Difference between revisions of "DASWorkshop2010"

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The 2010 DAS Workshop will be held on 7-9 April at the EBI Hinxton campus.
 +
* Information & registration: http://www.ebi.ac.uk/training/onsite/DAS_070410.html
 +
 +
 
=DAS Workshop 2010 Schedule=
 
=DAS Workshop 2010 Schedule=
 +
All 3 days will be held in the EBI training room.
 +
==Day 1==
  
 +
 +
{| class="wikitable" border="1"
 +
|- style="background:silver"
 +
! width="100px"|Time
 +
! Title
 +
! Speaker
 +
! Resources
 +
|-  style="background:#ffdead;"
 +
| 8:45 - 9:30
 +
| colspan="3" | Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
 +
|- style="background:#ffdead;"
 +
| 9:30 - 10:00
 +
| colspan="3" | Coffee is served outside the training room
 +
|-
 +
| 10:00 - 10:10
 +
| Welcome and Introduction to the Workshop
 +
| Jonathan Warren
 +
|
 +
|-
 +
| 10:10 - 10:30
 +
| DAS - Introduction/Overview
 +
| Andy Jenkinson
 +
| [http://www.ebi.ac.uk/~aj/das_workshop_2010/DAS-Introduction.pptx Basic Introduction] [http://www.ebi.ac.uk/~aj/das_workshop_2010/DAS-Introduction-Technical.pptx Technical Introduction]
 +
|-
 +
| 10:30 - 10:40
 +
| The DAS Game
 +
| Rafael Jimenez
 +
| [http://www.ebi.ac.uk/~rafael/talks/2010-04-07_workshop_das/dasGame/ Game cards]
 +
|-
 +
| 10:40 - 11:40
 +
| Hands on DAS Server Tutorials - Setting up a quick source for sharing data with your colleagues using Proserver or MyDAS - The room will be split into two groups: one for Java and one for Perl.
 +
| Andy Jenkinson, Gustavo Salazar
 +
| Introduction talk: [http://oware.cbio.uct.ac.za/~gustavo/DASservers.ppt PPT] Java:[http://code.google.com/p/mydas/wiki/MyDASTutorial MyDAS Part 1] Perl:[http://www.ebi.ac.uk/~aj/das_workshop_2010/proserver_tutorial_1.html ProServer Part 1]
 +
|-
 +
| 11:40 - 12:15
 +
| The DAS Registry and registering your source
 +
| Jonathan Warren
 +
|[http://www.biodas.org/wiki/RegistryTutorial2010 RegistryTutorial2010]
 +
|- style="background:#ffdead;"
 +
| 12:15 - 13:15
 +
| colspan="3" | Lunch break
 +
|-
 +
| 13:15 - 14:15
 +
| Tutorial - DAS servers continued
 +
| Andy Jenkinson, Rafael Jimenez, Gustavo Salazar
 +
| Java: [http://code.google.com/p/mydas/wiki/MyDASTutorial2ndPart MyDAS Part 2][http://code.google.com/p/mydas/wiki/MyDASTutorial3rdPart MyDAS Part 3]Perl:[http://www.ebi.ac.uk/~aj/das_workshop_2010/proserver_tutorial_2.html ProServer Part 2][http://www.ebi.ac.uk/~aj/das_workshop_2010/proserver_tutorial_3.html ProServer Part 3]
 +
|-
 +
|14:15 - 14:35
 +
|DAS clients - Putting it all together
 +
|Rob Finn
 +
| [http://www.biodas.org/workshop_2009/20090309ClientSpecReview.ppt 2009 Powerpoint]<br/>[http://www.biodas.org/workshop_2009/20090309ClientSpecReview.pdf 2009 PDF]
 +
|-
 +
|14:35 - 15:10
 +
|Talk and Tutorial -DAS client libraries to query DAS sources
 +
|Andy Jenkinson, Rafael Jimenez, Jose Villaveces
 +
|Javascript:[http://www.ebi.ac.uk/~jvillave/wiki/doku.php?id=jsdas JSDAS Tutorial], Java:[http://www.ebi.ac.uk/~rafael/dokuwiki/doku.php?id=das:courses:dasobert Dasobert Tutorial], Perl:[http://www.ebi.ac.uk/~aj/das_workshop_2010/daslite_tutorial.html Bio::Das::Lite]
 +
|-style="background:#ffdead;"
 +
| 15:10 - 15:30
 +
| colspan="3" | Cofee Break
 +
|-
 +
| 15:30 - 17:00
 +
| colspan="3" | Hands On Tutorial - continued
 +
|-  style="background:#ffdead;"
 +
|17:15
 +
| colspan="3" |Departure from Campus to Cambridge Leisure Park at circa 17:15 hrs.
 +
|}
  
