[Biopython] DOI for BioPython

[Leighton Pritchard]

On 22 Dec 2015, at 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:

http://dx.doi.org/10.1093/bioinformatics/btp163

(Or the more specific papers for Bio.Phylo, or PDB, etc)

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

2p:

- I’ve not found the Zenodo DOI assignment very straightforward. Maybe I’m doing it wrong?

- I take the point that citing the paper, rather than the specific software version, is not precise enough for replicability. However, for many of us (and I’m not on the paper, so don’t benefit from citation) we need to demonstrate some kind of value of contributing to Biopython during work time to our line managers/bosses, and citations for a paper still count much more than citations for specific releases. Citing the 2009 paper can still - in a real sense - ‘buy’ extra time from contributors, and is worth doing.

- The issue of indicating a specific release for reproducibility is satisfied with a DOI attached to that release, but also by the hash associated with that release, so you could refer to release v1.66 (which by itself is good enough) as c06a306 with no loss of precision relative to a DOI. This is a general principle that also applies to specific commit points in a repo.

L.

--
Dr Leighton Pritchard
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme
DG31, James Hutton Institute (Dundee)
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
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