Schedule
The course will be in rooms Air/Fire at SciLifeLab, Stockholm (see travel info).
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Time | Teacher(s) | Topic |
09:00 | LW, RÅ | Introduction to Reproducible Research [slides] |
09:45 | NJ | Data management [slides] |
10:15 | Fika break | |
10:45 | LW, RÅ, JS, PU |
Master your dependencies - environments and reproducibility
- Introduction to the package and environment manager Conda [slides] - Practical tutorial: Conda |
12:00 | Lunch | |
13:00 | LW, RÅ, JS, PU |
Organize your analysis using workflow managers
- Introduction to Snakemake [slides] - Practical tutorial: Snakemake |
16:15 | LW, RÅ | Wrap-up |
16:30 | Free time! | |
17:00 | Joint departure for dinner | |
17:30 | Dinner at Grappa Bar och Matsal, Sankt Eriksgatan 86 | |
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Time | Teacher(s) | Topic |
08:30 | LW, RÅ, JW |
Distributing and version tracking your code
- Introduction to version control and git [slides] - Practical tutorial: Git Computational notebooks - Introduction to Jupyter [slides] - Practical tutorial: Jupyter |
12:00 | Lunch | |
13:00 | LW, RÅ, OD |
Reproducible reports
- Introduction to R Markdown [slides] - Practical tutorial: R Markdown Containerization - Introduction to containers [slides] - Practical tutorial: Docker |
16:00 | LW, RÅ | Wrap-up [slides] |
16:30 | TGIF! |
Teachers:
JS - John Sundh
JW - Jakub Westholm
LW - Leif Wigge
NJ - Niclas Jareborg
OD - Olga Dethlefsen
PU - Per Unneberg
RÅ - Rasmus Ågren