 
==Day 2==
 
==Day 2==
Line 10: Line 82:
 
! Speaker
 
! Speaker
 
! Presentation
 
! Presentation
 +
|- style="background:#ffdead;"
 +
| 8:45 - 9:30
 +
| colspan="3" | Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
| 09:30 - 10:00
 
| 09:30 - 10:00
 
| colspan="3" | Arrival - Tea, Coffee.
 
| colspan="3" | Arrival - Tea, Coffee.
−
|-  
+
|-
 
|10:00
 
|10:00
 
|Opening talk  
 
|Opening talk  
 
|Tim Hubbard
 
|Tim Hubbard
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/200903DASworkshop.ppt presentation]
+
|[]
 
|-
 
|-
 
|10:20
 
|10:20
−
|Collaborative Annotation tool (MaDAS)
+
|Collaborative genomics with DAS- a new interactive DAS client
−
|Victor de la Torre
+
|Thomas Down
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/MaDAS_victor_de_la_torre.pptx presentation]
+
|[]
 
|-
 
|-
 
|10:40
 
|10:40
−
|Jalview / VAMSAS
+
|Progress to report on linking EMBOSS and DAS
−
|Jim Procter / Geoff Barton
+
|Peter Rice
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/Jalview_2009_DAS.pdf presentation]
+
|[http://www.biodas.org/workshop_2010/rice_emboss.ppt PPT]
 
|-
 
|-
 
|11:00
 
|11:00
−
|Pfam
+
|1.6 Spec Summary
−
|Rob Finn
+
|Jonathan Warren
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/20090309PfamDasWorkShop.ppt presentation]
+
|[http://www.biodas.org/workshop_2010/warren_1.6spec.ppt PPT]
 
|-
 
|-
 
|11:20
 
|11:20
−
|DASgenexp
+
|easyDAS: a hosted solution for DAS server creation
 
|Bernat Gel
 
|Bernat Gel
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/DASGenExp3.ppt presentation]
+
|[http://www.biodas.org/workshop_2010/bernat_easydas.ppt PPT]
 
|-
 
|-
 
|11:40
 
|11:40
−
|Dasty2
+
|Update on the DAS Registry
−
|Rafael Jimenez
+
|Jonathan Warren
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/rjimenez_dasworkshop2009_dasty2.ppt presentation]
+
|[http://www.biodas.org/workshop_2010/warren_registry.ppt PPT]
 
|-
 
|-
 
|12:00
 
|12:00
−
|EMBOSS as an efficient DAS annotation source
+
|DAS service to provide information on 3D motifs- PDBe
−
|Peter Rice, Mahmut Uludag
+
|Adel Golovin
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/DAS-Rice-Uludag.ppt presentation]
+
|[]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|12:15-13:30
 
|12:15-13:30
Line 53: Line 128:
 
|-
 
|-
 
|13:30
 
|13:30
−
|Ensembl
+
|DAS Writeback and its integration in Dasty2 as a proof of concept
−
|James Smith
+
|Gustavo Salazar
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/2009-das-talk-smith.ppt presentation]
+
|[http://www.biodas.org/workshop_2010/gustavo_writeback.ppt PPT] [http://www.slideshare.net/4ndr01d3/das-writeback SS]
 
|-
 
|-
 
|13:50
 
|13:50
−
|Integration of info on gene expression and its temporal and spatial localization
+
|KaryoDAS: An Interactive Genome Visualization Tool Using DECIPHER Data
−
|Jose Ramon Macias
+
|Manuel Corpas (and Eugene Bragin)
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/20090310_DAS_Workshop_DASxVO.ppt presentation]
+
|[http://www.biodas.org/workshop_2010/corpas_decipher.ppt PPT]
 
|-
 
|-
 
|14:10
 
|14:10
−
|DAS - writeback
+
|jsDAS: A javascript DAS client library
−
|Gustavo Salazar
+
|Jose Villaveces (and Bernat Gel)
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/DASwriteback.pdf presentation]
+
|[http://www.biodas.org/workshop_2010/jose_jsdas.ppt PPT]
 
