[Neuroimaging] Journal articles based on PRs

Wed Apr 13 08:46:23 EDT 2016

Hi, Chris.
The Zenodo solution is so cool.
I have not received the email about the this event. Please help me to check
it. My GitHub ID is Conxz. Thank you!

Best,
Xiangzhen

On Wed, Apr 13, 2016 at 4:47 AM, Chris Filo Gorgolewski <
krzysztof.gorgolewski at gmail.com> wrote:

> Hi Ariel,
> I have been recently thinking about the problem of giving academic credit
> to contributors. In Nipype we are facing exactly the same problem - people
> joining the project after the paper was published do not benefit from
> citations. The project is as strong as its community so we wanted to give
> people credit for their hard work. After some deliberations we have decided
> to go with a different approach then you are proposing. Beginning from the
> next release we will switch the main recommended citation from the
> Frontiers paper to a Zenodo <https://zenodo.org/> handle. In the past
> weeks we have been reaching out to Nipype contributors to get their
> permission and details to become coauthors of this Zenodo entry (please get
> in touch if you have contributed to Nipype and did not receive an email
> about this).
>
> Zenodo is a non profit organisation that provides citable DOIs for
> software (free of charge). It is indexed by Google scholar and is easy to
> set up and update. Thanks to this feature, with each release we will keep
> adding new contributors as coauthors. This solution has the following
> advantages:
> - Everyone contributing to nipype gets credit in the form of citations
> - There is one publication which makes citing easy (compare to Freesurfer
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, also
> consider that some journals limit the number of references)
> - There is no overhead of writing, submitting, and revising a manuscript
> on top of developing and revising code
>
> There is, however, one big drawback - there is only one first and one
> senior author on the Zenodo handle. I think this calls for a hybrid
> solution: an always up to date Zenodo entry combined with individual papers
> written by developers who feel they need such publication and are willing
> to put the extra effort of writing the manuscript. I would stay away from
> making a "deal" or explicitly recommending one particular commercial
> publisher. There are many outlets which publish software or software
> extensions (for example F1000Research has "Software Tool" category that
> often publishes small contributions: see
> http://f1000research.com/articles/2-192/v2 for example). I would leave it
> open to the developers to choose the venue where they want to publish using
> their best judgement. Why is it important? Most publishers are commercial
> entities and strongly recommending one over another benefits them
> financially. I think that as an open community, we should stay away from
> such decisions to avoid being accused of some shady internal deals. Let
> developers (and potential authors of such papers) decide by themselves.
>
> I hope this helps!
>
> Best,
> Chris
>
>
>
> On Tue, Apr 12, 2016 at 8:26 AM, Ariel Rokem <arokem at gmail.com> wrote:
>
>> Hi everyone,
>>
>> In a conversation I had with Rafael recently, he mentioned to me the
>> Journal of Open Research Software (
>> http://openresearchsoftware.metajnl.com/) that publishes articles about
>> open-source research software, and proposed this as a good place to publish
>> software contributions in our community. This is a good thing because it
>> provides a venue for articles specifically focused on software
>> implementations, even in cases where the methods have previously been
>> published as scientific articles. This provides a standard reference for
>> the software, and an opportunity for researchers who spend time writing
>> open-source software to get credit for the work they are doing.
>>
>> I propose to submit articles to JORS, based on newer additions to
>> libraries (particularly Dipy, but maybe others as well?), a PR, or series
>> of PRs that contribute substantial new features, or a substantial upgrade
>> to previous features. This addresses two major challenges:
>>
>> The first is the challenge we face in incentivizing new contributors to
>> join us. This is because if a standard reference article has already been
>> published for the software, their newer contributions might not get them
>> credit when this standard reference is cited. For example, Dipy
>> contributors who joined the project after 2014 get no credit when that
>> paper is cited.
>>
>> Two recent examples from Dipy are the work that Stephan Meesters has done
>> on contextual enhancement and fiber-to-bundle coherence measures (still in
>> progress in #828), and the work Rutger Fick is doing implementing Laplacian
>> regularization for MAP (#740). These are both implementations of previously
>> published scientific work (in these cases, work that these contributors
>> have been involved in). As you can all appreciate, the effort of
>> implementing these methods in Dipy is substantial, and we want to
>> incentivize these efforts and reward them. A journal article that other
>> researchers can cite is common currency for that.
>>
>> Another challenge we face is incentivizing code review. This is a serious
>> bottle-neck for progress. I propose to add code reviewers as authors to
>> these papers. This will incentivize the substantial effort that goes into
>> reviewing code. JORS allows author contributions to be specified and we
>> would clearly designate these kinds of contributions, so as to not diminish
>> from the effort made by the primary author of the code. But I would like to
>> include the people doing code review (if only because I have spent a lot my
>> own time in code review...). I hope that this will allow people to justify
>> spending time doing this crucial part of the work, and energize our code
>> review process a bit.
>>
>> I'd be happy to hear what people think about this idea.
>>
>> Cheers,
>>
>> Ariel
>>
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>>
>
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>

-- 
-----------------------------------------------------------------------------------------
Kong Xiangzhen
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University,
Beijing, China, 100875.
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