC (Wk 5)
Thanks to supercomputer resources, you can work with very large datasets at speed — running up to 100s of analyses in parallel, and using much larger amounts of memory and storage space than a personal computer has.
- We will use OSC throughout the course, and you’ll get a brief intro to it today.
- In week 5, we’ll learn to submit shell scripts as OSC “batch jobs” with Slurm, and use Conda to manage software.
Automated workflow management (Wk 6)
Using a workflow written with a workflow manager, you can run and rerun entire analysis pipeline with a single command, and easily change and rerun parts of it, too.
- We’ll use the workflow language Nextflow.
