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#format wiki
#language en
#pragma section-numbers off
#pragma hide-title true
#pragma keywords Bioinformatics, Open Source, Debian, Ubuntu, Meeting, Workshop, Sprint, Travemünde, Lübeck, 2011, January
#pragma description Meeting of the Debian and Ubuntu community to foster the development of an infrastructure for the research in bioinformatics
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 * where: [[http://www.travemuende.de/tourismus/geschichte/stadtportrait/en/index.html|Travemünde]], Germany ([[http://www.openstreetmap.org/?lat=53.96838&lon=10.88009&zoom=14|OSM]]) at the [[http://www.strandperle-travemuende.com?lang=en|Hotel Strandperle]].  * where: [[http://www.travemuende.de/tourismus/geschichte/stadtportrait/en/index.html|Travemünde]], Germany ([[http://www.openstreetmap.org/?lat=53.9588&lon=10.8712&zoom=14|OSM]]) at [[http://www.deutscher-kaiser-travemuende.de/|Hotel Deutscher Kaiser]].
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||No|| Name || Email || Organisation || Living in || Arrival at || Departure at ||
|| 1|| Steffen Möller || <moeller> || U Lübeck (Debian) || Lübeck (D) || 28.01.2011 || 31.01.2010 ||
|| 2|| Andreas Tille || <tille> || Debian || Wernigerode (D) || 28.01.2011 || 31.01.2010 ||
|| 3|| Tim Booth || tbooth_ceh.ac.uk || [[http://nebc.nerc.ac.uk/tools/bio-linux|NERC]] (BioLinux) || Oxford                 (UK) || 28.01.2011 || 31.01.2010 ||
|| 4|| Pjotr Prins || || U Wageningen (Debian) || Wageningen (NL)|| || ||
|| 5|| Alan Williams || || U Manchester (Taverna) || Manchester (UK) ||            || ||
|| 6|| Hajo Krabbenhöft || || U Lübeck (M.sc. student) || Lübeck (D) || 28.01.2011 || 31.01.2010 ||
|| 7|| Yask Gupta || || U Lübeck (Ph.D. student) || Lübeck (D) || 28.01.2011 || 31.01.2010 ||
|| 8|| Kushal Sejwal || || U Lübeck (Ph.D. student) || Würzburg (D) || 28.01.2011 || 31.01.2010 ||
|| 9|| Richard Holland || || Eaglegenomics (Debian) || Southampton (UK)||            || ||
||10|| Will Spooner || || Eaglegenomics || Babraham (UK) ||            || ||
||11|| Peter Rice || || EBI (EMBOSS) || Hinxton (UK) ||            || ||
||12|| Jim Procter || || U Glasgow (Jalview) || Glasgow (UK) ||            || ||
||13|| Michael Banck || <banck> || Debian || Munich (D) || 28.01.2011 || 31.01.2010 ||
||14|| Andreas Hildebrandt || || U Saarbrücken (BALLview) || Saarbrücken (D) || 28.01.2011 || 31.01.2010 ||
||15|| Sri Girish Srinivasa Murthy || || MPI Evol. Biol.|| Plön (D) || 28.01.2011 || 31.01.2011 ||
||16|| || || || || || ||
||17|| || || || || || ||
||18|| || || || || || ||
||19|| || || || || || ||
||20|| || || || || || ||

