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'''''Items added in advance. For report of actual outcomes and activities see below.'''''
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== Personal agendas == == Activities, outcomes and personal reports ==
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Please either add info directly here or else [[https://docs.google.com/document/d/1Hf_Sw-2tet4PIT7Brrc3AC7MaRAReGrQS60OOWmPwS8/edit|edit the shared Google doc]]
and we'll merge it in later.
[[DebianMed/Meeting/Aberdeen2014_Report|See the separate meeting report, compiled by Tim.]]
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[[DebianMed/Meeting/Aberdeen2014_Report|Meeting report is now being compiled.]]


=== Andreas Tille ===
 * Package uploads
  * Sponsored gnuhealth
  * New version of gnumed-server + gnumed-client
  * New version of flexbar, checking tests, contacted upstream about failing tests
  * Some changes at staden packaging
  * Worked with Detlef Wolf on upstream build system of bioinfo-c
  * seqtk (created in a life packaging session)
  * dnaclust (created in a life packaging session)
  * snp-sites sponsored for Jorge Soares
  * python3-fitbitscraper sponsored for Iain R. Learmonth
 * Introduction into [[DebianMed/MoM|Mentoring of the Month]]
 * Life packaging session at Saturday afternoon packaging randomly picked (simple) packages suggested by the audience
 * Discussing issues about creating an ontology based in data in UDD (debtags+descriptions) with EDAM people
 * Working on the FAQ section of the Blends documentation (relation to DebTags)
 * Working together with Luiz Ibanez on VistA packaging
 * Running around to help people gaining their first packaging experience after the life packaging session yesterday
 * Enabling [[http://kgb.alioth.debian.org/alioth.html|kgb]] for Git repositories
 * Other stuff than Debian Med
  * uscan enhancements
  * Sponsering libcitygml for Debian GIS
  * Activate 4096bit GPG key
  * Fixing Debian Games tasks

=== Iain Learmonth ===

 * Learnt Debian packaging through participating in Andreas' live packaging of dnaclust and seqtk.
  * Sorted out a man page for dnaclust
 * Packaged python3-fitbitscraper
 * Spoke with Luca and agreed to package HEAVyBASE once there is documentation available for the package
 * Gave a demo of a Python application visualising personal health data from FitBit ([[http://i.imgur.com/0NUpGc2.png|Screenshot]]).
 * Took some pictures, link below.
You may also see the original notes in the [[https://docs.google.com/document/d/1Hf_Sw-2tet4PIT7Brrc3AC7MaRAReGrQS60OOWmPwS8/edit|shared Google doc]], but all of this should now be in the report page on the Wiki.

Debian Med Sprint Weekend 2014, Stonehaven near Aberdeen

Following on from the previous event in Kiel, and earlier annual meetings, we invite enthusiastic hackers to attend the next Debian Med Sprint meeting in Stonehaven, near Aberdeen in Scotland (UK) http://www.stonehavenguide.net/.

Sights of Stonehaven

Location, Date

Dates and schedule

The main meeting will start at 5pm on Friday 31st January, then continue on through Saturday 1st and Sunday 2nd February. We hope that everyone can stay through to Sunday evening. A schedule and agenda have been added below and all attendees should contribute ideas. We hope to invite talks and tutorials (ideas welcome!) and to set some realistic goals for our hacking activities at the meeting.

Getting there

Stonehaven has a station served by frequent trains to/from from Aberdeen, Edinburgh and Glasgow. International direct flights arrive at Aberdeen airport from Amsterdam, Paris Charles de Gaul and Hamburg. National frlights arrive at Aberdeen from Heathrow and Gatwick. You can also travel to Aberdeen by bus http://uk.megabus.com/ and then take a local bus to Stonehaven. Try Transport Direct for planning rail and bus journeys in the UK.

Venue and costs

The meeting will be held at the Royal Hotel near the sea front in Stonehaven. We hope that all attendees can stay in the hotel. Regular prices are £65 for a single or £75 for a twin room per night (incl. breakfast), but Minke Informatics Limited will sponsor part of the cost. The discounted rate will be £55 a night for a room to yourself or £32.50 each if you are sharing with someone else. Please use the Royal Hotel web mail to book a room and ask for the discounted accomodation rate for our meeting.

We expect to cover at least refreshments and hopefully lunch through sponsorship too. Details to follow.

Organisers

Tony Travis and Tim Booth (see below) are the main organisers. Tony is our local boy in Aberdeen. Please feel free to contact us directly or to discuss the meeting with us via the Debian-Med mailing list.

Participants

Signing up

All attendees will need to pay in advance for the first night with a credit card to secure a hotel room and pay the balance on arrival at the hotel.

