DAS Workshop 2012 Schedule

All 3 days will be held in the EBI training room.

Day 1

Some knowledge/experience of PERL or Java and or Javascript would be beneficial for the hands on training day.

Example DAS commands can be found here as a DAS quick reference guide: DAS examples

The draft schedule for Day 1 is below. Please note that session times are a rough indication only and will vary according to progress on the day.

Time	Title	Speaker	Resources
9:15	Welcome and Information	JW
9:20	DAS - Introduction/Overview	AJ	DAS Introduction
9:40	The DAS Game	LG	The DAS Game
10:00	DAS - Technical Introduction	AJ	DAS Technical Introduction
10:20	Coffee break
10:40	Using DAS software, an introduction to some DAS implementations	RJ	Implementations Introduction
11:00	Demo: creating a DAS source from a file with EasyDAS	RJ	easyDAS tutorial
11:10	Hands-on: viewing DAS sources with Ensembl	AJ	DAS in Ensembl
11:20	Introduction to DAS server frameworks	JW	10 minute introduction to DAS servers
11:30	Hands-on programming tutorial: Creating a custom DAS source	AJ/JW/LG/RJ	MyDAS -or- ProServer
12:30	Lunch break
13:30	Tutorial - DAS servers continued	AJ/JW/LG/RJ
14:50	Introduction and hands-on: The DAS registry	JW	DAS Registry Tutorial
15:10	Coffee Break
15:30	Introduction to DAS client libraries	LG	Introduction to client libraries
15:40	Hands-on programming tutorial: DAS client libraries	AJ/JW/LG/RJ	Bio::Das::Lite-or- JDAS -or- JSDAS. Each will cover sources, sequence & features using the same examples
17:30	Departure from Campus to Whittlesford Station/Holiday Inn at circa 17:30 hrs.
19:00	Dinner at the Red Lion Whittlesford 7.00 pm for 7.30 pm sit down.

Day 2 and Day 3: Developer Hackathon

This year we will not have a day of talks as in previous years. Instead, both day 2 and day 3 will be “DAS developers’ days”. This may include some updates on progress since the last workshop, discussions, and a code hackathon. The exact format is yet to be decided.

Recent developments since the last workshop

DAS writeback
DAS search
Registry CRUD via a web service (get, post, put, delete) (JW)
Alternative content negotiation (e.g. the Registry supports JSON for all requests and responses) (AJ/JW)
Authentication/encryption in ProServer (AJ)

Suggestions for topics on Developers Days

Please feel free to add suggestions for discussions or code sprints.

JSON roll out to other servers and clients? (JW)
Firming up of the authentication DAS standard so the registry and writeback are consistent (JW)
Add support for conditional get (If-Modified-Since - reply only if modified since the modified since header) or ETags? (JW)
High density simple features such as SNPs - vcf format or simple json format without method and stop? (JW)

DAS Registry - new architecture and capabilities (JW)
DAS in personal genomics (MC/JW/BG)
Secure DAS trial (David Martin, Jim Procter, Thomas Down)

Useful links

DAS 1.6 specification spec

RelaxNG document for validation of features: relaxng

6 easy steps to setting up a genotype data source in the cloud/tomcat server’

[‘Sanger Proserver Adapters’ https://sangeradaptors.svn.sourceforge.net/svnroot/sangeradaptors/Bio/Das/ProServer/SourceAdaptor/]

Images

Pictures, mostly from day 2 are here http://www.flickr.com/photos/davidmam/sets/72157629110016398/

Outcomes from workshop 2012

A Ruby server is in development that implement the sources, sequence, features, types and soon entry_points request/responses : https://github.com/alexkalderimis/RubyDAS Bastian Greshaek and Alex Kalderimis

Mixed mode authentication for DAS servers specification http://www.biodas.org/wiki/DAS1.6E#Authentication. David Martin, Jim Proctor, Thomas Down, Andy Jenkinson.

SOLR based MyDAS gff current svn repository version of MyDAS. Rafael Jimenez

Firming up of the DAS JSON format (decided on “real” JSON rather than a convert from xml). Thomas Down, Andy Jenkinson, Jonathan warren.

DAS server code is being added to the Intermine project (MyDAS based). Alex Kalderimis

DAS support in the VectorNTI Genome Bench software is being updated. Ajish A Kahar

Additions to the JDAS (Java DAS library) code including authentication mixed mode mentioned above. Jim Procter, Leyla Garcia, Jonathan Warren.