[Biopython] DOI for BioPython

[Fields, Christopher J]

I agree re: tracking citations, etc, particularly for funding.  However, for attributing credit for developers it’s actually tricky, particularly with large projects that have an evolving group of core developers.

My personal example: I wasn’t on the original bioperl citation (joined after), yet I am now essentially managing bioperl development when I can.  My commits and releases are the things I could to point to, so it’s nice to have something of a compromise (e.g. an updated DOI via Zenodo).  Not to mention it shows that development has continued past the point of publication (sometimes with significant changes to the API), which as we all know isn’t true for a significant chunk of published software.

So in my opinion it’s never a bad thing to have an updated (officially sanctioned!) citation reflecting contributions from new developers or significant changes to the codebase.  The original citation will never go away.

chris

On Dec 22, 2015, at 10:38 AM, João Rodrigues <j.p.g.l.m.rodrigues at gmail.com<mailto:j.p.g.l.m.rodrigues at gmail.com>> wrote:


Having all citations concentrated in one paper with all the major contributors helps tracking citation data, which helps those major contributors and OBF in future funding ventures. Further, a new release does not change the entire code base, so if you were to use Bio.PDB in say release X and Y, where there weren't any changes to this module, you'd cite two different DOIs, which wouldn't make any sense from any point of view.

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.

What's better: citing the paper that describes the algorithm(s) or the pull request that fixed a typo in the documentation?

Cheers,

João

A ter, 22/12/2015, 16:05,  <c.buhtz at posteo.jp<mailto:c.buhtz at posteo.jp>> escreveu:
On 2015-12-22 15:10 Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:
> You can just say Biopython version 1.66 (for example) and
> cite the paper Cock et al 2009 and its DOI:

I need to cite the software not your paper about the software.
It is unscientific to do it like that. And somebody could say I just
want to say "thank you" in the way to increase your ImpfactFactor.

If there is no DOI I will just name the main website an the release
identifier (version number).

> Using Zenodo.org<http://zenodo.org> we'd have to register a DOI for each
> release, which does not seem that useful.

Exactly that would be useful and what DOIs are for - especially for a
scientific software like BioPython.
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