Schedule
Day 1
| Time | Topic | Teacher |
| 09:00 | Setting up | JS, JW, LM, TL |
| 10:00 | Introduction to Reproducible Research | EF |
| 10:30 | Break | |
| 10:45 | Data management and project organization | JS |
| 11:15 | Break-out rooms and ice breaker session | JS, JW, LM, TL |
| 11:30 |
Distributing and version tracking your code
- Introduction to version control and Git - Practical tutorial: Git |
JS |
| 12:00 | Lunch | |
| 13:00 |
… continued: Git tutorial |
JS, JW, LM, TL |
| 14:30 | Wrap-up day 1 | JS |
Day 2
| Time | Topic | Teacher |
| 09:00 |
Master your dependencies - environments and
reproducibility - Introduction to the package and environment manager Conda - Practical tutorial: Conda |
JS |
| 10:15 | Break | |
| 10:30 |
… continued: Conda tutorial |
JS, EP, LM, TL |
| 11:00 | Wrap up: Conda tutorial | JS |
| 11:15 |
Organize your analysis using workflow managers
- Introduction to Snakemake - Practical tutorial: Snakemake |
JS |
| 12:00 | Lunch | |
| 13:00 | … continued: Snakemake tutorial | JS, JW, LM, TL |
| 14:30 | Wrap-up day 2 | JS |
Day 3
| Time | Topic | Teacher |
| 09:00 | … continued: Snakemake tutorial | JS, JW, LM, TL |
| 10:15 | Break | |
| 10:30 | … continued: Snakemake tutorial | JS, JW, LM, TL |
| 11:00 | Wrap-up: Snakemake tutorial | JS |
| 11:15 |
Organize your analysis using workflow managers
- Introduction to Nextflow - Practical tutorial: Nextflow |
EF |
| 12:00 | Lunch | |
| 13:00 | … continued: Nextflow tutorial | JS, JW, LM, TL, EF |
| 14:30 | Wrap-up day 3 | EF |
Day 4
| Time | Topic | Teacher |
| 09:00 | … continued: Nextflow tutorial | JS, JW, LM, TL, EF |
| 10:00 | Wrap-up: Nextflow tutorial | EF |
| 10:15 | Break | |
| 10:30 |
Computational notebooks and reproducible reports
- Introduction to R Markdown - Practical tutorial: R Markdown |
JS |
| 12:00 | Lunch | |
| 13:00 |
Computational notebooks and reproducible reports
- Introduction to Jypyter - Practical tutorial: Jupyter |
JS |
| 14:30 | Wrap-up day 4 | JS |
Day 5
| Time | Topic | Teacher |
| 09:00 |
Containerization - Introduction to containers - Practical tutorial: Containers |
JS |
| 10:30 | Break | |
| 10:45 | … continued: Containers | JS, JW, LM, TL |
| 12:15 | Lunch | |
| 13:15 |
Putting the pieces together - How to put all the tools and procedures together - How to implement these procedures on a day-to-day basis |
JS |
| 14:30 | End of the course! | JS |
The above schedule is approximate; variations may occur.
| EF | Erik Fasterius |
| JS | John Sundh |
| VK | Verena Kutschera |
| TL | Tomas Larsson |
| JW | Jakub Westholm |
| LM | Lokesh Manoharan |
| EP | Estelle Proux-Wéra |