Debian Med 2016 Sprint

We fill this place with Life!

Location, Date

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

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

Participants

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

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?

Personal agendas

• a.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
• Sascha
  • Prepare a free alternative to barrnap's non-free HMMs
  • get into Groovy/Java packaging, work on Nextflow + deps
  • get some first hand advice on backports + Ubuntu interaction
  • if time is left: get all my packages autopkgtested

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.

Acknowledgements

the sprint has been possible thanks to:

• sponsors of DebConf15

• donations to the Debian project

• sponsor ...
• venue ...
• etc ...

CategorySprint