Attendees

As well as booking your room directly with the hotel, please fill your details in the table below.

No

Name

Email

confirmed

booked accom.

Organisation

Living in

Arrival at

Departure at

1

Tony Travis

tony.travis@minke-informatics.co.uk

yes

yes

Minke Informatics

Aberdeen

31 Jan 16:00

2 Feb 19:00

2

Tim Booth

tbooth@ceh.ac.uk

yes

yes

NEBC (Bio-Linux)

Wallingford

31 Jan 16:00

2 Feb 19:00

3

Steffen Möller

<moeller>

yes

yes

U Lübeck (Debian)

Lübeck (D)

31 Jan 16:00

3 Feb 19:00

4

Andreas Tille

<tille>

yes

yes

Debian

Wernigerode (D)

31 Jan

3 Feb

5

Olivier Sallou

<osallou>

yes

yes

U. Rennes 1

Rennes (F)

31 Jan

2 Feb

6

Luca Clivio

luca.clivio@marionegri.it

yes

yes

Mario Negri Institute

Milan (I)

31 Jan

2 Feb

7

Jim Procter

j.procter@dundee.ac.uk

yes

yes

University of Dundee

Dundee (UK)

31 Jan ~17:00

2 Feb ~18:00

8

Daniel Barker

db60@st-andrews.ac.uk

yes

yes

University of St Andrews

Fife (UK)

31 Jan

2 Feb

9

Brad Chapman

bchapman@hsph.harvard.edu

yes

yes

Harvard School of Public Health

Boston (US)

31 Jan (15:45)

2 Feb (22:25)

10

Jorge Soares

j.s.soares@gmail.com or js21@sanger.ac.uk

yes

yes

Wellcome Trust Sanger Institute

Cambridge (UK)

31 Jan (14:45)

2 Feb (15:25)

11

Detlef Wolf

detlef.wolf@roche.com

yes

yes

F. Hoffmann-La Roche AG

Basel (CH)

30 Jan (10:20)

3 Feb (11:00)

12

Kristoffer Rapacki

rapacki@cbs.dtu.dk

yes

yes

Danish ELIXIR Node

Copenhagen (DK)

31 Jan (before 5pm)

3 Feb (morning)

13

Niall Beard

niallbeard@gmail.com

yes

yes

University of Manchester

Manchester, UK

31 Jan (before 5pm)

3 Feb

14

Iain Learmonth

irl@fsfe.org

yes

yes

University of Aberdeen

Aberdeen

31 Jan ~15:00

2 Feb ~19:00

15

Peter Cock

no

no

?BioPython

Dundee

1 Feb

1 Feb

16

Piotr Chmura

pjchmura@cbs.dtu.dk

yes

yes

Danish ELIXIR Node

Copenhagen (DK)

31 Jan (before 5pm)

3 Feb (morning)

17

Emil Rydza

ekr@cbs.dtu.dk

yes

yes

Danish ELIXIR Node

Copenhagen (DK)

31 Jan (before 5pm)

3 Feb (morning)

18

Matúš Kalaš

matus.kalas@uib.no

yes

yes

U Bergen (EDAM)

Bergen (NO)

31 Jan ~11am

3 Feb ~4pm

Schedule

The bulk of the meeting is in a hackathon format, with people working in groups toward specific goals. Please edit the agenda below to add suggested topics. Please also volunteer to give a short talk about your area of interest and add it to the schedule. We will have a computer projector available. To get us in the mood, we will have a warm-up session on the Friday evening with short talks and updates (15min). All are invited to give a short presentation about their work, and if they were at a previous Sprint what has happened since the last time. We will also have presentations to start off the other two days (30min).

Friday 31st Jan

17:00

Meet up in hotel and get dinner

19:30

Registration for meeting Wiki and WiFi

20:00

Welcome

20:15

Update: Bioconductor, Flexbar and x2go (Tony)

20:30

Intro: EDAM - tool description model - tool registry (Kristoffer)

20:45

Upstream/down: Jalview and JABAWS (Jim and maybe TIM ;) )

21:00

Bioinformatics education: the 4273pi project (Daniel)

21:15

Talk about Bioinfo-C (Detlef Wolf). Slides: Roche_BioinfoC@DebianMed_Sprint_2014.pdf

21:30

Debian Med sprints and mentoring (Andreas Tille)

22:30

Retire to the bar

Saturday 1st Feb

09:30

Demo by invited speaker Brad Chapman, on Cloud BioLinux

10:30

Coffee break

11:00

Matúš presents the EDAM ontology

13:00

Lunch break

14:00

Review of agenda, prioritisation of tasks and output goals, formation of hacking groups

15:30

Coffee break

16:00

Hacking until...

