Debian Med 2017 Sprint

Location, Date

• January 12-16, 2017

This is an informal co-working and co-learning event, participants are welcome to attend on the days that work for their schedule.

Getting there

Splaiul Independenței 91-95
București 050095
România

Pictures of the walk from the hotel

Google Map, Directions

If arriving via airplane you may have a bus transfer from the plane to the airport terminal, so be prepared for temperatures approaching -13 °C.

Local travel: Taxis won't have working seat belts, Uber will

(M. Crusoe: Normally I recommend anything but Uber, but in Romania it is the only taxi option with seat belts)

Bus information: http://www.ratb.ro/eng/index.php (Google Maps has the schedules as well)

Route planner: http://www.ratb.ro/eng/calcul_ruta_en.php

Metro: run by a different company and it doesn't connect with the airport, so it is unlikely to be useful for most people

Hotel proposal

Olivier: I have a reservation at this place:

Hotel Trianon
Cobalcescu Grigore 9, Sector 1, 010191 Bucarest, Roumanie

http://www.hoteltrianon.ro/

There is free wifi, a restaurant and rooms with twin beds if you want to share a room. It is not far from Splaiul Independenței. Hotel is referenced on booking.com etc..

Food at the venue

TBD

Food nearby

TBD

Participants

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

Agenda

TBD

Personal agendas

M. Crusoe:

1. Getting existing CWL descriptions for tools inside packages, upstreaming them, and writing new descriptions.

2. Proof-of-concept for returning a Debian package name for a software identifier such as RRID (example: https://identifiers.org/rrid/RRID:SCR_001156 ) or bio.tools (example: https://bio.tools/tool/SignalP/version/4.1 )

It would also be great to see progress on packaging the various implementations https://github.com/common-workflow-language/common-workflow-language#implementations

S. Möller:

1. Decide about how to present Debian Med on scientific conferences. Would very much like to implement a routine workflow dynamically on a cloud.
2. Proceed on bio.tools integration with Matus and Jon

A. Tille:

1. Packaging
   • cytoscape
   • freebayes
   • gatk
   • kronatools
   • malt
   • sra-sdk update

   • sift/blimps -> free

   • dcm4che 3

2. Ask sprint participants to join me in nagging upstream to free their code

   • blat
   • paml
   • r-cran-edger (locfit)
   • segemehl
   • trf
   • varscan
3. Mentoring about packaging
4. Fixing bugs
5. Updating existing packages

O. Sallou

1. Update clustal omega
2. Look for biomaj3 packaging
3. CWL discussions
4. Fixing bugs

M. Kalas

1. Representing Debian Med packages in Bio.Tools
   • EDAM annotations in Debian (Med)
   • Export package descriptions in biotoolsSchema. Extended? Living on github?
   • Import to Bio.Tools
   • Directions for further improvements
2. Listing all relevant "bio" data/file formats in EDAM
   • Plus, how to proceed further with registering IANA media types?
3. How to provide a custom sequence annotation DB with minimum effort, using Debian building blocks?
   • This may ideally serve also as a platform for building data formats interoperability and data optimisation on top of it
4. How to convince computational biologists to use Debian?

Reports

Personal Reports

Acknowledgements

the sprint has been possible thanks to:

• the Faculty of Biology, University of Bucharest (Bucharest, Romania)

• the Common Workflow Language project

• donations to the Debian project

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