From mboxrd@z Thu Jan 1 00:00:00 1970 From: Amirouche Boubekki Subject: Re: Paper preprint: Reproducible genomics analysis pipelines with GNU Guix Date: Sun, 15 Apr 2018 07:50:19 +0000 Message-ID: References: <87604yndgh.fsf@elephly.net> <871sflfnq4.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="000000000000ee29b60569de5beb" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36917) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f7cQj-0002m5-Rx for guix-devel@gnu.org; Sun, 15 Apr 2018 03:50:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f7cQi-0000pm-Ui for guix-devel@gnu.org; Sun, 15 Apr 2018 03:50:33 -0400 In-Reply-To: <871sflfnq4.fsf@gnu.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Roel Janssen Cc: guix-devel , rb-general@lists.reproducible-builds.org, "guix-hpc@gnu.org" --000000000000ee29b60569de5beb Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Wow very great, thanks for sharing. On Wed, Apr 11, 2018 at 11:17 PM Roel Janssen wrote: > > Ricardo Wurmus writes: > > > Hey all, > > > > I=E2=80=99m happy to announce that the group I=E2=80=99m working with h= as 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 wit= h > > GNU Guix, and then looked at the degree to which the software achieves > > bit-reproducibility (spoiler: ~98%), analysed sources of non-determinis= m > > (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 =E2=80=9Ccontainers=E2=80=9D (or applica= tion 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. > > This looks really great! I also like how you leverage GNU Autotools. > > Finally there is a paper that uses GNU Guix as deployment tool for > scientific purposes. :) > > Kind regards, > Roel Janssen > > --000000000000ee29b60569de5beb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Wow very great, thanks for sharing.

On Wed, Apr 11, 2018 at 11:17 PM Roel Ja= nssen <roel@gnu.org> wrote:

Ricardo Wurmus <= rekado@elephly.net> writes:

> Hey all,
>
> I=E2=80=99m happy to announce that the group I=E2=80=99m working with = has released a
> preprint of a paper on reproducibility with the title:
>
>=C2=A0 =C2=A0 =C2=A0Reproducible genomics analysis pipelines with GNU G= uix
>=C2=A0 =C2=A0 =C2=A0https://www.biorxiv.o= rg/content/early/2018/04/11/298653
>
> We built a collection of bioinformatics pipelines and packaged them wi= th
> GNU Guix, and then looked at the degree to which the software achieves=
> bit-reproducibility (spoiler: ~98%), analysed sources of non-determini= sm
> (e.g. time stamps), discussed experimental reproducibility at runtime<= br> > (e.g. random number generators, kernel+glibc interface, etc) and
> commented on the idea of using =E2=80=9Ccontainers=E2=80=9D (or applic= ation 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.

This looks really great!=C2=A0 I also like how you leverage GNU Autotools.<= br>
Finally there is a paper that uses GNU Guix as deployment tool for
scientific purposes. :)

Kind regards,
Roel Janssen

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