Description
Jupyter notebooks are a popular vehicle these days to share data science workflows. To get an idea of best practices in this regard, it would be good to analyze a good number of them in terms of their reproducibility and other aspects of usability (e.g. documentation, ease of reuse).
A search in PubMed Central (PMC) reveals the following results:
With currently just 102 hits, a systematic reanalysis seems entirely doable and could perhaps itself be documented by way of reproducible notebooks that might eventually end up being mentioned in PMC.
A good starting point here could be An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study, for which both a Jupyter notebook and a Docker image are available.
I plan to give a lightning talk on this. Some background is in this recent news piece.