Schedule
Day 1#
| Time | Topic |
|---|---|
| 09:00 | Setting up |
| 10:00 | Introduction to Reproducible Research |
| 10:30 | Break |
| 10:45 | Data management and project organization |
| 11:15 | Break-out rooms and ice breaker session |
| 11:30 | Distributing and version tracking your code - Introduction to version control and Git - Practical tutorial: Git |
| 12:00 | Lunch |
| 13:30 | ... continued: Git tutorial |
| 15:00 | Wrap-up Git tutorial |
| 15:15 | Break |
| 15:30 | Master your dependencies - environments and reproducibility - Introduction to the package and environment manager Conda - Practical tutorial: Conda |
| 17:15 | Wrap up: Conda tutorial |
Day 2#
| Time | Topic |
|---|---|
| 09:00 | Organize your analysis using workflow managers - Introduction to Snakemake - Practical tutorial: Snakemake |
| 10:30 | Break |
| 10:45 | ... continued: Snakemake tutorial |
| 12:00 | Lunch |
| 13:30 | ... continued: Snakemake tutorial |
| 14:45 | Wrap-up Snakemake tutorial |
| 15:00 | Organize your analysis using workflow managers - Introduction to Nextflow - Practical tutorial: Nextflow |
| 15:45 | Break |
| 16:00 | Containerization - Introduction to containers - Practical tutorial: Containers |
| 17:45 | Wrap-up |
Day 3#
| Time | Topic |
|---|---|
| 09:00 | ... continued: Containers |
| 10:15 | Break |
| 10:30 | Computational notebooks and reproducible reports - Introduction to R Markdown - Practical tutorial: R Markdown |
| 12:00 | Lunch |
| 13:00 | Computational notebooks and reproducible reports - Introduction to Jypyter - Practical tutorial: Jupyter |
| 14:15 | Computational notebooks and reproducible reports - Introduction to Quarto - Practical tutorial: Quarto |
| 15:00 | Break |
| 15:15 | Wrap-up - Computational notebooks and reproducible reports |
| 15:30 | Putting the pieces together - How to put all the tools and procedures together - How to implement these procedures on a day-to-day basis |
| 16:30 | End of the course! |
The above schedule is approximate; variations may occur.