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Re: “Reproducible research articles, from source code to PDF”

From: Ludovic Courtès
Subject: Re: “Reproducible research articles, from source code to PDF”
Date: Thu, 18 Jun 2020 09:31:16 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux)

Hi Simon!

zimoun <> skribis:

> For example, they are future bridges to think: connect the Guix archive
> somehow with zenodo DOI and/or Software Heritage identifier.
> When I read this comment in the review [1]:
>         As  a final  note,  I  wonder if,  and  how  much, the  author's
>         approach to reproducible computation/automated report generation
>         is  feasible  for  the  average scientist,  in  particular  when
>         compared to tools with a smoother learning curve, such as Docker
>         containers,  Jupyter notebooks,  R  Markdown  documents and  the
>         like. A brief  analysis of this topic with  a clear presentation
>         of the  advantages of  the author's  approach in  the Discussion
>         session would be worthwhile.
> and then the Konrad's answer [2], I asked myself what pieces are
> missing.  And what could be the articulation of "guix pack -f docker",
> Guix-Jupyter or other notebooks (RMarkdown, Org)?  And what could be a
> practical workflow? (Keeping in mind that the average scientist is not a
> Linux guru but often run MacOS or Windows.)
> 1:
> 2:

I don’t like the phrase “average scientist”, and we’re talking about
people with a PhD who definitely know how to learn.

Apart from that, I agree with the comments above: putting it in the
hands of scientists will be the real challenge.  I think providing
modules and ready-to-use “templates” for people who use R+RMarkdown, or
LaTeX, or Jupyter, etc. is a necessary step.

> Half-related to the blog post.  You mention elsewhere this baby channel
> [3], maybe it could be worth to link it somewhere in the blog post.
> Moreover, totally unrelated, I feel it lacks a list of "Scientific"
> channels, as [4] or [5], maybe on
> 3:
> 4:
> 5:

<> has a list of channels.  I’ve added Guix
Past now.

Thanks for your feedback!


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