[Biopython] Support for Xdna, SnapGene and GCK formats

[Peter Cock]

On Thu, Aug 1, 2019 at 1:19 PM Damien Goutte-Gattat
<dgouttegattat at incenp.org> wrote:
>
> On Thu, Aug 01, 2019 at 10:01:22AM +0100, Peter Cock wrote:
> >> All the GCK files I have come from the "Drosophila Gateway Vector
> >> Collection" [1]; those files are not explicitly released under any free
> >> license (in fact there are no license terms at all), so I don't think we
> >> could bundle even one of them with the Biopython's source code, even if
> >> it is just to serve as a test file.
> >
> >The website [1] had a fairly liberal copyright statement at the bottom,
> >suggesting a sample file could be used with attribution (e.g. in the git
> >check in comment and where the test or example code used it)?
>
> The notice states "You are free to use the information contained on this
> page for non-profit purpose [...]". I am not sure this would be
> compatible with either the 3-clause BSD license or the Biopython License
> Agreement (neither of them excluding any kind of for-profit use).
>
> I am also slightly concerned by the following statement: "Portions of
> the material contained in the Drosophila Gateway Vector collection are
> subject to international patents [...]". I guess this refers to the
> vectors themselves and not merely to files containing their sequences,
> but I wonder if that could be subject to interpretation.
>
> Obviously I am no lawyer, so maybe I am just worrying too much. :)

Sadly I think you are right. I was thinking just about the immediate (and
to me clearly non-profit) step of validating Biopython functionality - there
is definitely a problem in redistribution to anyone using Biopython in a
for-profit setting, unless one sample file is judged fair use (and that is
a legal grey area).

> >Damien, you evidently know a lot more about email headers etc than me.
> >Are you also familiar with mailman, and how it might be better configured
> >on this specific point?
>
> Yes.
>
> Basically there's two options.
>
> ...
>
> Unfortunately, `from_is_list` has been introduced in Mailman 2.1.16 and
> `dmarc_moderation_action` in Mailman 2.1.18, but mailman.open-bio.org is
> running Mailman 2.1.15, so an upgrade would be needed before we can
> adopt that approach.

That seems worth looking at - I will forward this to the OBF mailman team.

Thank you,

Peter