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

Holger Levsen holger at layer-acht.org
Wed Apr 11 20:30:28 CEST 2018

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,

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?

	Holger, once again wishing he could read more (and more...)
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