Week overviews
- Week 1: Omics data and OSC
- Week 2: Project organization and Unix shell basics
- Week 3: Working with files in the Unix shell
- Week 4: Version control with Git and GitHub
- Week 5: Software management at OSC
- Week 6: Shell scripts and CLI tools
- Week 7: Slurm batch jobs at OSC
- Week 8: Catch-up (half-week)
- Week 9: Workflow and data management [TBA]
- Week 10: Coding with generative AI [TBA]
- Week 11: R – basics [TBA]
- Week 12: R – Quarto [TBA] (half-week)
- Week 13: R – data visualization [TBA]
- Week 14: R – omics data [TBA] (half-week)
- Week 15: Nextflow nf-core pipelines [TBA]
Exercises
- Week 3: Unix shell
- Week 5: GitHub and software at OSC
- Week 7: Shell scripts
- Week 9: Workflow and data management [TBA]
- Week 11: R basics [TBA]
- Week 12: Quarto [TBA]
- Week 14: R for omics data [TBA]
- Week 15: nf-core pipelines [TBA]
Assignments
- GRADED
- GA 1: Markdown and Unix shell basics (Week 2)
- GA 2: Unix shell data tools and Git (Week 4)
- GA 3: Shell scripts and software (Week 6)
- GA 4: Slurm batch jobs (Week 8)
- GA 5: Coding with generative AI (Week 10) [TBA]
- GA 6: Data analysis with R (Week 13) [TBA]
- UNGRADED
- UA 1: Pre-course survey (week 1)
- UA 2: OSC account setup (week 1)
- UA 3: GitHub account setup (week 4)
- UA 4: Local VS Code installation (week 9) (TBA)
- UA 5: Post-course survey (week 16) [TBA]
Final project

Week 5: Data and software management (at OSC)

Author

Affiliation

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Published

September 20, 2025

Overview

This week starts with a closer look at OSC, following up on the introduction to OSC you got in the first week of the course. Then, you will learn how you can access software that has and that has not been installed at OSC.

Learning goals

Some of the things you will learn this week:

A closer look at OSC

What cores are
In which context each of the different OSC file systems is useful
What different types of compute nodes are for

Software management

How to find and load OSC “modules” to use specific programs
Why containers and Conda are useful and reproducible alternative ways to use software
How to find and run Apptainer/Singularity containers to use specific programs
What the program FastQC does and how you can run it

Assignments and exercises

Exercises: GitHub, and software at OSC

Further resources

Optional self-study content on this site: Software management with Conda