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  * Prepare a free alternative to barrnap's non-free HMMs   * --(Prepare a free alternative to barrnap's non-free HMMs)--

Debian Med 2016 Sprint

We fill this place with Life!

hotel conference room it is nice out there

Location, Date

  • Thu 4th - Sun 7th February 2016
  • Sinatur Hotel Frederiksdal, Lyngby

Google maps http://www.sinatur.dk trip adivsor

A meeting room will be available from the morning of Thu, Feb 4. There is a projector and multiple extension cords. WiFi is up to standard (new installation).

Getting there

Public transportation:

  • From Copenhagen Airport to Nørreport Station: Metro
  • From Nørreport Station to Lyngby: S-train lines A and E
  • From Lyngby to Frederiksdal: bus 191 every 30min

The venue is a few minutes walk from the bus stop.

Alternatives: Taxi from Lyngby to venue is around DKK100. Or the adventurous may enjoy a pleasant hike from Lyngby instead.

Food at the venue

lunch: DKK50-225 ranging from a sandwich to full buffet

dinner: 6-9pm (not Sunday), DKK175-425, depending of the number of dishes (1-5)

Food nearby

Restaurant Nybro Kro, http://www.nybrokro.dk/, Nybrovej 376 - 2800 Kgs. Lyngby. Tel. +45 4587 0149, 20min walk or a few minutes by bus from the venue

Frederiksdal Fribad, fribad.dk, Frederiksdal Badesti 1, 2830 Virum, +45 45 83 81 85, 10min walk from the venue (inquiry about opening hours sent by email, no answer yet indicating they may be closed for the winter)

Participants

(tentative/final list of participants here before/after the sprint)

No

Name

Email

confirmed

booked accom.

Organisation

Living in

Arrival at

Departure at

1

Andreas Tille

tille at d.o

yes

via DTU

Debian

Germany

Thu, landing 10:15

Mon

2

Steffen Möller

moeller at d.o

Debian, Uni Rostock

Germany

3

Jon Ison

jison@cbs.dtu.dk

yes

DTU, ELIXIR-DK

GB

Thu morning

Sun afternoon

4

Kristoffer Rapacki

rapacki@cbs.dtu.dk

yes

DTU, ELIXIR-DK

Denmark

Thu

Sun

5

Sascha Steinbiss

sascha at steinbiss.name

yes

via DTU

WTSI

UK

Thu, landing 15:05

Sun, flight departs 19:00

6

Michael R. Crusoe

crusoe@ucdavis.edu

yes

via DTU

UCDavis; Common Workflow Language

Romania

Thu after 18

Mon

7

Luca Clivio

luca.clivio@marionegri.it

yes

Mario Negri Institute for Pharmacologic Research

Italy

Thu

Sun

8

Kevin Murray

spam@kdmurray.id.au

yes

Via DTU

CPEB, Australian National University

Australia

Thu after 18

Sat

9

Ross Gammon

retail@the-gammons.net

Not required

Debian

Denmark

Sat

Sun

10

Ruben Undheim

ruben.undheim@gmail.com

yes

Via DTU

Debian

Norway

Thu

Sun

11

Fabian Klötzl

kloetzl@evolbio.mpg.de

yes

via DTU

MPI for Evolutionary Biology

Germany

Thu

Sun

12

Wojtek Dabrowski

dabrowskiw@rki.de

yes

Robert Koch Institute

Germany

Thu

Fri evening, take off 19:45

13

Matúš Kalaš

matus.kalas@uib.no

yes

booked by DTU

University of Bergen

Norway

Thu, landing 10:10

Sat morning, take off 09:15

14

Hervé Ménager

hmenager@pasteur.fr

yes

Institut Pasteur

France

Thu

Fri

15

Petter Reinholdtsen

pere at d.o

no

Debian

Norway

Thu

Sun

16

Ioan Eugen Stan

eu at ieugen dot ro

yes

AirBnB

Debian

România

Landing Thu 17:00

Tue Take-off 11:00

Agenda

(tentative/final agenda here before/after the sprint)

  • Link to the ELIXIR-DB
    • workflow for automated updates
    • review of contributed annotations
  • Presentation of Debian Med / Bio-Linux / ... (?) on international conferences
    • booth
    • software collection
    • supporting-groups/people collection
    • workflows
  • Ideas for interactions with other blends? Debian initiatives?
    • Astronomy shares handling of large public data files
    • ARM and PowerPC vendors should have an interest to see the Debian Bioinformatics world ported. Where are they?
    • Discussing layout of tasks pages

