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 [TBA]
- Week 4: Version control with Git and GitHub [TBA]
- Week 5: Data and software management at OSC [TBA]
- Week 6: Shell scripts and CLI tools [TBA]
- Week 7: Slurm batch jobs at OSC [TBA]
- Week 8: Using generative AI when coding [TBA]
- Week 9: Automated pipelines with Nextflow [TBA]
- Week 10: Building Nextflow pipelines [TBA]
- Week 11: R – basics [TBA]
- Week 12: R – Quarto [TBA]
- Week 13: R – data visualization [TBA]
- Week 14: R – omics data [TBA]
- Week 15: Nextflow nf-core pipelines [TBA]
Exercises
- Week 3: Unix shell [TBA]
- Week 5: OSC data and software [TBA]
- Week 7: Slurm batch jobs [TBA]
- Week 9: Nextflow [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: Version control with Git and GitHub (Week 4) [TBA]
- GA 3: Shell scripting (Week 6) [TBA]
- GA 4: Slurm batch jobs at OSC (Week 8) [TBA]
- GA 5: Nextflow (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: Post-course survey (week 16)
Final project
- General info [TBA]
- FP 1: Proposal (week 12) [TBA]
- FP 2: Draft (week 14) [TBA]
- FP 3: Oral presentation (week 16) [TBA]
- FP 4: Final submission (week 16) [TBA]

Other
- Course references
- Course glossary [TBA]
- Collected further learning resources [TBA]
- OPTIONAL SELF-STUDY CONTENT:
- Unix data tools (week 3) [TBA]
- Misc. Unix shell (week 3) [TBA]
- Git (week 4) [TBA]
- Software management with Conda (week 5) [TBA]
- SSH connection (week 5) [TBA]
- OSC file transfer (week 5) [TBA]
- Shell scripting and looping (week 6) [TBA]
- Slurm batch jobs (week 7) [TBA]
- OSU Code Club
About

Ungraded assignment: OSC account setup

Week 1 (deadline: Wed Aug 27, 5 pm)

Author

Affiliation

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Published

August 22, 2025

Before you start

By 5 pm on Wed Aug 27, you should make sure that you have access to the Ohio Supercomputer Center (OSC), and the OSC Project for this course (PAS2880).

You will do much of your work during this course through your browser at the Ohio Supercomputer Center (OSC), starting this week’s class on Thursday.

To access OSC, you will need to have an account. This course has its own OSC “Project”, and membership of this specific project will allow you to access our shared files and to reserve computing resources.

What you should do

After completing the pre-course survey, you will receive an invitation email from OSC referencing the course’s project number PAS2880, and:

If you don’t have an OSC account yet
Follow the instructions in the email to create an OSC account.
If you already have an OSC account
The email will likely tell you that you have been added to the project and don’t have to do anything.
In either case, check whether you can log in
Go to https://ondemand.osc.edu and log in by typing your username and password on the left-hand side of the page. (If you just created your account, it can sometimes take up to half an hour or so before you can log in.)

If you have any questions about this or run into problems, don’t hesitate to contact Jelmer.