Practical Computing Skills for Omics Data
Ohio State PLNTPTH 5006 – Autumn 2026
| Week | Monday topic | Wednesday topic | Ex./GA/FP1 |
|---|---|---|---|
| 01 | 08/26: Course intro & Omics data | ||
| 02 | 08/31: Project organization & OSC intro | 09/02: VS Code & Markdown | Ex.1 |
| 03 | Labor day | 09/09: Unix shell – basics | GA1 |
| 04 | 09/14: Genomics files & Unix shell – files I | 09/16: Unix shell – files II | Ex.2 |
| 05 | 09/21: Version control – Git intro & hands-on | 09/23: Version control – GitHub | GA2 |
| 06 | 09/28: OSC – beyond the basics | 09/30: Software with modules and containers | Ex.3 |
| 07 | 10/05: Shell scripting I | 10/07: Shell scripting II | GA3 |
| 08 | 10/12: Generative AI in research and coding | 10/14: Generative AI in research and coding (cont.) | |
| 09 | 10/19: Coding with an AI agent | 10/21: Coding with an AI agent (cont.) | GA4 |
| 10 | 10/26: Slurm batch jobs | 10/28: Batch jobs and workflows | Ex.4 |
| 11 | 11/02: Running an nf-core pipeline (rnaseq) | 11/04: Data management | GA5 |
| 12 | 11/09: R & Quarto basics | Veteran’s day | FP1 |
| 13 | 11/16: Data wrangling in R | 11/18: Data visualization in R | Ex.5 |
| 14 | 11/23: Quarto – beyond the basics | Thanksgiving | FP2 |
| 15 | 11/30: R for omics data: RNA-seq count data | 12/02: R for omics data: metabolomics data | Ex.6 |
| 16 | 12/07: Student presentations I | 12/09: Student presentations II | FP4 |
NoteWeekly course activities
- Lectures: Monday & Wednesday 1:50–3:10 pm (required)
- Recitation: Friday 3–4 pm (optional)
- Jelmer’s office hours: Thursday 1–3 pm
- Kelsey’s office hours: Monday 11 am – 1 pm
Footnotes
Ex. = Exercises (ungraded); GA = Graded Assignment; FP = Final Project↩︎