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  * Had a look with Toni into [[http://www.openmicroscopy.org/|OpenMicroscopy]] noticing that it is a beast containing > 800 binary JAR files inside the source and will take a talented and very patient Java expert to copy with all this stuff   * Had a look with Tony Travis into [[http://www.openmicroscopy.org/|OpenMicroscopy]] noticing that it is a beast containing > 800 binary JAR files inside the source and will take a talented and very patient Java expert to copy with all this stuff

Debian Med sprint meeting in Southport

After the success of the last Debian Med sprint meeting in Lübeck we were granted the opportunity to organise a similar event in early 2012. This page assists in planning the event and records outcomes of the meeting.

The main organiser is Tim Booth (tbooth_ceh.ac.uk), the lead NEBC Bio-Linux developer.

Sponsorship

We would like to thank SciEngines for providing the FPGA tutorial on the Friday

We would like to thank Eucalyptus for sponsoring dinner on Saturday night

http://sciengines.com

http://eucalyptus.com

Location/Date/Capacity

The sprint will run from the 27th-29th January 2012 (Friday to Sunday). The main part of event will begin on Saturday morning. Friday is reserved for a tutorial on FPGA computing.

The venue will be the Dukes Folly Hotel Southport, UK. This is an independent hotel that will provide a similar atmosphere to the one we enjoyed in Lübeck-Travemünde, and we will have the place to ourselves for the duration. The hotel has only 17 bedrooms, but to accommodate up to 30 of us working in the daytime will not be a problem. For overspill, other hotels are nearby - see below. For after hours, our hotel has a fully licensed bar and Southport is also well supplied with places to eat and drink. Unfortunately, the famous funfair will not be open at this time of year.

Signing up/Cost

Update: On 14th December 2011 Tim contacted all attendees to confirm dates and room requirements. If you replied to this mail and are showing as "confirmed" in the table below then you have a room reserved in the hotel. If not, you need to contact Tim and say what you need.

Please add your name and other details to the table below. You will be contacted nearer the time to confirm details, so please check you have given a valid e-mail address and arrival/leaving dates. This table will be passed directly to the hotel to confirm reservations. If you have any special requirements you should contact the hotel directly on +44 1704 533355 - they are very friendly!

There is a flat rate per person of £35 per night for bed and breakfast. On the Saturday and Sunday the hotel will provide refreshments plus a full buffet lunch for £10 per person. So if you are staying for three nights the total cost to pay will be £125. For dinner each night and for lunch on the Friday/Monday we will make our own arrangements.

Getting to Southport

The Hotel is not far from the main rail station in Southport - less than 1km. (Click the thumbnail map for a larger version.)

http://nebc.nerc.ac.uk/static/images/southport2012/sp_map_big.gif

There are three international airports nearby:

Manchester Airport - trains run hourly direct from Manchester Airport Station to Southport, taking around 90 minutes

Liverpool John Lennon Airport - short bus or taxi ride into Liverpool, then trains run half-hourly to Southport

Blackpool Airport - is technically the closest, but there is no direct transport link to Southport, only a bus service via Preston.

For all public transport journeys in the UK, you should check http://www.transportdirect.info.

Overspill accommodation

If we end up filling the hotel, people may want to consider:

Talbot Hotel - Just around the corner, cheap. No on-line booking available.

Rosedale Hotel - Small hotel opposite Talbot. No on-line booking available.

Brittania Prince of Wales Hotel - Large hotel nearer to station. Headline prices are high but promotional offers may reduce the cost to under ~£43 per night. See website for bookings.

