Hackatathon: 27th June! Let redo ReScience C.

Hackatathon: 27th June! Let redo ReScience C.

[Simon TOURNIER]

Hi,

It's time to run the second Reproducible Research hackathon!  The first
one was from... 2020 [1], already!

The date: *Tuesday June, 27th*.  Start: 9h30 (CEST) End: 17h30

The plan is to discuss and pick some topics from 9h30 to 10h using one
BigBlueButton instance (link provided later).  Then, let work together!
For the ones who want, they can continue to use BBB for discussing, and
others can synchronise using IRC (channel provides later).  Around noon,
before lunch break, we all will report our progress on BBB.  Afternoon,
repeat.  Last, we end with a discussion summarizing the successes or the
roadblocks and draw the lines of the experiment report.

Well, anyone could come with their own topic they want to redo.

We suggest to pick articles from the ReScience C journal [2] -- they
provide a high level of transparency about the materials required for
redoing, IMHO.

Who’s in?

1: https://hpc.guix.info/blog/2020/07/reproducible-research-hackathon-experience-report/
2: http://rescience.github.io

Cheers,
simon

Re: [Spam:]Hackatathon: 27th June! Let redo ReScience C.

[Konrad Hinsen]

Simon TOURNIER <simon.tournier@inserm.fr> writes:

> It's time to run the second Reproducible Research hackathon!  The first
> one was from... 2020 [1], already!
>
> The date: *Tuesday June, 27th*.  Start: 9h30 (CEST) End: 17h30

Great initiative! Unfortunately, not a good date for me.

> We suggest to pick articles from the ReScience C journal [2] -- they
> provide a high level of transparency about the materials required for
> redoing, IMHO.

COMPUTO is now another good choice, for those looking for examples from
statistics:

   https://computo.sfds.asso.fr/

Cheers,
  Konrad
-- 
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: konrad DOT hinsen AT cnrs DOT fr
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: https://orcid.org/0000-0003-0330-9428
Mastodon: @khinsen@scholar.social
---------------------------------------------------------------------

Re: Hackatathon: 27th June! Let redo ReScience C.

[Etienne B. Roesch]

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Hi,

I am in. I have used both nix and guix, but I do consider myself a
beginner. I am also a plain old researcher in neuroscience, albeit with
formal training in software engineering. As such I think I would find it
more valuable to spend time figuring out the best way to describe "a best
practice" for people like me, onboarding newcomers, and write
documentation, rather than figuring out why a Makefile doesn't compile and
computer says no. I am also happy to join more experienced users, of
course, and follow the flow.

I have timeblocked the whole, and I am relatively free of my own movement,
but I can't promise I wouldn't be dragged into some boring meetings. I live
in the UK (+1h), and speak English and French. :D

Etienne

On Fri, May 12, 2023 at 2:53 PM Simon TOURNIER <simon.tournier@inserm.fr>
wrote:

> Hi,
>
> It's time to run the second Reproducible Research hackathon!  The first
> one was from... 2020 [1], already!
>
> The date: *Tuesday June, 27th*.  Start: 9h30 (CEST) End: 17h30
>
> The plan is to discuss and pick some topics from 9h30 to 10h using one
> BigBlueButton instance (link provided later).  Then, let work together!
> For the ones who want, they can continue to use BBB for discussing, and
> others can synchronise using IRC (channel provides later).  Around noon,
> before lunch break, we all will report our progress on BBB.  Afternoon,
> repeat.  Last, we end with a discussion summarizing the successes or the
> roadblocks and draw the lines of the experiment report.
>
> Well, anyone could come with their own topic they want to redo.
>
> We suggest to pick articles from the ReScience C journal [2] -- they
> provide a high level of transparency about the materials required for
> redoing, IMHO.
>
> Who’s in?
>
> 1:
> https://hpc.guix.info/blog/2020/07/reproducible-research-hackathon-experience-report/
> 2: http://rescience.github.io
>
> Cheers,
> simon
>
>

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Re: Hackatathon: 27th June! Let redo ReScience C.

[Ludovic Courtès]

Hi Etienne,

"Etienne B. Roesch" <etienne.roesch@gmail.com> skribis:

> I am in. I have used both nix and guix, but I do consider myself a
> beginner. I am also a plain old researcher in neuroscience, albeit with
> formal training in software engineering. As such I think I would find it
> more valuable to spend time figuring out the best way to describe "a best
> practice" for people like me, onboarding newcomers, and write
> documentation, rather than figuring out why a Makefile doesn't compile and
> computer says no. I am also happy to join more experienced users, of
> course, and follow the flow.

I guess the goal is to make progress on providing Guix files that would
let us re-run code submitted in ReScience C papers (for instance).  In
doing that, old-timers like me can of course provide guidance to onboard
newcomers: this exercise is meaningful if we make it approachable to a
wider scientific audience.

