4.2 Reproducible Research - CodeRefinery 2023 Sep
Channel: CodeRefinery
Date: 26/09/2023

If you can't get your code to do the same thing again, is it really science?  Or more practically, are you able to do your work?  Reproducibilty is a big deal, but we don't always learn how to do it.  In this lesson, we cover the basics, how to organize projects, record computational steps with Snakemake or other workflow managers, how to record environments with conda (and docker a bit), and sharing code and data (FAIR).

https://coderefinery.github.io/reproducible-research/

01:26 Introduction: how the whole workshop connects
05:36 Motivation
21:04 Organizing projects
28:46 Recording computational steps
33:25 Exercise: Snakemake
38:41 Q&A after exercise
44:13 Recording dependencies
49:58 Exercise: explore dependency management in conda/Python/R/Matlab
1:00:01 Recording environments (containers)
1:09:37 Exercise: Container
1:13:08 Discussion after exercise
1:14:50 Where do you go from here?  Practical advice

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This is part of the CodeRefinery September 2023 workshop.  The videos are available to everyone, but may be most useful to the people who attended the workshop and want to review later.

Playlist: https://www.youtube.com/playlist?list=PLpLblYHCzJADyLxv8GRyxFiRJBhQ-G0NQ

Workshop webpage: https://coderefinery.github.io/2023-09-19-workshop/

CodeRefinery: https://coderefinery.org/