Personal agendas

  • Andreas Tille
    • check for other packages ?BioLinux might need

    • Mentoring newcomers
    • General bug fixing
    • Finalising web sentiel tasks pages from GSoC
    • Trying to understand debhelper and make use of it for edam files and references in debian/upstream/metadata files
    • Teammetrics: Sponsoring graph, time dependent graph for maintainer per package, recently active maintainers
    • Fix ${R:depends} to not only add the r-base package version but also the packages specified in Build-Depends
    • Write script to check JSON syntax of debian/upstream/metadata files
    • Finalise new version of seqan
    • Check binary JARs of igv to see if it can be freed
    • New upstream version of sitplus with split off library
    • Cleanup tasks files (help needed!)
  • Sascha
    • Prepare a free alternative to barrnap's non-free HMMs

    • get into Groovy/Java packaging, work on Nextflow
      • Finish grengine as a dependency

      • Contact upstream about dropping capsule support

    • get some first hand advice on backports + Ubuntu interaction
    • if not done until then: update htslib + samtools to 1.3 (requirement for reapr)

    • try to get SPAdes working (requirement for circlator and ariba)
    • Key signing
  • l.clivio
    • asking help for packaging heavybase, the peer to peer database for data sharing in clinical trials
    • exploring/studying/discussing with anyone may be interested algorithms for fully decentralized and secure peer to peer data sharing database for big data
  • K Murray
    • Get seqan packaged optimally and working
    • Pop many mayhem bugs
    • Investigate packaging TASSEL
    • Finish my unfinished packages
  • Wojtek Dabrowski
    • Talk about benchmarking collaboration between Debian Med, ELIXIR, GMI, RKI and potentially de.NBI - preferably with a short presentation on Friday
  • Fabian Klötzl
    • Prepare new upstream release of andi and update package
    • Create package for indelible
    • Otherwise I am free and happy to accept tasks from others
  • Michael R. Crusoe
    • Generating bio.tools descriptions from Common Workflow Language tool descriptions
    • Generating a debian/upstream/metadata template from a CWL tool description
    • Packaging the CWL reference implementation

Collaboration with ELIXIR

The Tools and Data Services Registry provides essential scientific and technical information about analytical tools and data services for bioinformatics. The registry is provided by a community effort coordinated by the Danish node of ELIXIR - the European infrastructure for biological information. Debian Med already includes packages for many key tools in bioinformatics and we’re working to forge a vibrant collaboration between ELIXIR and Debian Med to ensure:

  • the package descriptions are annotated to the standard required by the registry and

  • establish a permanent mechanism for registration, updates and sharing of the package descriptions

To these ends, ELIXIR-DK would like to support this sprint by sponsoring an “extra day” (Thu - Fri) dedicated to registry work:

  • ELIXIR-DK will pay for the meeting room at the hotel on Thursday 4th - Sunday 7th inclusive
  • In addition, for anyone arriving on Thursday Feb 4th to help out, ELIXIR-DK will pay for a European flight and a hotel room and evening meal for Thursday night

In practical terms, package registration should be straightforward given a sensible data sharing mechanism, which we can settle at the meeting. The time-consuming part is the annotation, so we’d like to focus on 10 attributes which are mandatory in the ELIXIR registry. This includes terms from the EDAM vocabulary to describe the package “topic” (broad scientific category), “operation” (exactly what a tool does) and “data” (input and output type of data) which can also include “format” (specific data formats): EDAM developers will be on-hand to help with this.

Any questions? For enquiries about venue, hotel etc. please mail Myhanh Nguyen. For technical enquries please mail registry@elixir-dk.org, alternatively mail Jon Ison and Kristoffer Rapacki directly.

Reports

(pointers to communication about the sprint)

  • announcement: (e.g. link to lists.d.o archives)
  • report: (e.g. link to lists.d.o archives)
  • other:
  • other:
  • ...
  • report proposal by Luca Clivio: Decentralized data management in 'hostile' environments: safety and security for clinical research data sharing in hospitals with commodity hardware surviving the IT restrictions.

Personal Reports

Andreas Tille

  • Sponsored uploads done:
    • poretools
    • libzstd
    • roary
    • snakemake
    • samtools
    • salmon
    • trinityrnaseq
    • python-rdflib-jsonld
    • khmer
    • indelible
    • axe-demultiplexer
  • Uploaded:
    • ngs-sdk
  • Introduction into Debian infrastructure (together with Petter and Steffen)
  • Wrote SQL query against UDD to export all data relevant for EDAM

Acknowledgements

the sprint has been possible thanks to:


CategorySprint