Lessons are grouped by topic and numbered in the order they build on each other: the LTEE project you create in lesson 02 grows with every lesson after it, and each tutorial lists what it needs at the top. When each lesson is taught is in the schedules: 7-week course and workshop.
slides · slides (PDF) · tutorial
| Getting started |
00 Setup |
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| Introduction |
01a Reproducibility |
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01b Open science |
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| Project organization and data management |
02 Project organization |
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03 Data management and FAIR |
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| Version control |
04 Git and GitHub |
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| Software environments |
05 Pixi |
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05b Pixi and Conda compared |
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| Notebooks and reports |
06 Jupyter |
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07 Quarto |
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| Containers |
08 Containers |
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| Workflows |
09 Snakemake |
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10 Nextflow |
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| Documentation and sharing |
11 Documentation |
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12 Putting it all together |
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| Extras |
Markdown |
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Take-down |
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Bash 101 |
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Terminal editors and sessions |
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YAML, TOML and JSON |
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| Extras (optional) |
Package and share your tool |
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Also: cheat sheets · the LTEE example project · glossary · LTEE project hand-in · capstone rubric · sources and credits