We seasoned users (Simon, Konrad, myself, and anyone who feels
qualified) should prepare upfront to get a more precise idea of the
tasks involved and how we can onboard people.

> I have timeblocked the whole, and I am relatively free of my own movement,
> but I can't promise I wouldn't be dragged into some boring meetings. I live
> in the UK (+1h), and speak English and French. :D

Awesome.  :-)

BTW, the event will be in English but we can definitely onboard those
who might prefer to speak French or German.

Ludo’.

Re: Hackatathon: 27th June! Let redo ReScience C.

[Etienne B. Roesch]

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Hi!

As an editor for resci, I of course welcome .scm files and scripts, as
examples that could be provided to future submissions. I would particularly
looove a bullet-proof .scm config for the editorial process, which... is
somewhat documented but has gaps: I have been working on this for one of
the submissions I am handling at the moment; at the moment, I have mostly
made sure to use guix for running the code submitted (python notebooks),
which I'll push to the author's repo, and have not *yet* moved to the
editorial process.

The above task I have started as editor overlaps completely with the theme
of the hackathon, I suppose ;) Happy to do just that and finally tick it
off my todo list. I am sure Nicolas will be pleased.
That may also create that opportunity to learn that I had in mind in my
previous email.

Also happy to serve as a guinea pig and help create onboarding procedures.
:)

Have an amazing week everyone!

Etienne

On Wed, May 24, 2023 at 2:31 PM Ludovic Courtès <ludovic.courtes@inria.fr>
wrote:

> Hi Etienne,
>
> "Etienne B. Roesch" <etienne.roesch@gmail.com> skribis:
>
> > I am in. I have used both nix and guix, but I do consider myself a
> > beginner. I am also a plain old researcher in neuroscience, albeit with
> > formal training in software engineering. As such I think I would find it
> > more valuable to spend time figuring out the best way to describe "a best
> > practice" for people like me, onboarding newcomers, and write
> > documentation, rather than figuring out why a Makefile doesn't compile
> and
> > computer says no. I am also happy to join more experienced users, of
> > course, and follow the flow.
>
> I guess the goal is to make progress on providing Guix files that would
> let us re-run code submitted in ReScience C papers (for instance).  In
> doing that, old-timers like me can of course provide guidance to onboard
> newcomers: this exercise is meaningful if we make it approachable to a
> wider scientific audience.
>
> We seasoned users (Simon, Konrad, myself, and anyone who feels
> qualified) should prepare upfront to get a more precise idea of the
> tasks involved and how we can onboard people.
>
> > I have timeblocked the whole, and I am relatively free of my own
> movement,
> > but I can't promise I wouldn't be dragged into some boring meetings. I
> live
> > in the UK (+1h), and speak English and French. :D
>
> Awesome.  :-)
>
> BTW, the event will be in English but we can definitely onboard those
> who might prefer to speak French or German.
>
> Ludo’.
>

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Re: Hackatathon: 27th June! Let redo ReScience C.

[Konrad Hinsen]

Hi Etienne,

> examples that could be provided to future submissions. I would particularly
> looove a bullet-proof .scm config for the editorial process, which... is
> somewhat documented but has gaps: I have been working on this for one of

Is that for ReScience X? ReScience C is moving to a new platform, and
thus to a different editorial process, so it's not worth investing much
effort into the old one.

Cheers,
  Konrad.
-- 
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: konrad DOT hinsen AT cnrs DOT fr
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: https://orcid.org/0000-0003-0330-9428
Mastodon: @khinsen@scholar.social
---------------------------------------------------------------------

Re: Hackatathon: 27th June! Let redo ReScience C.

[Etienne B. Roesch]

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ReSci C… I have heard of the “new platform” for a while. Is there an ETA?

Etienne


On Thu, 25 May 2023 at 13:20, Konrad Hinsen <konrad.hinsen@cnrs.fr> wrote:

> Hi Etienne,
>
> > examples that could be provided to future submissions. I would
> particularly
> > looove a bullet-proof .scm config for the editorial process, which... is
> > somewhat documented but has gaps: I have been working on this for one of
>
> Is that for ReScience X? ReScience C is moving to a new platform, and
> thus to a different editorial process, so it's not worth investing much
> effort into the old one.
>
> Cheers,
>   Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: konrad DOT hinsen AT cnrs DOT fr
> http://dirac.cnrs-orleans.fr/~hinsen/
> ORCID: https://orcid.org/0000-0003-0330-9428
> Mastodon: @khinsen@scholar.social
> ---------------------------------------------------------------------
>

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Re: Hackatathon: 27th June! Let redo ReScience C.

[Konrad Hinsen]

"Etienne B. Roesch" <etienne.roesch@gmail.com> writes:

> ReSci C… I have heard of the “new platform” for a while. Is there an ETA?