 * Pending: Goettingen, Lübe
ck, Darmstadt
||No|| Name  || Email || Organisation || Living in || Arrival at || Departure at ||
|| 1|| Steffen Möller  || <moeller>        || U Lübeck (Debian) || Lübeck (D) || 28.01.2011 || 31.01.2011 ||
|| 2|| Andreas Tille  || <tille> || Debian || Wernigerode (D) || 27.01.2011 20:30 || 31.01.2011 ||
|| 3|| Tim Booth  || tbooth_ceh.ac.uk || [[http://nebc.nerc.ac.uk/tools/bio-linux|NERC]] (Bio-Linux) || Oxford (UK) || 28.01.2011 || 30.01.2011 ||
|| 4|| Pjotr Prins  || || U Wageningen (Debian) || Wageningen (NL)|| || ||
|| 5|| Alan Williams  || || U Manchester (Taverna) || Manchester (UK) || 28.01.2011 || 31.01.2011 ||
|| 6|| Hajo Krabbenhöft  || || U Lübeck (M.sc. student) || Lübeck (D) || 28.01.2011 || 31.01.2011 ||
|| 7|| Yask Gupta  || || U Lübeck (Ph.D. student) || Lübeck (D) || 28.01.2011 || 31.01.2011 ||
|| 8|| Kushal Sejwal  || || U Lübeck (Ph.D. student) || Würzburg (D) || 28.01.2011 || 31.01.2011 ||
|| 9|| Richard Holland  || || Eaglegenomics (Debian) || Southampton (UK)|| 28.01.2011 || 31.01.2001 ||
||10|| Will Spooner  || || Eaglegenomics || Babraham (UK) || 29.01.2001 || 31.01.2001 ||
||11|| Peter Rice  || || EBI (EMBOSS) || Hinxton (UK) || 29.01.2001 || 30.01.2001 ||
||12|| Jim Procter  || || U Dundee ([[http://www.jalview.org/|Jalview]]) || Dundee (UK) || 28.01.2011 || 31.01.2011 ||
||13|| Michael Banck        || <mbanck>         || Debian                   || Munich (D)      || 28.01.2011 || 30.01.2011 ||
||14|| Andreas Hildebrandt  || || U Saarbrücken (BALLview) || Saarbrücken (D) || 28.01.2011 || 31.01.2011 ||
||15|| Jürgen Doenitz || || U Göttingen (Göbix) || Göttingen (D) || 28.01.2011 || 31.01.2011 ||
||16|| Tony Travis || || U Aberdeen || Aberdeen (UK) || 28.01.2011 || 31.01.2011 ||
||17|| Christian
Steigies || <cts> || U Kiel (Debian) || Kiel (D) || 30.01.2011 || 30.01.2011 ||
||18|| Antje Krause || || FH Bingen || Mainz (D) || 28.01.2011 || 31.01.2011 ||
||19|| Olivier Sallou || || IRISA (symbiose) || Rennes (F) || 28.01.2011 || 31.01.2011 ||
||20|| David Wit
hers || || U Manchester || Manchester (UK) || 28.01.2011 || 31.01.2011 ||
||21|| Joel Hedlund || || U Linköping || Linköping (
S) || 28.01.2011 || 31.01.2011 ||
||22|| Alexander Mestiash
vili|| || TU Dresden || Dresden (D) || || ||
||23||
Manuel Prinz || <manuel> || U Duisburg-Essen (Debian)|| Essen (D) || 28.01.2011 || 31.01.2011 ||
||24|| Pablo Di Tomasso || || U
Barcelona || Barcelona (E) || || ||
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   * external tool activity in Taverna
     * plan for next release of Taverna
     * harmonization with other tool descriptions
     * extension of invocation environments
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   * first joint paper recently accepted in BMC Bioinformatics
   * discuss paper on getData
   * [[http://www.biomedcentral.com/1471-2105/11/S12/S5|first joint paper]] recently accepted in BMC Bioinformatics
   * discuss paper on [[getData]]
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== Program ==

We should have Saturday (29th) and Sunday (30th) to truly concentrate on our work. Participants should (and most do) arrive on Friday (28th) and leave on Monday (31th). Teams will split and summarise at coffee breaks on their respective status/issues.

Friday is the day for setups, individual training and learning about the novel developments and on-hand insights into problems at another site, allowing for the teams' detailed scheduling for Saturday and Sunday. Monday will be used to wrap up, literally and in writing.
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TBA ==== ''teamJava'': bio related Java packaging subgroup ====
Objectives:
Etherpad: [[http://192.168.1.23:9000/JNsYKrs0X8]]
 * www.jalview.org related
  * create biolinux/debMed package for Jalview 2.6.x
  * create experimental [[http://www.compbio.dundee.ac.uk/jabaws|JABAWS]] package for biolinux
 * Examine and Resolve dependency issues :
  i. Jmol
Participants:
  i. Jim Procter
  ii. MichaelBanck (Jmol packaging)

==== ''teamTaverna'': Taverna relationship subgroup ====
Objectives:
  * examine other tool description formats
    * soaplab
    * galaxy
    * biopieces
    * GIMIAS
    * BOINC wrapper
    * any more?
  * how to publish tool descriptions
  * check architecture of external tool activity to ensure extensibility
  * look at data referencing issues
  * Runtime Environment specification
  * roadmap for invocation mechanisms
  * [[DebianMed-Taverna-20110130 | External tool notes]]
Participants:
  i. Alan Williams
  i. David Withers