Attendees

No

Name

Email

Organisation (Interests)

Living in

Arrival at

Departure at

Booked room

Travelling details

1

Steffen Möller

<moeller>

U Lübeck (Debian)

Lübeck (D)

Thu 26.1.2012

Mon 30.1.2012

confirmed 14/12

2

Andreas Tille

<tille>

Debian

Wernigerode (D)

Thu 26.1.2012

Mon 30.1.2012

confirmed 14/12

BE869 Southampton -> Manchester 16:30

3

Tim Booth

tbooth_ceh.ac.uk

NERC (Bio-Linux)

Wallingford (UK)

Late Thursday

Monday

confirmed

Car or Rail from Oxford

4

Alan Williams

alanrw_cs.man.ac.uk

U Manchester (Taverna)

Manchester (UK)

Friday

Monday

Confirmed 14/12

From Manchester with Stuart+Quyen

5

Tony Travis

ajt_minke.ukfsn.org

Unemployed (Bio-Linux)

Banchory (UK)

Fri

Monday

confirmed 15/12

6

Olivier Sallou

pre.sur_irisa.fr

U Rennes 1

Rennes (FR)

Friday

Monday

confirmed 18/12

7

Piero Fariselli

pre.sur_unibo.it

U Bologna (1D->2.5D)

Bologna (IT)

Thur

Mon

confirmed 11/1/12

8

Ivo Maintz

pre.sur_biologie.hu-berlin.de

HU (Sys Biol)

Berlin (D)

Thur

Sun

confirmed 07/11

9

Laszlo Kajan

lsur_rostlab.org

Rostlab (1D->2.5D)

Munich (D)

Thu 26.01.12

Mon 30.01.12

confirmed 19/12

10

Sascha Steinbiss

sur_zbh.uni-hamburg.de

U Hamburg

Hamburg (D)

Friday

Monday

confirmed 14/12

11

Stuart Owen

U Manchester (Seek)

Manchester (UK)

Friday Eve

Monday

confirmed 14/12

From Manchester with Alan+Quyen

12

Brian Thomason

pre.sur_eucalyptus.com

Eucalyptus (cloud)

Santa Barbara (US)

Friday

Monday

confirmed 14/12

13

H. Soon Gweon

hyugwe_ceh

Bio-Linux

Wallingford (UK)

Late Thursday

Late Saturday

confirmed 20/12

Travelling with Tim from Oxford

14

Quyen Nguyen

pre.sur_h-its.org

HITS (Seek)

Heidelberg (D)

Friday

Monday

confirmed 14/12

From Manchester with Alan+Stuart

15

Martin Steghöfer

msteghofer_cistib.upf.edu

CISTIB/Gimias (workflows)

Barcelona (E)

Fri 27.01.12

Sun 29.01.12

confirmed 18/1/12

16

Matus Kalas

pre.sur_bccs.uib.no

U Bergen (BioXSD, EDAM)

Bergen (N)

Thu

Sun morning

confirmed 11/1/12

17

Stefan Baumgart

presur_sciengines.com

?SciEngines

Kiel (D)

Thu

Sun

confirmed 20/1

Staying at Carlton House

18

Daniel Siebert

?SciEngines

Kiel (D)

Thu

Sun

confirmed 20/1

Staying at Carlton House

19

William Spooner

pre.sur@eaglegenomics.com

Eagle Genomics

Babraham (UK)

Fri

Mon

confirmed 9/1/12

Staying at Rosedale. May have to cancel at last minute due to deadline

20

Jim Procter

jsur_compbio.dundee.ac.uk

U Dundee (Jalview,java in debian, osgi)

Dundee (UK)

Cancelled

Cancelled

Cancelled

Dundee

Agenda

The meeting addresses the following topics over Saturday and Sunday - please add yours. Work and discussions will happen in parallel in the same room. The schedule is determined on Friday evening when most of us are expected to have arrived on site.

As a special feature, just like with bigger conferences, only better, this year brings us a 'hands-on' tutorial on FPGA computing for application acceleration. It is planned to take up all of Friday and this way only enriches and not disturbs the remainder of the meeting. Respective attendees are expected to arrive already on Thursday.

