Difference between revisions of "DASWorkshop2011"

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|Opening talk  
 
|Opening talk  
 
|Tim Hubbard
 
|Tim Hubbard
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/th201103_das_workshop.pdf PDF]
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/th201103_das_workshop.pdf PDF][http://www.scivee.tv/node/28137 Video]
 
|-
 
|-
 
|10:20
 
|10:20
 
|Dalliance- a new interactive DAS client
 
|Dalliance- a new interactive DAS client
 
|Thomas Down
 
|Thomas Down
−
|[http://www.biodalliance.org/people/thomas/dalliance-201103/dalliance.html HTML Slides]
+
|[http://www.biodalliance.org/people/thomas/dalliance-201103/dalliance.html HTML Slides][http://www.scivee.tv/node/28151 Video]
 
|-
 
|-
 
|10:40
 
|10:40
 
|DAS search
 
|DAS search
 
|Gustavo Salazar
 
|Gustavo Salazar
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/41/gustavo_advancesearch.ppt PPT], [http://www.biotnet.org/training-materials/das-advance-search BTN]
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/41/gustavo_advancesearch.ppt PPT], [http://www.biotnet.org/training-materials/das-advance-search BTN][http://www.scivee.tv/node/28152 Video]
 
|-
 
|-
 
|11:00
 
|11:00
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|easyDAS: a hosted solution for DAS server creation
 
|easyDAS: a hosted solution for DAS server creation
 
|Bernat Gel
 
|Bernat Gel
−
|[http://www.biotnet.org/training-materials/easydas-presentation BTN]
+
|[http://www.biotnet.org/training-materials/easydas-presentation BTN][http://www.scivee.tv/node/28108 Video]
 
|-
 
|-
 
|11:40
 
|11:40
 
|Update on the DAS Registry
 
|Update on the DAS Registry
 
|Jonathan Warren
 
|Jonathan Warren
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/das_registry_update2.pptx PPT]
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/das_registry_update2.pptx PPT][http://www.scivee.tv/node/28112 Video]
 
|-
 
|-
 
|12:00
 
|12:00
 
|WebApollo: Extending JBrowse to support DAS and genome annotation editing
 
|WebApollo: Extending JBrowse to support DAS and genome annotation editing
 
|Gregg Helt
 
|Gregg Helt
−
|[http://s3.amazonaws.com/WebApollo/presentations/WebApollo+-+DAS+Workshop+2011.pptx PPTX], [http://s3.amazonaws.com/WebApollo/presentations/WebApollo+-+DAS+Workshop+2011.pdf PDF]
+
|[http://s3.amazonaws.com/WebApollo/presentations/WebApollo+-+DAS+Workshop+2011.pptx PPTX], [http://s3.amazonaws.com/WebApollo/presentations/WebApollo+-+DAS+Workshop+2011.pdf PDF][http://www.scivee.tv/node/28130 Video]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|12:15-13:30
 
|12:15-13:30
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|EBI Search
 
|EBI Search
 
|Andy Jenkinson
 
|Andy Jenkinson
−
|[http://www.ebi.ac.uk/~aj/das_workshop_2011/EBI-Search.pptx PPTX]
+
|[http://www.ebi.ac.uk/~aj/das_workshop_2011/EBI-Search.pptx PPTX][http://www.scivee.tv/node/28153 Video]
 
|-
 
|-
 
|13:50
 
|13:50
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|Dasty update
 
|Dasty update
 
|Jose Villaveces
 
|Jose Villaveces
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/42/dasty_1.ppt PPT]
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/42/dasty_1.ppt PPT][http://www.scivee.tv/node/28154 Video]
 
|-
 
|-
 
|14:30
 
|14:30
 
|EMBOSS as a DAS client
 
|EMBOSS as a DAS client
 
|Peter Rice, Mahmut Uludag
 
|Peter Rice, Mahmut Uludag
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/premboss-das2011.ppt PPT]
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/premboss-das2011.ppt PPT][http://www.scivee.tv/node/28159 Video]
 
|-
 
|-
 
|14:50
 
|14:50
 
|Jalview Update
 
|Jalview Update
 
|James Procter
 
|James Procter
−
|[http://www.jalview.org/talks/2011_DASJalviewUpdate.pdf PDF]
+
|[http://www.jalview.org/talks/2011_DASJalviewUpdate.pdf PDF][http://www.scivee.tv/node/28160 Video]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|15:10-15:30
 
|15:10-15:30
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|Setting up a BAM based DAS source in GBrowse experience.
 
