Re: [dealii-developers] Code DOI's via Zenodo

[Timo Heister]

JP,

I would like to get back to the question if it is a good idea to
create DOI for all steps:
1. Several tutorials are a community effort and not contributed by a
single individual. This probably holds for 1 - 19. It is difficult to
decide on authorship here. This might be enough of a reason to not
assign DOIs for them.
2. How do you decide between a community and individual effort? Can
the latter become the former at some point?
3. When do you want to create a new DOI? It is weird that you can
change authors for a specfic DOI and I assume google scholar can't
deal with that...
4. What is the threshold to become an author on a tutorial? I hate
applying metrics to this. Can I just go and make some documentation
improvements to become an author on every single tutorial? Or phrased
in a different way: Might assigning authors discourage improving
existing programs?

These are a lot of questions we need to think about.


On Wed, Mar 22, 2017 at 9:46 AM, Timo Heister  wrote:
>> Quick question - what was the rationale behind categorising it as a "data 
>> set" as opposed to "software"?
>
> This seems to be a bug. I selected "software" of course. Note that the
> word "data set" doesn't appear in the bibtex text.
>
> On Wed, Mar 22, 2017 at 9:38 AM, Timo Heister  wrote:
>> Please keep in mind that a zenodo DOI creates a reference to a
>> specific version of the source code.
>>
>>> Timo, is it possible to edit any of the entries after a request for a DOI 
>>> has been submitted?
>>
>> You can edit most of the meta data including authors. I just updated
>> the title for example.
>>
>>> A way around it would be to retire each step number that becomes obsolete 
>>> and is removed from the documentation.
>>
>> I would like to avoid producing a large number of unused tutorial numbers.
>>
>>
>>
>>
>> On Wed, Mar 22, 2017 at 4:18 AM, Jean-Paul Pelteret
>>  wrote:
>>> An alternative would be to just create a new DOI for a program that has
>>> either undergone significant work by someone not already an author, or that
>>> has been reworked to the point where it is a different program.
>>>
>>> Newer releases would then simply reference the new DOI.
>>>
>>>
>>> Yes, this would seem to be a sensible solution to the problem.
>>>
>>> I’ve started to collate the necessary information for the tutorials and code
>>> gallery examples. What I’ve done so far can be found here:
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_spreadsheets_d_1yaKP8mnVIrVZ6aoGGhi396VGEiY3OR0XfWvgDEeKLio_edit-3Fusp-3Dsharing=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=Z4XPlf-AfJ0AaWG75t_f3G-tMWEAOI10qqR_2aT-KSc=6MfQzHpCjq9L8K9YojGf_2AizEbwmk5QWUXL5yNH3pc=
>>>  
>>>
>>> Should I create a generic deal.II account on Zenodo for us all to share, and
>>> thereby manage the entries related to the tutorials etc? If desirable, we
>>> can also create a community page to collect all of the other deal.II related
>>> uploads to Zenodo.
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "deal.II developers" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to dealii-developers+unsubscr...@googlegroups.com.
>>> For more options, visit 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=Z4XPlf-AfJ0AaWG75t_f3G-tMWEAOI10qqR_2aT-KSc=DivbN68JQR6x5wnjE2H2Y5G7Wc3QydXxEmn0vH4HgRM=
>>>  .
>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [dealii-developers] Code DOI's via Zenodo

[Timo Heister]

> Quick question - what was the rationale behind categorising it as a "data 
> set" as opposed to "software"?

This seems to be a bug. I selected "software" of course. Note that the
word "data set" doesn't appear in the bibtex text.