19:30

Beer and pizza provided by sponsors

23:00

More hacking and beer

Sunday 2nd Feb

09:30

Talk about Qlustar, Tony Travis (Minke Informatics)

10:00

Kristoffer speaks of possibilities of batch upload of package info into the tools registry

10:30

Coffee break

11:00

Talk about ?P2Pdb, Luca Clivio. A peer to peer approach to data sharing for clinical trials and translational research

11:45

Update on Bio-Linux from Tim, and update of hackathon activities and outputs

13:00

Lunch break

14:00

Detlef - demo of PubmedSearch on bioinfoc

14:15

Continuation of hackathon activities

16:00

Compilation of activities and output reports from all hackers

17:00

Thanks and close

Agenda

Items added in advance. For report of actual outcomes and activities see below.

  • Packaging Galaxy for Bio-Linux - the Debian way [Tim, Steffen]
    • Related: Installing and updating Galaxy in a contolled, isolated environment for handling sensitive data [Matúš]
  • Priorisation of Java-based tools [Steffen, someone else from pkg-java]
    • Taverna - mostly hopeless to address without cheating, we should decide how to cheat [Steffen]
    • biojava [Olivier]: fix biojava and package update of biojava3
    • libgo-perl [Olivier]: fix test bug in new release and upload new release
    • package new NGS softwares [Olivier]: discosnp and mapsembler2
    • Jalview refresh and prototype non-free JABAWS package (If Sasha Sherstnev agrees ;) )

    • OBO-Edit [Sascha]
    • ... please add packages you are interested in ...
  • Tutorials - Debian Med Live
  • Reviews - where are we
    • ?BioConductor [Andreas? Tony?]

    • Data handling [Steffen]
  • EDAM ontology in DebianMed packages? [ olivier ]: being able to search for Debian tools based on EDAM ontologies

    • note [Matus]: preliminary brainstorming on this topic has been done by László, Jon Ison, Matúš (+Steffen, Hervé, Bertrand, Kristoffer Rapacki. Notes connected to attributes to annotate are in this section of the CodefestOntoDoc) - Let's get more people on board and decide and make concrete steps in Stonehaven!

  • Development of bioinformatics tools registry and opportunities for synergy with Debian Med, Bio-Linux, Galaxy, Mobyle, ... [Kristoffer, Matúš]
  • Community development, licensing, and potentially packaging of "standards" (incl. ontologies, schemata, ...) - what are the good, sustainable ways? Interested: Matus
  • p2pDB [Luca] - beyond the web: a peer to peer approach to data sharing for clinical trials and translational research
  • Bioinformatics education on the Raspberry Pi - 4273pi [Daniel]

  • Automated creation of Docker containers with specific combinations of Debian-Med and external packages using Cloud. Work in progress is bcbio-nextgen-vm, with a Dockerfile. [Brad]

    • [note O. Sallou] might be worth looking at/contributing to build-debian-cloud (python branch). It can be used for the moment to build EC2 or VirtualBox/Vagrant and KMV images. It also supports the addition of plugins.
    • There is also packer which provides a nice general soluation. [Brad]

  • Automated methods to add large biological data next to existing Docker containers. Allows lightweight distributions with ability to share data among multiple instances. [Brad]
  • Provide automated manifest of software versions installed on image, prioritizing biological software. Previous work in ?CloudBioLinux: script and output files. [Brad]

  • Review of Qlustar HPC as a Bio-Linux terminal server [Tony]
  • Tackling some larger packages [Andreas]
    • staden (finalise merge of Tim's and Jonas' work on this)

    • ensembl (we just had this, it should be reinjected)
    • check for other packages ?BioLinux might need

  • Mentoring newcomers [Andreas]
  • Personal health monitoring (pedometer, blood pressure, sleep quality, water intake, CPAP compliance, etc.) using free software [Iain]
  • Maintaining trusted repositories of software for isolated computing environments which handle sensitive data - how much can Debian, Bio-Linux, or ?CloudBioLinux help? [Matus]

Activities, outcomes and personal reports

See the separate meeting report, compiled by Tim.

You may also see the original notes in the shared Google doc, but all of this should now be in the report page on the Wiki.

Photos

Photos taken by Iain Learmonth are available here. Photos taken by Detlef from the surroundings of the venue are here.

Acknowledgements

  • This event is supported by

    Balaenoptera acutorostrata FLOSS UK NERC Environmental 'Omics Synthesis Centre

    Q-Leap Qlustar Eagle Genomics