== Travel ==

 * Hotel rooms are already reserved for you have not expressed the wish to organise it yourself.
 * When coming by train, use [[http://reiseauskunft.bahn.de]] and select ''Lübeck-Travemünde Hafen'' as destination. From there it is 150m or so to the Hotel. If you miss that one and exit at ''Lübeck-Travemünde Strand'', at daylight with not too much luggage, just have a 20 minutes walk at the water for about a mile or so till you arrive at the Hotel. Every non-tourist should know it. If it is dark already then just stay seated in the train that is going back and forth to Lübeck and will stop at ''Travemünde Hafen'' again, anyway. Lübeck is on the connection between Hamburg and Copenhagen and we have another ICE to Munich plus all the local trains to the well-connected Hamburg.
 * When flying in, be aware of RyanAir nicely serving Lübeck. I collect you from there or you can make it by public transport. Hamburg Fuhlsbüttel is about 90km away. There are busses going to Lübeck (look for AUTOKRAFT) but I usually take the trains. When you arrive close in time, you can also share a cab (there are big ones), but let me order it from here .... should then be about 80 Euros.
 * When coming by ferry to Travemünde Skandinavienkai, take a bus from the Terminal to Travemünde itself. Lines 30 or 31 will drop you right in front of the Hotel after two kilometers or so.

== Keysigning ==

When dealing with Debian packages it is always a good idea if you have a GPG key signed by a Debian Developer. So this meeting is a good chance to get your key signed. If you are not comfortable with GPG creation and signing just have a look here:
 * [[Keysigning]]
 * [[http://keyring.debian.org/creating-key.html]]
Make sure you have a printout of your GPG key and a passport at hand. [[http://www.debian.org/events/materials/business-cards/|Here]] are nice templates for business cards where you can include your Fingerprint easily.

== Results ==

A summary was sent to [[http://lists.debian.org/debian-project/2011/02/msg00026.html]]. Andreas had already provided a more detailed list. Will blogged about it [[http://www.eaglegenomics.com/2011/02/getting-involved-in-debian-med/|here]]. Others may follow suit.

==== Andreas Tille ====
 * Short intro for newcomers into [[DebianMed|Debian Med]]
 * Worked on packaging of [[http://debian-med.alioth.debian.org/tasks/bio#bowtie|bowtie]] together with Yask Gupta and Antje Krause which is now in [[http://ftp-master.debian.org/new/bowtie_0.12.7-1.html|new packages queue]]
 * Adopted on packaging of [[http://debian-med.alioth.debian.org/tasks/bio#mothur|mothur]] which is now in [[http://ftp-master.debian.org/new/mothur_1.15.0-1.html|new packages queue]]
 * Helped Steffen Möller and Tim Booth finalising [[http://debian-med.alioth.debian.org/tasks/bio#tm-align|tm-align]] which is now in [[http://ftp-master.debian.org/new/tm-align_20110130-1.html|new packages queue]]
 * Worked together with Alexander Mestiashvili on [[http://debian-med.alioth.debian.org/tasks/bio#vienna-rna|vianna-rna]] which advanced a lot [[http://svn.debian.org/wsvn/debian-med/trunk/packages/vienna-rna/trunk/debian/#_trunk_packages_vienna-rna_trunk_debian_| in SVN]] and is close to state where it can be uploaded
 * Created a new Debian Med task [[http://debian-med.alioth.debian.org/tasks/bio-ngs|Debian Med Next generation sequencing packages]] and added prospective packages there
 * Spended some time on polishing [[http://debian-med.alioth.debian.org/tasks/bio#meme|meme]] packaging in [[http://svn.debian.org/wsvn/debian-med/trunk/packages/meme/trunk/#_trunk_packages_meme_trunk_|SVN]] which is interesting because it contains newer code for our package glam2, but has stalled this effort because meme is non-free
 * Helped Richard Holland and Steffen Möller in finalising [[http://debian-med.alioth.debian.org/tasks/bio#ensembl|ensembl]] which is now in [[http://ftp-master.debian.org/new/ensembl_57-5.html|new packages queue]]
 * Helped William Spooner to work on [[http://debian-med.alioth.debian.org/tasks/bio#wgs-assembler|wgs-assembler]] in [[http://svn.debian.org/wsvn/debian-med/trunk/packages/wgs-assembler/trunk/#_trunk_packages_wgs-assembler_trunk_|SVN]]
 * Discussed with Tim Booth about future cooperation between [[DebianMed|Debian Med]] and [[http://nebc.nerc.ac.uk/tools/bio-linux/||Bio-Linux]]
 * Discussed with Olivier Sallou how I can help him packaging [[http://debian-med.alioth.debian.org/tasks/bio#biomaj|biomaj]] which is subject of further work in [[http://svn.debian.org/wsvn/debian-med/trunk/packages/biomaj/trunk/#_trunk_packages_biomaj_trunk_|SVN]]
 * Had a lot of interesting discussions with Tony Travis (about Ubuntu and other derivatives), Tim Booth, Pjotr Prins, Joel Hedlund, all the DDs and for sure the other participants
 * Something I forgot to mention here most probably on this quite exciting weekend
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the sprint has been possible thanks to: the [[Sprints|sprint]] has been possible thanks to:
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 * we still hope for some external contributions  * Debian Society

