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  * [[https://lists.debian.org/debian-med/2013/02/msg00154.html|Report from Olivier Sallou]]
  * [[https://lists.debian.org/debian-med/2013/03/msg00013.html|Report from Andreas Tille]]

Debian Med 2013 Sprint

Location, Date

http://www.urlaub-schoenberger-strand.de/images/ostsee-schoenberger-strand.jpg

When:

23rd/24th of February, 2013

Where:

Schönberger Strand near Kiel, Germany Wikipedia OpenStreetMap

Haus Felsenburg (literally: "House Rock Castle" ... fits our distro)

As for last years we managed to avoid the (nice and well connected, though) University buildings and found a family-run hotel at the Waterkant. It is at €50 per night and kindly just add your name below and do not to seek accommodation independently, so we all find our slots to talk to everyone, unconstrained of daytime schedules.

Who:

Enthusiasts and enthusiastic professionals in Medical-/Bioinformatics working with Debian/Ubuntu/Bio-Linux.

Travel:

Within Germany you may prefer one of the high speed trains going directly to Kiel. Otherwise, fly to Hamburg on the 22nd, preferably, and inform us so we get some joint transport organised. When you arrive at Hamburg Airport, do NOT take a train from Hamburg main station, take the Kielius or KielExx. When flying to Lübeck, or getting there easily from Copenhagen or from Stettin, you can share a car with one of us. If you go directly to Kiel (via Kielius, KielExx or train) you arrive at the main train station. From there you can take an hourly direct bus (Line 201) to Schönberg. The tour takes ca. 35 minutes and costs 4,30 €. From the bus stop (which is the final one) you can easily walk to the hotel.

Registration:

Free!

Please arrive at the 22nd if possible, so we have a warm start on the 23rd.

Participants

Needing Accommodation

No

Name

Email

confirmed

needs accom.

Organisation

Living in

Arrival at

Departure at

1

Steffen Möller

<moeller>

yes

yes

U Lübeck (Debian)

Lübeck (D)

22.2.

24.2.

2

Andreas Tille

<tille>

yes

yes

Debian

Wernigerode (D)

22.02. 16:02

25.02. 06:12

3

Ivo Maintz

pre.sur_biologie.hu-berlin.de

yes

yes

HU (Sys Biol)

Berlin (D)

4

Laszlo Kajan

lsur_rostlab.org

yes

yes

Rostlab / Debian

Munich (D)

22/02 17:21 Kiel Main St.

24/02 17:21 Kiel Main St.

5

Alex Mestiashvili

yes

yes

TU Dresden / Debian

Dresden (D)

6

Sascha Steinbiss

sur_zbh.uni-hamburg.de

yes

yes

U Hamburg / Debian

Hamburg (D)

22/02

24/02

7

Olivier Sallou

<osallou>

yes

yes

U Rennes 1 (Debian)

Rennes (F)

22/02 16:55 (Hamburg Airport))

25/02

8

Tony Travis

tony.travis_ed.ac.uk

yes

yes

U Edinburgh

Banchory (Scotland, UK)

22/02 17:50 (Hamburg Airport)

25/02

9

Christoph Gille

pre.sur_charite.de

yes

Charité

Berlin (D)

10

Tim Booth

tsur_ceh.ac.uk

yes

yes

NERC, Bio-Linux

Oxford (UK)

22/02

24/02

11

Uwe Beckert

yes

yes

Rechenkraft.net

Berlin (D)

22/02

25/02

12

Christian Beer

djangofett_gmx.net

yes

yes

Rechenkraft.net

22/02

25/02

2 Personen

13

Fabian Kloetzl

presur_t-online.de

yes

yes

U Luebeck

Luebeck (D)

22/02

24/02

Mattus and Dirk cannot come.

Locals

No

Name

Email

confirmed

needs accom.

Organisation

Living in

Arrival at

Departure at

1

Ingo Thomsen

i.sur_ikmb.uni-kiel.de

yes

local

U Kiel

Kiel (D)

2

Michael Banck

<mbanck>

yes

no

Debian

Munich (D)

23/02

24/02

3

Hajo Krabbenhöft

<moeller>

yes

no

Uni Lübeck

Lübeck (D)

4

Christian Steigies

<cts>

yes

no

CAU / Debian

Kiel (D)

Agenda

This preliminary collection of topics will transform more into team building once the list of attendees becomes more stable.

