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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/.
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 |
confirmed |
booked accom. |
Organisation |
Living in |
Arrival at |
Departure at |
|
1 |
Tony Travis |
yes |
yes |
Minke Informatics |
Aberdeen |
31 Jan 16:00 |
2 Feb 19:00 |
|
2 |
Tim Booth |
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 |
yes |
yes |
Mario Negri Institute |
Milan (I) |
31 Jan |
2 Feb |
|
7 |
Jim Procter |
yes |
yes |
University of Dundee |
Dundee (UK) |
31 Jan ~17:00 |
2 Feb ~18:00 |
|
8 |
Daniel Barker |
yes |
yes |
University of St Andrews |
Fife (UK) |
31 Jan |
2 Feb |
|
9 |
Brad Chapman |
yes |
yes |
Harvard School of Public Health |
Boston (US) |
31 Jan (15:45) |
2 Feb (22:25) |
|
10 |
Jorge Soares |
yes |
yes |
Wellcome Trust Sanger Institute |
Cambridge (UK) |
31 Jan (14:45) |
2 Feb (15:25) |
|
11 |
Detlef Wolf |
yes |
yes |
F. Hoffmann-La Roche AG |
Basel (CH) |
30 Jan (10:20) |
3 Feb (11:00) |
|
12 |
Kristoffer Rapacki |
yes |
yes |
Danish ELIXIR Node |
Copenhagen (DK) |
31 Jan (before 5pm) |
3 Feb (morning) |
|
13 |
Niall Beard |
yes |
yes |
University of Manchester |
Manchester, UK |
31 Jan (before 5pm) |
3 Feb |
|
14 |
Iain Learmonth |
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 |
yes |
yes |
Danish ELIXIR Node |
Copenhagen (DK) |
31 Jan (before 5pm) |
3 Feb (morning) |
|
17 |
Emil Rydza |
yes |
yes |
Danish ELIXIR Node |
Copenhagen (DK) |
31 Jan (before 5pm) |
3 Feb (morning) |
|
18 |
Matúš Kalaš |
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]
- 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.