Re: My sprint report (Was: Annual Debian Med sprint: 04.-07. February 2016 in Copenhagen)
On behalf of ELIXIR / DTU I'd like to say thanks to the Debian guys, had a real blast and it's a pleasure with such hard
A slight clarification (this is often mixed up): EDAM is a simple controlled vocabulary (for bio-topics, operations data
and data formats). It is used to describe the tools in the bio.tools registry. So in due course (in the way Andreas
described) we'll be exposing the Debian package info in bio.tools, and linking back. All good!
> 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 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 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 M�ller.
> 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
>  https://github.com/bio-tools/biotoolsConnect/tree/master/DebianMed
> On Wed, Nov 25, 2015 at 07:00:40PM +0100, Andreas Tille wrote:
>> 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
>> 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