  • Welcome
    • Schedule: Friday late night
    • Preparation/Organisation: Ingo, Andreas
  • Joint discusion: Positioning of Debian Med as a community and resources we should reserve for it
    • Schedule: Friday and Sunday
    • Tops:
      • Knowledge transporter and archive
        • legacy applications, snapshot.d.o

        • wiki
        • inter/personal and inter-organisational network
        • connects to EU projects, Conferences
      • Should we have a dedicated machine for us? Cloud presence?
      • DebianMed <-> Debian Science <-> Debichem <-> Bio-Linux

      • ...?
    • Preparation/Organisation: Steffen
  • Presentations from participants:
    • Schedule: any time
    • Add yourself here

    • Tim Booth - Live USB and Cloud environments as a practical teaching platform
  • Isolating/addressing technical issues with packages in Debian today
    • Participants: everyone, problem-specific team building
    • Schedule: Friday/early Saturday - and the rest of the meeting
    • Preparation/Organization: Laszlo, Andreas (please!)
  • Identification of packages missing for today's and future routine workflows
    • Participants: everyone
    • Tops:
      • Next generation sequencing (Ingo)
      • Structural computing (Michael)
      • System biology (Ivo)
      • Taverna (if anyone fancies tackling it? - Tim) (Steffen contributes pkg-escience)

      • ...
    • Schedule: Saturday evening
    • Preparation/Organization: Ingo, Michael, Ivo
  • Debian packages for complete BOINC projects

    • Participants: everyone interested
    • Preparation/Organisation: Uwe, Steffen
    • Ideas:
      • extended outreach of computational biology
      • promotion of Debian's cross-platformness
      • unlimited resources for research groups
  • Tour through Kiel labs
    • Participants: everyone interested
    • Preparation/Organisation: Ingo
  • Certain packaging projects

* Group photo

Personal Agendas

Uwe Beckert

Andreas Tille

  • Wrote draft article for Indian health care magazin

  • Short talk proving the importance of sprints

  • Packaging
    • Worked with T. Travis on flexbar and uploaded the package

    • Worked with Ch. Gille on strapbase and uploaded the package

    • Discussed strategy how to strip glam2 source from meme upstream with T. Booth (I will take over this if time permits)

    • Discussed igv packaging issues with O. Sallou (he volunteered to have a look into this package)

    • Worked together with I. Maintz on cellprofiler

    • Worked together with I. Maintz on a couple of R packages as predependencies
  • Discussing / chatting
    • Some chat with Ch. Steigies (Debian Games, Debian m68k, Debian Science)
    • Short discussion with M. Banck about ?DebiChem

  • Little bit of MoM
  • Maintain Debian Med tasks files about newly commited packages
  • General infrastucture issues
    • Issues with machine-readable files importer into UDD
    • Try to revive PET data in UDD (#701533)

    • Work on installation of future blends.debian.net host (install needed packages, create UDD clone)

Olivier Sallou

Package libgenome-perl and libgenome-model-tools-music

Package above dependencies:

  • libur-perl
    • libgetopt-complete-perl
    • libclass-autoloadcan-perl
    • libtest-fork-perl

Fix beast-mcmc bug (698497)

List goby Java required libs not available in Debian repository.

Package IGV: first version ok, updating it to use as many debian libs as possible.

Sascha Steinbiss

Aragorn packaging

  • Improve manpage, waiting for upstream to update source on web page

?RepeatMasker dependencies

  • understand overlap between rmblast and ncbi-blast
  • try to build rmblast source with ncbi-blast's rules file

Improve ?GenomeTools as a dependency for other software

  • try to resolve last remaining non-API deps of Parseval to Gt to finally enable packaging Parseval w/o requiring non-API headers
  • investigate and fix performance-related bugs in Gt
  • work on detaching Gt domain search from HMMER source (can't link statically for licensing reasons)

Laszlo Kajan

  • Listened to BOINC presentation.
  • Intermittently worked on 'freecontact' documentation and test suite.
  • Gave talk on PredictProtein in Debian, had discussion about creating a Debian wiki page DebianMed/PredictProtein on getting started with PredictProtein on a Debian system.

  • Listened to Tony Travis' ?X2Go presentation.

  • Listened to Tim Booth's ?BioLinux presentation: '?BioLinux as a tool for bioinformatics training'.

  • Got a quick overview of STRAP from Christoph Gille.
  • Worked on gridengine with Alexandre Mestiashvili.

  • Discussed details of Makefile usage with Tony Travis.
  • Listened to STRAP talk from Christoph Gille.

  • Attended tour of Kiel Labs.

MichaelBanck

  • Discussed gridengine packaging with LaszloKajan

  • Uploaded updated debian-med-related Debichem packages: gamgi, rdkit
  • Uploaded updated Debichem packages: cclib, gausssum
  • Updated debichem taskfile per discussion with AndreasTille

  • Discussed Scalalife packaging with SteffenMoeller and ?AlexMestiashvili

    • Evaluated licensing for DALTON, DISCRETE, MUSIC, XMIPP
    • Packaged and Uploaded ErgoSCF for Debichem
  • Worked on updating debian-med-related Debichem packages (incomplete): jmol

Reports

(pointers to communication about the sprint)

See also

Acknowledgements

the sprint has been possible thanks to:

  • donations to the Debian project

  • sponsor DeltaComputer for lending us an exceptionally nice machine as a Debian-server for this weekend-event.


CategorySprint DebianMed