[CIG-MC] CIG-MC Digest, Vol 122, Issue 7

Tue Mar 6 13:49:47 PST 2018

I second the idea of a community statement as to what we consider to be
data and what we consider the standard of reproducibility to be. This has
come up a lot recently, and there has not been a satisfactory response from
funding agencies and  journals. As stated, if we do indeed need to archive
and make available large amounts of data (TB scale) as suggested for JGR
Planets, I worry what the implications are for early career researchers?
Those who may move institutions frequently, and who may have limited to
non-existent funding? The idea of maintaining large amounts of data on
personal servers, as done in tomography, is not a very robust option. It
creates a potentially significant barrier to publishing, perhaps even
barring publication in extreme cases...  at least without a clear and well
articulated definition of 'data' and a standard of reproducibility within
the community and at large.

well, that's as far as my 2-cents go.

On Tue, Mar 6, 2018 at 3:15 PM, <cig-mc-request at geodynamics.org> wrote:

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>    1. Re: AGU's new data policy (Cooper, Catherine M)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 6 Mar 2018 17:28:04 +0000
> From: "Cooper, Catherine M" <cmcooper at wsu.edu>
> To: "cig-mc at geodynamics.org" <cig-mc at geodynamics.org>
> Subject: Re: [CIG-MC] AGU's new data policy
> Message-ID: <277B34AD-D981-4A95-B8D6-586EF8DB3706 at wsu.edu>
> Content-Type: text/plain; charset="utf-8"
>
>
> I wonder if it wouldn’t be helpful to have a community statement as to
> what we consider “data” and what we agree needs to be shared for
> reproducibility (which we all agree is important)?  But it seems like we
> might need to do some outreach on this if there is some misunderstanding
> about model output as data amongst AGU and NASA (this has come up in
> proposal reviews).
>
>
> On Mar 6, 2018, at 9:01 AM, Juliane Dannberg <judannberg at gmail.com<mailto:
> judannberg at gmail.com>> wrote:
>
> My experience with this is similar to what Thorsten describes. I also
> regularly have TB-sized model output, and usually include the doi of the
> version of the code I used in the paper, upload all input files/scripts
> etc. I used as supplementary material, and include a sentence that "all
> input files necessary to reproduce the model results are included in the
> supplementary material". So far, that seemed to be an acceptable solution,
> also for AGU journals.
>
> But I agree that there doesn't seem to be a good way to archive TB-sized
> model output over long periods of time...
>
> Best,
> Juliane
>
> ----------------------------------------------------------------------
> Juliane Dannberg
> Postdoctoral Fellow, Colorado State University
> http://www.math.colostate.edu/~dannberg/<https://urldefense.
> proofpoint.com/v2/url?u=http-3A__www.math.colostate.edu_-
> 257Edannberg_&d=DwMDaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-
> Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=HfT2q7BUNv7lwQ4rNBn6WCxad64-
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>
>
> Am 3/6/2018 um 9:39 AM schrieb Thorsten Becker:
> The way I have interpreted AGU's guidelines for geodynamic studies as AGU
> editor is to not ask for archiving of model output, but to ask for general
> access to all material that would be needed to recreate that output, or
> some simpler version of it that is proof of concept. I.e. input data, input
> files, and a DOI to version of code, for example, if a community code is
> used.
>
> The general idea is, of course, to make things reproducible, and AGU and
> Wiley are among those who realize that this can cause problems, and are
> working on solutions with the community.
>
> One particular issue is that I have not asked for verification that
> results are actually reproducible, and taken authors assurances that codes
> will be shared at face value (besides when the publications were of
> technical nature, and we ask reviewers to actually try to download and run
> the software, for example (which usually never works)). I think that part
> might change, in that publishers may ask for a code access link and somehow
> archive this.
>
> I can also see some solutions akin to asking for a Docker set up, archived
> somewhere, that will allow anyone to rerun the models. There are
> interesting challenges involved, but in the end, I think moving to more
> openness and reproducibility is a good thing, and the success of CIG shows
> how some issues that were raised before we moved into this model resolved
> themselves. Things are perfect, but we're making progress.
>
> My personal experience with publishing numerical stuff in highly visible
> journals is that, within a week, there are people actually asking to get
> all the code and all the input files to rerun our models, and we've always
> shared all of our stuff, of course. I realize that this is a significant
> workload (particularly for my grad students who actually put this stuff
> together...) and somehow AGU and publishers need to do more to support
> people with large data volumes, seismological inversions being another
> example.
>
>
> Thorsten Becker - UTIG & DGS, JSG, UT Austin<https://urldefense.
> proofpoint.com/v2/url?u=http-3A__www-2Dudc.ig.utexas.edu_
> external_becker_&d=DwMDaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-
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>
> On Tue, Mar 6, 2018 at 7:17 AM, Scott King <sdk at vt.edu<mailto:sdk at vt.edu>>
> wrote:
>
> AGU journals have a new data policy requiring that all the data from the
> work must be in a publicly accessible repository.  In general I think this
> is a good thing.   They provide several possible solutions.   From the
> editor letter…
>
> "AGU requires that data needed to understand and build upon the published
> research be available in public repositories following best practices<
> https://urldefense.proofpoint.com/v2/url?u=http-3A__publications.agu.org_
> author-2Dresource-2Dcenter_publication-2Dpolicies_data-
> 2Dpolicy_data-2Dpolicy-2Dfaq_&d=DwMDaQ&c=C3yme8gMkxg_
> ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=3iAcC0lqlf3gOx4_NidEiA&m=
> HfT2q7BUNv7lwQ4rNBn6WCxad64-R40vEvd3Ehweq84&s=
> ySxEBeS3cBYIOD8hSSkU7WymnOp8M-wucwrFXLBFHss&e=>. This includes an
> explicit statement in the Acknowledgments section on where users can access
> or find the data for this paper. Citations to archived data should be
> included in your reference list and all references, including those cited
> in the supplement, should be included in the main reference list. All
> listed references must be available to the general reader by the time of
> acceptance.”
>
> They list several possible repositories, none of which seem appropriate
> for 2.9 TB of CicomS results. Set aside the philosophical issue that model
> results are not “data” (they don’t accept that).   I have the output used
> in the published figures down to a reasonable size but. I’m curious what
> others are doing.  Has anyone else run into this yet?  (If not you will.)
> I’m curious if there is a community consensus regarding a repository where
> all geodynamics results would/could end up, as opposed to ending up with
> them scattered across 3-4 (or more) potential repositories.  Maybe that’s
> not something to worry about, but since this is new and to me at least I’ve
> had no time to think it through, I’m curious what others are doing.
>
> Thoughts?
>
> Cheers,
>
> Scott
>
>
>
>
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