Debian Med Blend meeting in Lübeck

It seems somewhat amazing, but most of the Debian Med contributors have never met in person before. We think that to maximise the user experience, we shall get together, talk about more than our individual packages and identify some lower and some not-so-low-hanging fruits.

Location, Date

Participants

No

Name

Email

Organisation

Living in

Arrival at

Departure at

1

Steffen Möller

<moeller>

U Lübeck (Debian)

Lübeck (D)

28.01.2011

31.01.2011

2

Andreas Tille

<tille>

Debian

Wernigerode (D)

27.01.2011 20:30

31.01.2011

3

Tim Booth

tbooth_ceh.ac.uk

NERC (Bio-Linux)

Oxford (UK)

28.01.2011

30.01.2011

4

Pjotr Prins

U Wageningen (Debian)

Wageningen (NL)

5

Alan Williams

U Manchester (Taverna)

Manchester (UK)

28.01.2011

31.01.2011

6

Hajo Krabbenhöft

U Lübeck (M.sc. student)

Lübeck (D)

28.01.2011

31.01.2011

7

Yask Gupta

U Lübeck (Ph.D. student)

Lübeck (D)

28.01.2011

31.01.2011

8

Kushal Sejwal

U Lübeck (Ph.D. student)

Würzburg (D)

28.01.2011

31.01.2011

9

Richard Holland

Eaglegenomics (Debian)

Southampton (UK)

28.01.2011

31.01.2001

10

Will Spooner

Eaglegenomics

Babraham (UK)

29.01.2001

31.01.2001

11

Peter Rice

EBI (EMBOSS)

Hinxton (UK)

29.01.2001

30.01.2001

12

Jim Procter

U Dundee (Jalview)

Dundee (UK)

28.01.2011

31.01.2011

13

Michael Banck

<mbanck>

Debian

Munich (D)

28.01.2011

30.01.2011

14

Andreas Hildebrandt

U Saarbrücken (BALLview)

Saarbrücken (D)

28.01.2011

31.01.2011

15

Jürgen Doenitz

U Göttingen (Göbix)

Göttingen (D)

28.01.2011

31.01.2011

16

Tony Travis

U Aberdeen

Aberdeen (UK)

28.01.2011

31.01.2011

17

Christian Steigies

<cts>

U Kiel (Debian)

Kiel (D)

30.01.2011

30.01.2011

18

Antje Krause

FH Bingen

Mainz (D)

28.01.2011

31.01.2011

19

Olivier Sallou

IRISA (symbiose)

Rennes (F)

28.01.2011

31.01.2011

20

David Withers

U Manchester

Manchester (UK)

28.01.2011

31.01.2011

21

Joel Hedlund

U Linköping

Linköping (S)

28.01.2011

31.01.2011

22

Alexander Mestiashvili

TU Dresden

Dresden (D)

23

Manuel Prinz

<manuel>

U Duisburg-Essen (Debian)

Essen (D)

28.01.2011

31.01.2011

24

Pablo Di Tomasso

U Barcelona

Barcelona (E)

Agenda

  • improving our interaction with BioLinux

  • integration of public resources
    • brainstorm about how data.debian.org could help
    • review getData and link it with several packages

  • review of latest developments
    • Bio* roundup
    • Ensembl
    • Immunoinformatics
    • Cloud computing
    • Next generation sequencing
    • BioLib

      • strategies for packaging with minimal redundancy across packages
      • first upload to experimental
    • Taverna

      • formulating joint workflows
      • identify missing packagings
      • plan for packaging Taverna itself
      • external tool activity in Taverna
        • plan for next release of Taverna
        • harmonization with other tool descriptions
        • extension of invocation environments
  • organisational issues
    • ties to pkg-java

    • relation to other Blends

    • identify missing packages and setting priorities
  • strategies for further development
    • thinning the line between Debian and upstream
    • thinning the line between Debian and educators
    • outreach
      • first joint paper recently accepted in BMC Bioinformatics

      • discuss paper on getData

      • papers citing or mentioning us
      • books and book chapters

Program

We should have Saturday (29th) and Sunday (30th) to truly concentrate on our work. Participants should (and most do) arrive on Friday (28th) and leave on Monday (31th). Teams will split and summarise at coffee breaks on their respective status/issues.

