PRACS-AU25

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

Practical Computing Skills for Omics Data
Ohio State PLNTPTH 5006 - Autumn 2025

Week	Tue session	Thu session	Ex	GA/FP
01	08/26: Course intro (slides) & Omics data (slides)	08/28: The Ohio Supercomputer Center (OSC)
02	09/02: Project organization	09/04: VS Code + Markdown & Unix shell: Basics		GA 1
03	09/09: Unix shell: Working with files I	09/11: Unix shell: Working with files II	Ex 1
04	09/16: Version control: Git	09/18: Version control: GitHub		GA 2
05	09/23: Reproducibility & Data management	09/25: OSC part II & Software: modules and containers	Ex 2
06	09/30: Shell scripting: basics	10/02: Shell scripting: running CLI software		GA 3
07	10/07: Slurm batch jobs I	10/09: Slurm Batch jobs II	Ex 3
08	10/14: Coding with generative AI	Fall break		GA 4
09	10/21: Workflow management intro	10/23: Building Nextflow pipelines I	Ex 4
10	10/28: Building Nextflow pipelines II	10/30: Building Nextflow pipelines III		GA 5
11	11/04: Intro to R & R vectors and data types	11/06: Tabular data in R	Ex 5
12	Veteran’s day	11/13: R notebooks with Quarto	Ex 6	FP 1
13	11/18: Data visualization in R	11/20: Bioconductor: R for omics data		GA 6
14	11/25: RNA-Seq count data analysis in R	Thanksgiving	Ex 7	FP 2
15	12/02: Running nf-core pipelines I	12/04: Running nf-core pipelines II	Ex 8
16	12/09: Student presentations			FP 4

= Week overview page Ex / = Exercises GA/FP = Graded Assignment / Final Project