[rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix

[Holger Levsen]

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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