Friday is the day for setups, individual training and learning about the novel developments and on-hand insights into problems at another site, allowing for the teams' detailed scheduling for Saturday and Sunday. Monday will be used to wrap up, literally and in writing.

Teams / subgroups

Objectives: Etherpad: http://192.168.1.23:9000/JNsYKrs0X8

  • www.jalview.org related
    • create biolinux/debMed package for Jalview 2.6.x
    • create experimental JABAWS package for biolinux

  • Examine and Resolve dependency issues :
    1. Jmol

Participants:

  1. Jim Procter

    ii. MichaelBanck (Jmol packaging)

''teamTaverna'': Taverna relationship subgroup

Objectives:

  • examine other tool description formats
    • soaplab
    • galaxy
    • biopieces
    • GIMIAS
    • BOINC wrapper
    • any more?
  • how to publish tool descriptions
  • check architecture of external tool activity to ensure extensibility
  • look at data referencing issues
  • Runtime Environment specification
  • roadmap for invocation mechanisms
  • External tool notes

Participants:

  1. Alan Williams
  2. David Withers

Travel

  • Hotel rooms are already reserved for you have not expressed the wish to organise it yourself.
  • When coming by train, use http://reiseauskunft.bahn.de and select Lübeck-Travemünde Hafen as destination. From there it is 150m or so to the Hotel. If you miss that one and exit at Lübeck-Travemünde Strand, at daylight with not too much luggage, just have a 20 minutes walk at the water for about a mile or so till you arrive at the Hotel. Every non-tourist should know it. If it is dark already then just stay seated in the train that is going back and forth to Lübeck and will stop at Travemünde Hafen again, anyway. Lübeck is on the connection between Hamburg and Copenhagen and we have another ICE to Munich plus all the local trains to the well-connected Hamburg.

  • When flying in, be aware of ?RyanAir nicely serving Lübeck. I collect you from there or you can make it by public transport. Hamburg Fuhlsbüttel is about 90km away. There are busses going to Lübeck (look for AUTOKRAFT) but I usually take the trains. When you arrive close in time, you can also share a cab (there are big ones), but let me order it from here .... should then be about 80 Euros.

  • When coming by ferry to Travemünde Skandinavienkai, take a bus from the Terminal to Travemünde itself. Lines 30 or 31 will drop you right in front of the Hotel after two kilometers or so.

Keysigning

When dealing with Debian packages it is always a good idea if you have a GPG key signed by a Debian Developer. So this meeting is a good chance to get your key signed. If you are not comfortable with GPG creation and signing just have a look here:

Make sure you have a printout of your GPG key and a passport at hand. Here are nice templates for business cards where you can include your Fingerprint easily.

Results

A summary was sent to http://lists.debian.org/debian-project/2011/02/msg00026.html. Andreas had already provided a more detailed list. Will blogged about it here. Others may follow suit.

Andreas Tille

  • Short intro for newcomers into Debian Med

  • Worked on packaging of bowtie together with Yask Gupta and Antje Krause which is now in new packages queue

  • Adopted on packaging of mothur which is now in new packages queue

  • Helped Steffen Möller and Tim Booth finalising tm-align which is now in new packages queue

  • Worked together with Alexander Mestiashvili on vianna-rna which advanced a lot in SVN and is close to state where it can be uploaded

  • Created a new Debian Med task Debian Med Next generation sequencing packages and added prospective packages there

  • Spended some time on polishing meme packaging in SVN which is interesting because it contains newer code for our package glam2, but has stalled this effort because meme is non-free

  • Helped Richard Holland and Steffen Möller in finalising ensembl which is now in new packages queue

  • Helped William Spooner to work on wgs-assembler in SVN

  • Discussed with Tim Booth about future cooperation between Debian Med and http://nebc.nerc.ac.uk/tools/bio-linux/

  • Discussed with Olivier Sallou how I can help him packaging biomaj which is subject of further work in SVN

  • Had a lot of interesting discussions with Tony Travis (about Ubuntu and other derivatives), Tim Booth, Pjotr Prins, Joel Hedlund, all the DDs and for sure the other participants
  • Something I forgot to mention here most probably on this quite exciting weekend

Acknowledgements

the sprint has been possible thanks to:

  • travel support by U Manchester, NERC, U Glasgow, Eaglegenomics, European Bioinformatics Institute
  • Debian Society


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