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Re: [rb-general] Paper preprint: Reproducible genomics analysis pipeline
From: |
Holger Levsen |
Subject: |
Re: [rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix |
Date: |
Wed, 11 Apr 2018 18:30:28 +0000 |
Hi Ricardo,
On Wed, Apr 11, 2018 at 02:18:38PM +0200, Ricardo Wurmus wrote:
> I’m happy to announce that the group I’m working with has released a
> preprint of a paper on reproducibility with the title:
>
> Reproducible genomics analysis pipelines with GNU Guix
> https://www.biorxiv.org/content/early/2018/04/11/298653
>
> We built a collection of bioinformatics pipelines and packaged them with
> GNU Guix, and then looked at the degree to which the software achieves
> bit-reproducibility (spoiler: ~98%), analysed sources of non-determinism
> (e.g. time stamps), discussed experimental reproducibility at runtime
> (e.g. random number generators, kernel+glibc interface, etc) and
> commented on the idea of using “containers” (or application bundles)
> instead.
wow, just wow. very very nice to see that!
> The middle section is a bit heavy on genomics to showcase the features
> of the pipelines, but I think the introduction and the
> discussion/conclusion may be of general interest.
As you might guess I have just skimmed over the text but it's really
super cool to see reproducible builds used in science! and diffoscope,
too!
just one thing/question: in the keywords you have "reproducible
software" but not "reproducible builds", which is kind of our "marketing
term". Do you think you could squeeze that in?
--
cheers,
Holger, once again wishing he could read more (and more...)
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