Schedule
Day 1
| Time | Topic | Teachers |
| 09:00 | Setting up and troubleshooting installations | EF, JS, LM, TL, EP |
| 10:00 | Lecture: Introduction to Reproducible Research | EF |
| 10:25 | Break | |
| 10:40 | Lecture: Data management and project organization | JS |
| 11:10 |
Version tracking and distributing your code - Lecture: Introduction to version control and Git - Practical tutorial: Git |
EF |
| 12:00 | Lunch | |
| 13:00 | … continued: Git | EF, JS, LM, TL, EP |
| 14:40 | Break | |
| 15:00 |
Mastering your environment - Lecture: Introduction to the package and environment manager Conda - Practical tutorial: Conda |
JS |
| 16:45 | Wrap-up day 1 | EF |
Day 2
| Time | Topic | Teachers |
| 09:00 |
Organize your analyses using workflow managers - Lecture: Introduction to Snakemake - Practical tutorial: Snakemake |
JS |
| 10:20 | Break | |
| 10:40 | … continued: Snakemake | EF, JS, LM, TL, EP |
| 12:00 | Lunch | |
| 13:00 | … continued: Snakemake | EF, JS, LM, TL, EP |
| 14:40 | Break | |
| 15:00 |
Organize your analyses using workflow managers - Lecture: Introduction to Nextflow - Practical tutorial: Nextflow |
EF |
| 16:45 | Wrap-up day 2 | JS |
| 18:00 | Course dinner at Grappa | EF, JS, LM, TL, EP |
Day 3
| Time | Topic | Teachers |
| 09:00 | … continued: Nextflow | EF, JS, LM, TL, EP |
| 10:20 | Break | |
| 10:40 | … continued: Nextflow | EF, JS, LM, TL, EP |
| 12:00 | Lunch | |
| 13:00 |
Writing computational notebooks and reproducible
reports - Lecture: Introduction to Quarto - Practical tutorial: Quarto |
EF |
| 14:30 | Break | |
| 14:50 | … continued: Quarto | EF, JS, LM, TL, EP |
| 15:20 |
Writing computational notebooks and reproducible
reports - Lecture: Introduction to Jypyter - Practical tutorial: Jupyter |
JS |
| 16:45 | Wrap-up day 3 | EF |
Day 4
| Time | Topic | Teachers |
| 09:00 | … continued: Jupyter | EF, JS, LM, TL, EP |
| 09:45 |
Working with containers - Lecture: Introduction to containers - Practical tutorial: Containers |
JS |
| 10:30 | Break | |
| 10:50 | … continued: Containers | EF, JS, LM, TL, EP |
| 12:00 | Lunch | |
| 13:00 | … continued: Containers | EF, JS, LM, TL, EP |
| 14:20 | Break | |
| 14:40 | … continued: Containers | EF, JS, LM, TL, EP |
| 16:45 | Wrap-up day 4 | JS |
Day 5
| Time | Topic | Teachers |
| 09:00 |
Putting it all together - Lecture: How to put all the tools together and seeing the big picture - Practical tutorial: Start using the tools in your own projects |
EF |
| 10:20 | Break | |
| 10:40 | … continued: Putting it all together | EF, JS, LM, TL, EP |
| 12:00 | Lunch | |
| 13:00 | … continued: Putting it all together | EF, JS, LM, TL, EP |
| 14:20 | Break | |
| 14:40 | … continued: Putting it all together | EF, JS, LM, TL, EP |
| 15:45 | Final wrap-up and end of the course! | JS |
The above schedule is approximate; variations may occur.
| EF | Erik Fasterius |
| JS | John Sundh |
| TL | Tomas Larsson |
| LM | Lokesh Manoharan |
| EP | Estelle Proux-Wéra |