Comment by flopsamjetsam
6 hours ago
> Every result is instantly reproducible. When you read a paper claiming that a new drug reduces symptoms by 30%, you click a link and watch the exact analysis run in your browser. The data processing, statistical tests, and visualizations execute in seconds using the same environment the authors used—preserved perfectly through reproducible containers.
At least some journals have this as a stipulation e.g. https://www.nature.com/nature-portfolio/editorial-policies/r...
Particularly the "data availability" and "Availability and peer review of computer code and algorithm".
However, in my limited experience, of trying to reproduce certain scRNA-seq processing pipelines, in practice it's never available as just a Github link. I can understand that some/many researcher's code is not in good shape, so I think it'll be quite a stretch to have this available.
I do think it's laudable though, to try and make it available. It would certainly have been very useful for me in the past.
I try to do something like this with my publications, and encourage others to. My goal is to have the pipeline from raw data to complete figures and manuscript in a repository, with cached data for computationally expensive analysis and for stochastic simulation results, and the option for the user to just use those or run the full pipeline, with or without the same random seeds. I just make clear that the code was run-once code and is going to be messy compared to code refined over time and diverse uses. I generally use Zenodo to a GitHub repo, however, in case GitHub decides to do something bad in the future. Making sure things run far in the future can also be a challenge. Sure, you can use a container: will the base of that container be available in 30 years?
And with that said, for experimental work, this approach does not make things fully reproducible; it only makes the analysis reproducible. There are always factors that influence experiments: research is by definition at the edge of our understanding, and reality has countless variables, including ones no one has thought of, known about or thought important.