Difference between revisions of "DASWorkshop2011"
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| − | | [http://www.biotnet.org/training-materials/bio-das- | + | | [http://www.biotnet.org/training-materials/bio-das-lite-tutorial Bio::Das::Lite]-or- [http://www.biotnet.org/training-materials/jdas JDAS] -or- [http://code.google.com/p/jsdas/wiki/tutorial JSDAS]. Each will cover sources, sequence & features using the same examples |
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Revision as of 15:47, 2 March 2011
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
Contents
- 1 DAS Workshop 2011 Schedule
- 1.1 Day 1
- 1.2 Day 2
- 1.3 Day 3
- 1.4 Discussion about fitting alternative data formats into the DAS ecosystem (TAD)
- 1.5 Security - authorization and authentication for clients, servers, registry (GS, AJ, JW)
- 1.6 Genome alignments in DAS (TAD)
- 1.7 Improving interactivity of DAS data (TAD)
- 1.8 Dasobert 2
- 1.9 Pagination in features response
- 1.10 Philosophy of validation, spec compliance - client vs server expectations
DAS Workshop 2011 Schedule
The first 2 days will be held in the EBI training room. 3rd day room to be announced.
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 | [] |
| 10:40 | DAS search | Gustavo Salazar | PPT, BTN |
| 11:00 | Short break | [] | |
| 11:20 | easyDAS: a hosted solution for DAS server creation | Bernat Gel | PPT |
| 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 Autorization for writeback and secure DAS data sources | Gustavo and Andy | [], [] |
| 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 Floating room in the Morgan Building at the Sanger institute.
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 Travellodge in order for people to get planes and trains etc back home.
Finish at 4pm.
Suggested Topics:
Discussion about fitting alternative data formats into the DAS ecosystem (TAD)
See proposal from 2010 workshop.
Also Binary data support in Dalliance.
Security - authorization and authentication for clients, servers, registry (GS, AJ, JW)
Genome alignments in DAS (TAD)
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)
