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 8: Halfway recap / catch-up

Author

Affiliation

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Published

October 13, 2025

1 Overview

This week, we will only meet on Tuesday because Wed-Fri is fall break. We will use this lecture to catch up as we have been one lecture behind schedule for a while now. Furthermore, we will give a brief initial overview of expectations around your Final Project for this course

2 Readings

Final Project: general information

3 Exercises & assignments

Graded assignment: Slurm batch jobs with shell scripts (Due 10/20)