|Setting up a BAM based DAS source in GBrowse experience.
 
|Frank Schwach
 
|Frank Schwach
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/fsdas_workshop_march11.pdf PDF], []
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/38/fsdas_workshop_march11.pdf PDF], [http://www.scivee.tv/node/28133 Video]
 
|-
 
|-
 
|15:50
 
|15:50
 
|Authentication and Authorization for writeback and secure DAS data sources
 
|Authentication and Authorization for writeback and secure DAS data sources
 
|Gustavo and Andy
 
|Gustavo and Andy
−
|[http://www.biotnet.org/sites/biotnet.org/files/documents/41/dassecurity.ppt PPT], [http://www.biotnet.org/training-materials/das-security BTN]
+
|[http://www.biotnet.org/sites/biotnet.org/files/documents/41/dassecurity.ppt PPT], [http://www.biotnet.org/training-materials/das-security BTN][http://www.scivee.tv/node/28136 Video]
 
|-
 
|-
 
|16:10
 
|16:10
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==Day 3==
 
==Day 3==
 +
* [[DASWorkshop2011/day3/topics|Suggested Topics]]
 +
* [[DASWorkshop2011/day3/minutes|Minutes]]
 +
* [[DASWorkshop2011/day3/actionplan|Action Plan]]
 +
* [[DASWorkshop2011/day3/paperproposal|DAS Paper proposal]]
 +
 +
 
Location is the EBI Training Room
 
Location is the EBI Training Room
 
  As per other days -Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
 
  As per other days -Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
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  Departure 16:00 hrs form campus to Travelodge in order for people to get planes and trains etc back home.
 
  Departure 16:00 hrs form campus to Travelodge in order for people to get planes and trains etc back home.
 
Finish at 4pm.
 
Finish at 4pm.
−
 
−
===Suggested Topics:===
 
−
 
−
==Discussion about fitting alternative data formats into the DAS ecosystem (TAD)==
 
−
 
−
See [[DAS1.6E#Support_for_alternative_content_formats|proposal from 2010 workshop]].
 
−
 
−
Also [http://www.biodalliance.org/bin.html Binary data support in Dalliance].
 
−
 
−
==Security - authorization and authentication for clients, servers, registry (GS, AJ, JW)==
 
−
==Genome alignments in DAS (TAD)==
 
−
[[DAS1.6E#Alignment|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)
 

Latest revision as of 10:40, 5 April 2011

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


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 Introduction Technical Introduction
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 PDFVideo
10:20 Dalliance- a new interactive DAS client Thomas Down HTML SlidesVideo
10:40 DAS search Gustavo Salazar PPT, BTNVideo
11:00 Short break []
11:20 easyDAS: a hosted solution for DAS server creation Bernat Gel BTNVideo
11:40 Update on the DAS Registry Jonathan Warren PPTVideo
12:00 WebApollo: Extending JBrowse to support DAS and genome annotation editing Gregg Helt PPTX, PDFVideo
12:15-13:30 Lunch break
13:30 EBI Search Andy Jenkinson PPTXVideo
13:50 Dealing with Personal Genomes using DAS Manuel Corpas []
14:10 Dasty update Jose Villaveces PPTVideo
14:30 EMBOSS as a DAS client Peter Rice, Mahmut Uludag PPTVideo
14:50 Jalview Update James Procter PDFVideo
15:10-15:30 coffee break
15:30 Setting up a BAM based DAS source in GBrowse experience. Frank Schwach PDF, Video
15:50 Authentication and Authorization for writeback and secure DAS data sources Gustavo and Andy PPT, BTNVideo
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.

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