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My sprint report (Was: Annual Debian Med sprint: 04.-07. February 2016 in Copenhagen)


I'd like to give a short report about our Debian Med sprint.  Thanks to
the invitation of ELIXIR-DK we stayed in a nice hotel close to
Copenhagen.  Despite the close location to the Danish capital it felt
like in the middle of nowhere in the woods between two lakes - a great
place for not beeing distracted from hacking.  This was the first sprint
with rock solid and fast internet connection from the first to the last
minute at any place of the venue which was an extra plus. :-)  Food and
accomodation was very good - thanks a lot for the organisation to DTU.

Regarding participants some long standing sprinters were missing but
we've got some additional help by members of other Blends (namely Petter
Reinholdtsen/Debian Edu, Ross Gammon/Debian GIS, Ruben Undheim/Debian
Science) as well as some newcomers as usual.  There were also some
Elixir members with no direct connection to Debian who intended to use
the rich resource of metadata assembled in UDD via the Debian Med team
packaging work to feed this data into EDAM ontology and to help
enhancing Debian Med DebTags.

I need to admit that I blatantly "failed" to work down the personal
agenda I had created for myself due to more urgent issues coming up at
the sprint.  However, I consider this a positive result since my
original work items were basically things that I can do on my own and
the sprint was dominated by coordinated work with Elixir members which
finally was made way better to do in common.  So the only item of my
original schedule was sponsoring packages from other sprinters.

My main work in the first half of the sprint was creating an UDD example
query[1] that is gathering metadata from UDD relevant for EDAM.  This
script should not be considered a ready tool but rather an example how
to fetch the data from UDD and to provide ideas how UDD could be used in

In the second part I created a UDD gatherer of the debian/upstream/edam
files created by other sprint participants to make a cross link between
Debian and EDAM.  The UDD gatherer fetches the data from these files and
is exposing the data again in the query script[1] together with all
other metadata about bioinformatics tools inside Debian.

I also started an overhaul of Biology DebTags inspired by a list of
possible tags generated by Jon Ison.

Other activities were an introduction about metadata provided by the
Debian packaging which was kindly supported by Petter Reinholdtsen and
Steffen Möller.

Thanks to all people who supported and took part in our sprint which was
a great experience again as every year.  The efficient work in these
sprints might trigger an even higher meeting frequence as yearly -
perhaps two sprints per year might be a good idea.

Kind regards


[1] https://github.com/bio-tools/biotoolsConnect/tree/master/DebianMed

On Wed, Nov 25, 2015 at 07:00:40PM +0100, Andreas Tille wrote:
> Hi,
> I would like to inform the sprints list (and DPL) about our annual
> Debian Med sprint.  It will be organised by ELIXIR-DK (thanks a lot).
> More information can be obtained from the Wiki page
>     https://wiki.debian.org/Sprints/2016/DebianMed2016
> Everybody, also those who do not (yet) feel like a Debian Med member is
> welcome to work on Debian Med in specific or Blends in general.
> Participants should try to add some personal work plan to the wiki page.
> See you in Copenhagen
>        Andreas.
> -- 
> http://fam-tille.de


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