  • How do we see Debian Med changed / do we actively change Debian Med with what we learn from
    • Interaction of with Ubuntu (MOTU) maintainers
    • Interaction with bioinformatics research groups
      • having their work packaged by us
      • packaging it themselves
      • packaging their third party tools
    • Interaction with service groups in academia and industry
  • Review of latest developments
    • Cloud computing progress - priority tools for Cloud (eg. Cloudman)

    • BOINC
    • GPU / FPGA application acceleration
  • Workflows
    • Infrastructure with Taverna and Galaxy
    • Can we find ways to present such more visibly?
    • What packages are missing in Debian to render new kinds of workflows a reality with Debian?
  • getData / BioMaj

    • first packages using it
    • standardising interaction between databases and packages/Debian policy - (consider extensions to APT? - Tim)
    • better integration with above workflows
    • effectiveness in Cloud/cluster environments
    • comparison with the data management configuration in Galaxy
    • other further developments?!?
  • Review of what came up on the mailing list
    • Renaming of user-executable files to fully comply with Debian Policy for scientific packages (like omitting .pl suffix)
  • License checking session: Lets do a collaborative try to write upstream of non-free programs to consider relicensing

Personal Agendas

Andreas Tille

  • Ensembl packaging specifically working on installation in unstable without any conflicts (=trying to solve libwww issue)
    • problematic package is actually liblwp-parallel-perl (need more input from previous maintainer)
  • Beast-mcmc finishing
    • last problematic JAR mtj.jar is a mess of other included JARs based on f2j blas/arbapck JARs with no visible source
  • Continuing with current MoM; presenting MoM to the audience to gather more potential students

    • Kept on mentoring the student
  • Finishing sofa-framework which needs to be updatet to new version
  • Bug squashing of Debian Med team maintained packages
    • Solved #657827 and #648167
  • If time permits work on some Beast related phylogeny packages
    • Uploaded phy-spread package
  • Checking status of Debian Med tasks
    • tasks tools are broken because of technical changes in Debian Infrastructure, needs sorting out
  • Spontaneous mentoring of people
    • Introductional talk about Debian and Blends structure
    • Mentoring Quyen, Laszlo and others about gpg keys
  • Working on Blends sentinel bugs overview
    • Terribly blocked by non-functional fetching translations from ddtp.debian.net which is down. Caring for alternatives to at least get tasks pages updated again but no success so far.
  • Helping others packaging and sponsoring
    • Sponsored chado (gmod suite) prepared by Olivier Sallou
    • Helped Charles getting snappy-java using Debian packaged library (see below external wishlist)
    • Worked with Ivo on copasi
    • Helped Martin with Python packaging
    • Had a look with Tony Travis into OpenMicroscopy noticing that it is a beast containing > 800 binary JAR files inside the source and will take a talented and very patient Java expert to copy with all this stuff

    • Looked into packages prepared by Piero
  • License checking

External wishlist

Schedule

  • Thursday: Arrival of participants / trainers for FPGA tutorial
  • Friday:
    • 9-19: FPGA tutorial, breaks for coffee and lunch as it fits
    • 19-21: dinner
    • 21-22: icebreaking 7-15min talk series: how Debian helps today and after this sprint
      • Laszlo and Piero: structure prediction
      • Stuart and Ivo: system biology
      • Tim and Soon: Bringing the Galaxy server to Debian
    • 23-24: discussions and planning of synchronisation points on Sat/Sun
  • Saturday/Sunday: roundtable work, planning, discussion and writing
    • unplanned discussions over breakfast
    • teams start whenever breakfast ends
    • joint lunch
    • coffee+tea+biscuits?
    • joint dinner
    • more teamwork
  • Monday: joint breakfast and group travel to airports

It's worth noting for those not in the know that there is some symbiosis between this sprint event and the annual BOSC Codefest which is held before the ISMB conference. Though the meetings are quite different in focus, they have recently engaged many of the same people and projects.

See also