|-
 
|-
 
|14:30
 
|14:30
 
|Interaction DAS
 
|Interaction DAS
 
|Hagen Blankenburg
 
|Hagen Blankenburg
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/20090310_Blankenburg_DASMI.pdf presentation]
+
|[http://www.biodas.org/workshop_2010/hagen_dasformi.pdf PDF]
 
|-
 
|-
 
|14:50
 
|14:50
−
|DAS for ENCODE data coordination
+
|Data integration in ENFIN using standards; the EnCore DAS service
−
|Felix Kokocinski
+
|Rafael Jimenez
−
|[http://www.sanger.ac.uk/~fsk/DAS_workshop09.pdf pdf]
+
|[http://www.ebi.ac.uk/~rafael/talks/2010-04-07_workshop_das/2010-07-07_workshop_das_encore.pdf PDF], [http://www.ebi.ac.uk/~rafael/talks/2010-04-07_workshop_das/2010-07-07_workshop_das_encore.ppt PPT]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|15:10-15:30
 
|15:10-15:30
Line 81: Line 156:
 
|-
 
|-
 
|15:30
 
|15:30
−
|A web resource for selecting epitopes for antibodies
+
|<del>Text Mining DAS source</del>
−
|Niall Haslam
+
|<del>Maximilian Haussler</del>
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/NiallHaslamDAS2009.pdf presentation]
+
|
 
|-
 
|-
 
|15:50
 
|15:50
−
|DAS Searches
+
|Update on the collaborative, web-based version of Apollo
−
|Andreas Prlic
+
|Gregg Helt
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/DAS_searches_20090310.pdf presentation]
+
|[]
 
|-
 
|-
 
|16:10
 
|16:10
−
|A karyotype DAS client
+
|From Pfam Das Alignments to Widgets
−
|Rafael Jimenez
+
|Prasad Gunasekaran
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/rjimenez_dasworkshop2009_KDC.ppt presentation]
+
|[http://www.biodas.org/workshop_2010/prasad_pfam.pdf PDF]
 
|-
 
|-
 
|16:30
 
|16:30
−
|DASher, a standalone Java client for DAS protein sequence features
+
|Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups
−
|David Messina
+
|
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/Messina_DASconf09.keynote.zip presentation] [http://www.sanger.ac.uk/Software/analysis/das/presentations/Messina_DASconf09.pdf pdf]
+
|
 
|-
 
|-
 
|16:50
 
|16:50
−
|Data Federation - BioMart & DAS
+
|
−
|Syed Haider
+
|
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/BioMart_DAS_2009.ppt presentation]
+
|
−
|-
+
|- style="background:#ffdead;"
 
|17:10
 
|17:10
−
|Trellis DAS2 framework- which includes the DAS1-->DAS2 proxy and alpha UCSC DAS2 server
+
|Bus Leaves for Cambridge Travel Lodge
−
|Gregg Helt
+
|
−
|[http://www.sanger.ac.uk/Software/analysis/das/presentations/Trellis_Mar2009.pptx presentation]
+
|
−
|-
+
|- style="background:#ffdead;"
−
|17:30
+
|19:00
−
|Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups
+
|Dinner at [http://restaurantalimentum.co.uk/index.php Alimentum] The Private Dining Room 7.00 pm for 7.30 pm sit down.
 
|
 
|
 
|
 
|
 
|-
 
|-
 
|}
 
|}
 +
 +
==Day 3==
 +
 +
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:===
 +
 +
[http://www.doodle.com/cvb5btwmrzz9avgh doodle poll for expressing interest in topics]
 +
 +
Content negotiation and efficient data formats
 +
 +
how / if the big amounts data can be served via das
 +
 +
DAS for high-density quantitative data.
 +
 +
1: From molecules to sets. 2: Other dimensions: Samples.
 +
 +
Writing a DAS client in C
 +
 +
Running DAS on amazon or google app engine. And seeing what changes have to be made to the dazzle code to enable this. I'd favour app engine.
 +
 +
speeding up annotation retrieval for multiple segment IDs (e.g. retrieving all features for a big alignment)
 +
 +
using jsDas with JalviewLite
 +
 +
The semantic web, RDF and DAS.
 +
 +
DAS authentication and security
 +
 +
Actual topics that we discussed:
 +
 +
Authentication and security - see the proposed spec.[http://www.biodas.org/wiki/DAS1.6E#Authentication|spec]
 +
 +
Content Negogation and efficient formats- see proposal spec.[http://www.biodas.org/wiki/DAS1.6E#Support_for_alternative_content_formats 1.6E content neg].
 +
 +
RDF.

