<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 22 Dec 2015, at 15:10, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" class="">p.j.a.cock@googlemail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">You can just say Biopython version 1.66 (for example) and</div>
<div class="">cite the paper Cock et al 2009 and its DOI:</div>
<div class=""><br class="">
</div>
<div class=""><a href="http://dx.doi.org/10.1093/bioinformatics/btp163" class="">http://dx.doi.org/10.1093/bioinformatics/btp163</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">(Or the more specific papers for Bio.Phylo, or PDB, etc)</div>
<div class=""><br class="">
</div>
<div class="">Using <a href="http://zenodo.org" class="">Zenodo.org</a> we'd have to register a DOI for each</div>
<div class="">release, which does not seem that useful.</div>
</div>
</div>
</blockquote>
<br class="">
</div>
<div>2p:</div>
<div><br class="">
</div>
<div>- I’ve not found the Zenodo DOI assignment very straightforward. Maybe I’m doing it wrong?</div>
<div><br class="">
</div>
<div>- 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.</div>
<div><br class="">
</div>
<div>- 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.</div>
<div class=""><br class="">
</div>
<div class="">L.</div>
<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; orphans: 2; text-indent: 0px; widows: 2; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; orphans: 2; text-indent: 0px; widows: 2; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<span class="Apple-style-span" style="border-collapse: separate; orphans: 2; text-indent: 0px; widows: 2; border-spacing: 0px;">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
--<br class="">
Dr Leighton Pritchard<br class="">
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme<br class="">
DG31, James Hutton Institute (Dundee)<br class="">
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA<br class="">
e: <a href="mailto:leighton.pritchard@hutton.ac.uk" class="">leighton.pritchard@hutton.ac.uk</a> w:
<a href="http://www.hutton.ac.uk/staff/leighton-pritchard" class="">http://www.hutton.ac.uk/staff/leighton-pritchard</a><br class="">
gpg/pgp: 0xFEFC205C tel: +44(0)844 928 5428 x8827 or +44(0)1382 568827<br class="">
<br class="">
</div>
</span></div>
</span></div>
</span></div>
</span></div>
</div>
</div>
<br class="">
<br /><br />
<p>This email is from the James Hutton Institute, however the views expressed by the sender are not necessarily the views of the James Hutton Institute and its subsidiaries. This email and any attachments are confidential and
are intended solely for the use of the recipient(s) to whom they are addressed.</p>
<p>If you are not the intended recipient, you should not read, copy, disclose or rely on any information contained in this email, and we would ask you to contact the sender immediately and delete the email from your system. Although the James Hutton Institute has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and any attachments.</p>
The James Hutton Institute is a Scottish charitable company limited by guarantee.
<br />
Registered in Scotland No. SC374831
<br />
Registered Office: The James Hutton Institute, Invergowrie Dundee DD2 5DA.
<br />
Charity No. SC041796<p></p></body>
</html>