On Wed, Mar 22, 2017 at 9:38 AM, Timo Heister  wrote:
> Please keep in mind that a zenodo DOI creates a reference to a
> specific version of the source code.
>
>> Timo, is it possible to edit any of the entries after a request for a DOI 
>> has been submitted?
>
> You can edit most of the meta data including authors. I just updated
> the title for example.
>
>> A way around it would be to retire each step number that becomes obsolete 
>> and is removed from the documentation.
>
> I would like to avoid producing a large number of unused tutorial numbers.
>
>
>
>
> On Wed, Mar 22, 2017 at 4:18 AM, Jean-Paul Pelteret
>  wrote:
>> An alternative would be to just create a new DOI for a program that has
>> either undergone significant work by someone not already an author, or that
>> has been reworked to the point where it is a different program.
>>
>> Newer releases would then simply reference the new DOI.
>>
>>
>> Yes, this would seem to be a sensible solution to the problem.
>>
>> I’ve started to collate the necessary information for the tutorials and code
>> gallery examples. What I’ve done so far can be found here:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_spreadsheets_d_1yaKP8mnVIrVZ6aoGGhi396VGEiY3OR0XfWvgDEeKLio_edit-3Fusp-3Dsharing=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=xlkbb1e_zxM1NT74AYTBJog40AxVtOft-lhf-ctjMLY=QBiXKDw42wIbaMu8czOhIRC9Jm-aeJhjsZd_WgLmQbg=
>>  
>>
>> Should I create a generic deal.II account on Zenodo for us all to share, and
>> thereby manage the entries related to the tutorials etc? If desirable, we
>> can also create a community page to collect all of the other deal.II related
>> uploads to Zenodo.
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "deal.II developers" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to dealii-developers+unsubscr...@googlegroups.com.
>> For more options, visit 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=xlkbb1e_zxM1NT74AYTBJog40AxVtOft-lhf-ctjMLY=otVUGY9FNvMp6tWhHMf3YfUmE_hlQ_MEfRZg5aM15cY=
>>  .
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [dealii-developers] Code DOI's via Zenodo

[Timo Heister]

Please keep in mind that a zenodo DOI creates a reference to a
specific version of the source code.

> Timo, is it possible to edit any of the entries after a request for a DOI has 
> been submitted?

You can edit most of the meta data including authors. I just updated
the title for example.

> A way around it would be to retire each step number that becomes obsolete and 
> is removed from the documentation.

I would like to avoid producing a large number of unused tutorial numbers.




On Wed, Mar 22, 2017 at 4:18 AM, Jean-Paul Pelteret
 wrote:
> An alternative would be to just create a new DOI for a program that has
> either undergone significant work by someone not already an author, or that
> has been reworked to the point where it is a different program.
>
> Newer releases would then simply reference the new DOI.
>
>
> Yes, this would seem to be a sensible solution to the problem.
>
> I’ve started to collate the necessary information for the tutorials and code
> gallery examples. What I’ve done so far can be found here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_spreadsheets_d_1yaKP8mnVIrVZ6aoGGhi396VGEiY3OR0XfWvgDEeKLio_edit-3Fusp-3Dsharing=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=NnEXND6kzagXO4G4yd7vfa9PXN9r53LPFyaNqKp59Wc=h02X5YqDxtVMCHz9L3C1ZVE8LYMcgvZtRghLyerUzu8=
>  
>
> Should I create a generic deal.II account on Zenodo for us all to share, and
> thereby manage the entries related to the tutorials etc? If desirable, we
> can also create a community page to collect all of the other deal.II related
> uploads to Zenodo.
>
> --
> You received this message because you are subscribed to the Google Groups
> "deal.II developers" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to dealii-developers+unsubscr...@googlegroups.com.
> For more options, visit 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=NnEXND6kzagXO4G4yd7vfa9PXN9r53LPFyaNqKp59Wc=11YqQOvmcDPbjEVeG7VkRnJ4wjw3d70yQ7WYBPQ_wFw=
>  .



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [dealii-developers] Code DOI's via Zenodo

[Timo Heister]

> To put this in context, Andrew and I were having a discussion related to the
> use of the step-44 tutorial as a basis for further research.

You could also consider submitting to 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.archnumsoft.org_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=VLl3-Z5XpHPGLgAFp2LNQI8jgD7xjFq9hP1DOfg5SdE=q5Rhh4lreSUkROMqR1828ermzE20AzYNksRY_nvW9t8=
 
Maybe Guido can offer some guidance if this is acceptable even though
it already is a tutorial program. You could always extend it for a
publication there.

> True, this definitely seems to be the case. You have to upload at least one
> file when making a new entry in Zenodo.