Latest revision as of 10:14, 22 February 2011

The 2010 DAS Workshop will be held on 7-9 April at the EBI Hinxton campus.


DAS Workshop 2010 Schedule

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

Day 1

Time Title Speaker Resources
8:45 - 9:30 Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
9:30 - 10:00 Coffee is served outside the training room
10:00 - 10:10 Welcome and Introduction to the Workshop Jonathan Warren
10:10 - 10:30 DAS - Introduction/Overview Andy Jenkinson Basic Introduction Technical Introduction
10:30 - 10:40 The DAS Game Rafael Jimenez Game cards
10:40 - 11:40 Hands on DAS Server Tutorials - Setting up a quick source for sharing data with your colleagues using Proserver or MyDAS - The room will be split into two groups: one for Java and one for Perl. Andy Jenkinson, Gustavo Salazar Introduction talk: PPT Java:MyDAS Part 1 Perl:ProServer Part 1
11:40 - 12:15 The DAS Registry and registering your source Jonathan Warren RegistryTutorial2010
12:15 - 13:15 Lunch break
13:15 - 14:15 Tutorial - DAS servers continued Andy Jenkinson, Rafael Jimenez, Gustavo Salazar Java: MyDAS Part 2MyDAS Part 3Perl:ProServer Part 2ProServer Part 3
14:15 - 14:35 DAS clients - Putting it all together Rob Finn 2009 Powerpoint
2009 PDF
14:35 - 15:10 Talk and Tutorial -DAS client libraries to query DAS sources Andy Jenkinson, Rafael Jimenez, Jose Villaveces Javascript:JSDAS Tutorial, Java:Dasobert Tutorial, Perl:Bio::Das::Lite
15:10 - 15:30 Cofee Break
15:30 - 17:00 Hands On Tutorial - continued
17:15 Departure from Campus to Cambridge Leisure Park at circa 17:15 hrs.

Day 2

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 Collaborative genomics with DAS- a new interactive DAS client Thomas Down []
10:40 Progress to report on linking EMBOSS and DAS Peter Rice PPT
11:00 1.6 Spec Summary Jonathan Warren PPT
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 DAS service to provide information on 3D motifs- PDBe Adel Golovin []
12:15-13:30 Lunch break
13:30 DAS Writeback and its integration in Dasty2 as a proof of concept Gustavo Salazar PPT SS
13:50 KaryoDAS: An Interactive Genome Visualization Tool Using DECIPHER Data Manuel Corpas (and Eugene Bragin) PPT
14:10 jsDAS: A javascript DAS client library Jose Villaveces (and Bernat Gel) PPT
14:30 Interaction DAS Hagen Blankenburg PDF
14:50 Data integration in ENFIN using standards; the EnCore DAS service Rafael Jimenez PDF, PPT
15:10-15:30 coffee break
15:30 Text Mining DAS source Maximilian Haussler
15:50 Update on the collaborative, web-based version of Apollo Gregg Helt []
16:10 From Pfam Das Alignments to Widgets Prasad Gunasekaran PDF
16:30 Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups
16:50
17:10 Bus Leaves for Cambridge Travel Lodge
19:00 Dinner at Alimentum The Private Dining Room 7.00 pm for 7.30 pm sit down.

Day 3

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:

doodle poll for expressing interest in topics 

Content negotiation and efficient data formats

how / if the big amounts data can be served via das

DAS for high-density quantitative data.

1: From molecules to sets. 2: Other dimensions: Samples.

Writing a DAS client in C

Running DAS on amazon or google app engine. And seeing what changes have to be made to the dazzle code to enable this. I'd favour app engine.

speeding up annotation retrieval for multiple segment IDs (e.g. retrieving all features for a big alignment)

using jsDas with JalviewLite

The semantic web, RDF and DAS.

DAS authentication and security

Actual topics that we discussed: 

Authentication and security - see the proposed spec.[1]

Content Negogation and efficient formats- see proposal spec.1.6E content neg.

RDF.
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