Debian Med 2013 Sprint
Location, Date
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 |
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 |
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
- ...?
- Knowledge transporter and archive
- 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
meme: A. Tille, T. Booth
flexbar: A. Tille, T. Travis
goby A. Tille, O. Sallou
?OpenMM, revisiting rogue package: Steffen (priority with Taverna)
Suggestion: freecontact - a free, fast protein contact predictor that implements direct-coupling analysis (DCA)(EVfold) and PSICOV algorithms: L. Kajan
Genome Music: O. Sallou
gt Ruby bindings, rmblast, maybe ?RepeatMasker: S. Steinbiss
* 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)
- report: (e.g. link to lists.d.o archives)
?Overview and reports on past meetings since 2011
Debian Med activities
Packages in Next Generation Sequencing
Overview on all tasks of Debian Med
See also
pre-BOSC/ISMB Codefest 2013 in Berlin
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.