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Analyze all Jupyter notebooks mentioned in PubMed Central #25

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@Daniel-Mietchen

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@Daniel-Mietchen

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.

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