[Biopython] DOI for BioPython

[João Rodrigues]

Since this is a python library I'd go with the mantra of there is only one
way to do things, thus, one citation to keep things simple :)

More seriously, I'd be much happier with a convention where you'd cite the
major biopython paper, the specific module papers if there are any, and
include the hash of the revision you used. This should be included in the
wiki page where we define 'citation guidelines'. It is simple, helps
everyone (although occasional contributors might feel robbed), and is fully
reproducible.

Including DOIs for every release is only partially reproducible, since it
relies on a third party service to map between the DOI and the release,
which adds an unnecessary, in my opinion, extra layer of complexity. Also,
it doesn't help those that do not know biopython to learn about it since
they will have to Google it's publication.

It's a good discussion and a good point to raise, but there are still major
rules in science we have to play by in order to keep people interested and
generally move forward.

As Tiago, I'm also against implementing pre-release DOIs. It'll create too
much entropy that has no real benefits other than ideology.

A qua, 23/12/2015, 01:03, Tiago Antao <tra at popgen.net> escreveu:

> On Tue, 22 Dec 2015 16:38:37 +0000
> João Rodrigues <j.p.g.l.m.rodrigues at gmail.com> wrote:
>
> > Also, Peter's paper is not *his* paper about the software. It's the
> > entire team, or almost, on that paper and it describes the different
> > modules and their purpose and functionality.
>
> One can discuss if it is good or bad, but basic pragmatism dictates
> that the proper citing object is the 2009 paper, period. This for the
> reasons stated here by others already. Myself I would not be able to
> have contributed over the years if there was not a high-cited paper to
> put forward as a justification.
>
> Having another (non-paper) citing object will damage the project and
> has my full frontal objection. Things in science work as they work, and
> while I might object to paper citation metrics, that is the
> world we live in. I believe Biopython already lives too much on the
> volunteering of a few individuals, removing the only thing that
> provides "income" would be fatal. We actually need more (not less)
> forms of "income".
>
> That being said, and at the risk of opening a can of worms, I find it
> very unfair that many people that have recently contributed hard to the
> project are not on the author list of the 2009 paper (you, for
> example. Bow is another). That would be fixed with a new paper. Deciding
> on the author list would be the can of worms. We all can agree that it
> would be another Cock et al paper, but getting the list of people that
> are the "et al" would be complex.
>
> Tiago
>
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