DASWorkshop2011

The 2011 DAS Workshop will be held on 2-4 Marchl at the EBI Hinxton campus.

• Information & registration: http://www.ebi.ac.uk/training/onsite/110302DAS.html

DAS Workshop 2011 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

Time	Title	Speaker	Resources
8:45 - 9:30	Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
9:30 - 09:50	Coffee is served outside the training room
09:50 - 10:00	Welcome and Introduction to the Workshop	Jonathan Warren
10:00 - 10:20	DAS - Introduction/Overview	Andy Jenkinson
10:20 - 10:35	The DAS Game	Rafael Jimenez	The DAS Game
10:35 - 11:25	Hands-on tutorial: using DAS software, 10 minute introduction of some DAS implementations (Bernat)	Bernat Gel, Thomas Down, Jose Villavaces	Implementations. PPT Creating DAS sources from GFF files supplied using easyDAS (Bernat), Viewing DAS sources using Dalliance (Thomas) PDF-or- Dasty3 (Jose) PDF
11:25 - 12:15	Hands-on programming tutorial: Creating a custom DAS source	Gustavo, Andy	10 minute introduction to DAS servers, MyDAS -or- ProServer
12:15 - 13:15	Lunch break
13:15 - 14:50	Tutorial - DAS servers continued	Andy Jenkinson and Gustavo Salazar	Perl(ProServer) and Java(MyDAS)
14:50 - 15:10	Hands on Tutorial The DAS registry: Short introduction talk then hands on tutorial	Jonathan Warren	DAS Registry Tutorial
15:10 - 15:30	Cofee Break
15:30 - 17:15	Hands-on programming tutorial: DAS client libraries, 10 minute introduction	Andy, Rafael, Leyla, Jose, Bernat	Bio::Das::Lite-or- JDAS -or- JSDAS. Each will cover sources, sequence & features using the same examples
17:30	Departure from Campus to Cambridge Travel Lodge and Leisure Park at circa 17:30 hrs.
19:00	Dinner at Browns directions from Travel lodge The Private Dining Room 7.00 pm for 7.30 pm sit down. There is a large bus for this journey at 17.30 and so we encourage campus people who would normally use the campus bus to take the workshop bus. Browns is approx 25 minute walk from the travel lodge we are currently suggesting a pub stop at The Snug on the way. People will be responsible for getting back to their hotel or home after the restaurant.

Day 2

Preliminary schedule where the order and content may still change considerably.

Time	ProjectName	Speaker	Presentation
8:45 - 9:30	Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
09:30 - 10:00	Arrival - Tea, Coffee.
10:00	Opening talk	Tim Hubbard	[]
10:20	Dalliance- a new interactive DAS client	Thomas Down	HTML Slides
10:40	DAS search	Gustavo Salazar	PPT, BTN
11:00	Short break		[]
11:20	easyDAS: a hosted solution for DAS server creation	Bernat Gel	BTN
11:40	Update on the DAS Registry	Jonathan Warren	PPT
12:00	WebApollo: Extending JBrowse to support DAS and genome annotation editing	Gregg Helt	[]
12:15-13:30	Lunch break
13:30	EBI Search	Andy Jenkinson	[]
13:50	Dealing with Personal Genomes using DAS	Manuel Corpas	[]
14:10	Dasty update	Jose Villaveces	PPT
14:30	EMBOSS as a DAS client	Peter Rice, Mahmut Uludag	[]
14:50	Jalview Update	James Proctor	[], []
15:10-15:30	coffee break
15:30	Setting up a BAM based DAS source in GBrowse experience.	Frank Schwach	[], []
15:50	Authentication and Authorization for writeback and secure DAS data sources	Gustavo and Andy	PPT, BTN
16:10	Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups		[]
16:30
16:50
17:10	Bus Leaves for Cambridge Travel Lodge

Day 3

Location is the EBI Training Room

As per other days -Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.

Start at 10am

Departure 16:00 hrs form campus to Travelodge in order for people to get planes and trains etc back home.

Finish at 4pm.

Discussion about fitting alternative data formats into the DAS ecosystem (TAD)

See proposal from 2010 workshop.

Also Binary data support in Dalliance.

Genome alignments in DAS (TAD)

Some background.

Briefly: there's a pretty good alignment data model, but the query syntax currently has a few issues which limit its use for genomic alignments. Most significantly, there's not a good way to fetch a subset of the alignment based on sequence coordinates (e.g. "give me all alignment blocks overlapping the segment 22:30000000,30100000 from human NCBI36").

Improving interactivity of DAS data (TAD)

Can we extend DAS to give better support for more interactive client navigation? Things like next/previous feature buttons.

Customized html labels/pop ups? (JW)

Dasobert 2

Improvements, Schema Driven? (JW, RJ))

Pagination in features response

For search functionality (or in general?) (GS, AJ, RJ, JW, LG)

Philosophy of validation, spec compliance - client vs server expectations

Should the DAS registry say list all sources and just give information on their validity rather than archiving sources. Should clients do all they can to accommodate poor data sources or should they link to validation data and encourage correct data source compliance?(JW)

Also: how aggressively should the registry check for and prune dead datasources? Should there be some expectation of "maximum reasonable response time" for a DAS request? (TAD)

Maxbins strategies

As simple as it can seem, binning strategies for the maxbins attribute are not evident. Although the binning startegy is very dependant on data type, it would be nice to have a small set of standard simple binning algorithms so maxbins can be easily added to new DAS sources. (BG)