You can manually upload the .cc and reference the deal.II repo. Here,
I did an experiment:
https://urldefense.proofpoint.com/v2/url?u=http-3A__doi.org_10.5281_zenodo.400995=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=VLl3-Z5XpHPGLgAFp2LNQI8jgD7xjFq9hP1DOfg5SdE=OFCA8kbF8irN9mIMWW_bI38XJuia6TFs1ZcM7UNvvmY=
 

-- 
Timo Heister
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Re: [dealii-developers] Code DOI's via Zenodo

[Jean-Paul Pelteret]

Thanks for the replies thus far. Interesting points that you both have 
raised. I was only introduced to Zenodo this last week and have just 
created an account, so I wasn't fully aware of how it could / would have to 
be used.

To put this in context, Andrew and I were having a discussion related to 
the use of the step-44 tutorial as a basis for further research. We've 
never had any metrics on how widespread its application has been. For him, 
without this data, its been difficult to justify as third-party 
contributors (as we were when we wrote the tutorial) in the writing funding 
proposals the merits of contributing to open-source software. On a more 
selfish note, as young researchers it may also have been beneficial to us 
to boost those annoying but supposedly important citation metrics that we 
rely on to advance our careers. It goes without saying that, like everyone 
who contributes, we remain very much in agreement of the altruistic nature 
of open-source software and the community around it. But on this particular 
point it would be great if we could somehow inject an extra dose of 
pragmatism without upsetting the spirit in which the contributions are made 
in the first place.
 

> > But we could create DOIs for the tutorials that really only list the 
> > (original) authors of that program. Presumably, people who cite them 
> would 
> > also cite deal.II itself. 
>

Thats pretty much what I envisioned could/would happen. Same goes for the 
code-gallery contributions, which are more easy to claim ownership over as 
they're distanced from the main repository. Also, I couldn't see the case 
for someone citing only one or the other. 
 

> I don't know how to do this in a simple way. Zenodo takes a github 
> repo and a specific release tag and creates a DOI for it. Unless you 
> manually upload the tutorial source code separately, there is no way 
> to give it a different title or list of authors. 
>

True, this definitely seems to be the case. You have to upload at least one 
file when making a new entry in Zenodo.

Thanks for being willing to have this discussion!

Best,
J-P
 

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Re: [dealii-developers] Code DOI's via Zenodo

[Timo Heister]

> But we could create DOIs for the tutorials that really only list the
> (original) authors of that program. Presumably, people who cite them would
> also cite deal.II itself.

I don't know how to do this in a simple way. Zenodo takes a github
repo and a specific release tag and creates a DOI for it. Unless you
manually upload the tutorial source code separately, there is no way
to give it a different title or list of authors.

> I don't actually know how it came up with the author list -- it may simply
> be the complete list of committers to the github repo

Yes, but I can edit this list and remove authors. Any suggestions on
what I should do?

>. It's also not a [Data
> set].

I am not sure how to remove that. It doesn't appear in the bibtex code, though.

-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [dealii-developers] Code DOI's via Zenodo

[Timo Heister]

Hey,

I think it is valuable having the option to cite a specific tutorial:
be it as a starting point (if somebody wants to do this) or, to claim
ownership (like I ask my students who contributed a tutorial do). I
already generate zenodo DOIs for deal.II, for example
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.5281_zenodo.61430=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=bIZ1PN9GFeiDFVPWRQ7rHwsFOCnh0BavuhRERQ4RDWGqJOxfLu0FfCOxyifWO5wc=QBOg_BDNEv2oxreDNyMg5qlOXr0VonBbmR-nJnozly4=m-02g5Xa9gAtLPafL-gUa_jIap1nABF7b_EYozeVaHA=
 
The problem is that the tutorials are a part of the deal.II repo, so
you can not cite the tutorial directly (and the author list is
incorrect).

I can not think of a good solution for this, so I just create a
citation linking to the .html page of the tutorial.



On Sat, Mar 18, 2017 at 2:07 AM, Jean-Paul Pelteret
 wrote:
> Dear all,
>
> I've recently been made aware of Zenodo, a facility to give code and
> scientific datasets a DOI number. What are your views on giving the
> tutorials (and, if the individual authors wanted it, the code-gallery
> examples) a DOI? It could be of benefit (and an "extra reward") to the
> authors of those particular pieces of work in terms of increasing their
> citation count. On the other hand, it may go against the spirit of sharing
> that is a core part of the deal.II project, and many of the tutorials are
> strongly interlinked so promoting the citation of one tutorial over the host
> of others that it builds on is not particularly fair.
>
> Best,
> J-P
>
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>  .



-- 
Timo Heister
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