We are aiming for something like October. The new platform is ready and
being tested. Then we have to move over the content from the old one.

Cheers,
  Konrad.
-- 
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: konrad DOT hinsen AT cnrs DOT fr
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: https://orcid.org/0000-0003-0330-9428
Mastodon: @khinsen@scholar.social
---------------------------------------------------------------------

Re: Hackatathon: 27th June! Let redo ReScience C.

[Simon Tournier]

Hi Ludo,

On Wed, 24 May 2023 at 15:31, Ludovic Courtès <ludovic.courtes@inria.fr> wrote:

> We seasoned users (Simon, Konrad, myself, and anyone who feels
> qualified) should prepare upfront to get a more precise idea of the
> tasks involved and how we can onboard people.

Are you volunteering? ;-)

It could be nice if we can have a list of papers from ReScience C.
Then, it could helpful to spot out the tasks and how to start for
Guixifying the paper.

Well, I am pretty busy until Monday, 19th of June but I can dedicate
some time for preparing these tasks after this date.

WDYT about first collect some papers from ReScience C?


Cheers,
simon

Re: Hackatathon: 27th June! Let redo ReScience C.

[Etienne B. Roesch]

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Ludo, Simon,

I'll spare you the details, but I am organising a hackathon with students
from various campuses, in a few weeks, and I have decided to propose as a
project that we review the doc for guix, hoping that managing a (small)
horde of beginners will identify gaps and maybe produce useful
insights/content.
Any comment, recommendations, steer welcome.

Thanks for your talk Ludo this week, very cool!

Etienne (Reading, UK)

On Wed, May 31, 2023 at 11:33 AM Simon Tournier <zimon.toutoune@gmail.com>
wrote:

> Hi Ludo,
>
> On Wed, 24 May 2023 at 15:31, Ludovic Courtès <ludovic.courtes@inria.fr>
> wrote:
>
> > We seasoned users (Simon, Konrad, myself, and anyone who feels
> > qualified) should prepare upfront to get a more precise idea of the
> > tasks involved and how we can onboard people.
>
> Are you volunteering? ;-)
>
> It could be nice if we can have a list of papers from ReScience C.
> Then, it could helpful to spot out the tasks and how to start for
> Guixifying the paper.
>
> Well, I am pretty busy until Monday, 19th of June but I can dedicate
> some time for preparing these tasks after this date.
>
> WDYT about first collect some papers from ReScience C?
>
>
> Cheers,
> simon
>

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RE: Hackatathon: 27th June! Let redo ReScience C.

[Simon TOURNIER]

Hi

Tomorrow, do not miss the second Reproducible Research hackathon
using Guix:

    *Tuesday June, 27th*.  Start: 9h30 (CEST) End: 17h30

Please join at 9h30 the BigBlueButton instance,

    https://bbb.inria.fr/cou-pmi-g09-ute

More details in [1].  Especially a PAD for keeping track of the plan and progress,

We suggest to pick articles from the ReScience C journal [2] -- they
provide a high level of transparency about the materials required for
redoing, IMHO.  The aim of the day is to learn altogether how to produce research
reproducible papers [3] using Guix.  The key points are:

 + writing the manifest file
 + describing the channel file
 
with various bonus points as archiving on Software Heritage.

1: https://hpc.guix.info/blog/2023/05/reproducible-research-hackathon-let-redo/
2: http://rescience.github.io
3: https://hpc.guix.info/blog/2023/06/a-guide-to-reproducible-research-papers/

Cheers,
simon

Hackatathon let redo, experience report.

[Simon TOURNIER]

Hi,

Please give a look at the last Hackathon about redoing published paper using Guix:

https://hpc.guix.info/blog/2023/07/reproducible-research-hackathon-experience-report/

Have a nice "summer".

Cheers,
simon

Re: Hackatathon: 27th June! Let redo ReScience C.

[Peter Polidoro]

> From: "Etienne B. Roesch" <etienne.roesch@gmail.com>

> I am also a plain old researcher in neuroscience, albeit with
> formal training in software engineering.

Just out of curiousity, do you know of other neuroscientists using 
Guix or are you one of the few?

I also work with neuroscientists and have been telling them about 
Guix for a couple of years now, but I have not yet been able to 
convince any to even try it.

They often complain about problems they have, like struggling to 
package polyglot software, that Guix could solve for them, but 
seem reluctant, perhaps because of fear of lisp or not being able 
to run natively on their operating system or because it is so 
different than what they know.

> As such I think I would find it
> more valuable to spend time figuring out the best way to 
> describe "a best
> practice" for people like me, onboarding newcomers, and write
> documentation, rather than figuring out why a Makefile doesn't 
> compile and
> computer says no.

Such a "best practice" would be very valuable and I would be 
interested in helping if possible.