all messages for Guix-related lists mirrored at yhetil.org
 help / color / mirror / code / Atom feed
* Paper preprint: Reproducible genomics analysis pipelines with GNU Guix
@ 2018-04-11 12:18 Ricardo Wurmus
  2018-04-11 18:30 ` [rb-general] " Holger Levsen
                   ` (3 more replies)
  0 siblings, 4 replies; 13+ messages in thread
From: Ricardo Wurmus @ 2018-04-11 12:18 UTC (permalink / raw)
  To: guix-devel; +Cc: rb-general, guix-hpc@gnu.org

Hey all,

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.

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.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

^ permalink raw reply	[flat|nested] 13+ messages in thread

end of thread, other threads:[~2018-05-13  8:58 UTC | newest]

Thread overview: 13+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2018-04-11 12:18 Paper preprint: Reproducible genomics analysis pipelines with GNU Guix Ricardo Wurmus
2018-04-11 18:30 ` [rb-general] " Holger Levsen
2018-04-11 18:40   ` Ricardo Wurmus
2018-04-11 19:00     ` Holger Levsen
2018-04-11 18:31 ` Holger Levsen
2018-04-11 21:16 ` Roel Janssen
2018-04-15  7:50   ` Amirouche Boubekki
2018-04-23  8:20 ` [rb-general] " Ludovic Courtès
     [not found]   ` <87fu30fsra.fsf@elephly.net>
2018-05-11  8:10     ` Ludovic Courtès
2018-05-11  8:19       ` Ricardo Wurmus
2018-05-11  9:39         ` Catonano
2018-05-13  5:07           ` Ricardo Wurmus
2018-05-13  8:58             ` Catonano

Code repositories for project(s) associated with this external index

	https://git.savannah.gnu.org/cgit/guix.git

This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.