Difference between revisions of "DASWorkshop2011"

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The 2011 DAS Workshop will be held on 2-4 Marchl at the EBI Hinxton campus.
 
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
+
* Information & registration: http://www.ebi.ac.uk/training/onsite/110302DAS.html
  
  
 
=DAS Workshop 2011 Schedule=
 
=DAS Workshop 2011 Schedule=
−
The first 2 days will be held in the EBI training room. 3rd day room to be announced.
+
All 3 days will be held in the EBI training room.
 
==Day 1==
 
==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: [http://www.dasregistry.org/DASCommandExamples.jsp DAS examples]===
  
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
Line 18: Line 19:
 
| colspan="3" | Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
 
| colspan="3" | Departure from the Travelodge Cambridge Leisure Park at 08:45 hrs to Campus.
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
−
| 9:30 - 10:00
+
| 9:30 - 09:50
 
| colspan="3" | Coffee is served outside the training room  
 
| colspan="3" | Coffee is served outside the training room  
 
|-
 
|-
−
| 10:00 - 10:10
+
| 09:50 - 10:00
 
| Welcome and Introduction to the Workshop
 
| Welcome and Introduction to the Workshop
 
| Jonathan Warren
 
| Jonathan Warren
 
|
 
|
 
|-
 
|-
−
| 10:10 - 10:30
+
| 10:00 - 10:20
 
| DAS - Introduction/Overview
 
| DAS - Introduction/Overview
 
| Andy Jenkinson
 
| 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]
+
| [http://www.biotnet.org/training-materials/introduction-das Introduction] [http://www.biotnet.org/training-materials/technical-introduction-das Technical Introduction]
 
|-
 
|-
−
| 10:30 - 10:40
+
| 10:20 - 10:35
 
| The DAS Game
 
| The DAS Game
 
| Rafael Jimenez
 
| Rafael Jimenez
−
| [http://www.ebi.ac.uk/~rafael/talks/2010-04-07_workshop_das/dasGame/ Game cards]
+
| [http://www.biotnet.org/training-materials/das-game The DAS Game]
 
|-
 
|-
−
| 10:40 - 11:40
+
| 10:35 - 11:25
−
| 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.
+
| Hands-on tutorial: using DAS software, 10 minute introduction of some DAS implementations (Bernat)
−
| Andy Jenkinson, Gustavo Salazar
+
| Bernat Gel, Thomas Down, Jose Villavaces
−
| 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]
+
| Implementations. [http://www.lsi.upc.edu/~bgel/research/easydas/tutorial/Implementations.ppt PPT] [http://code.google.com/p/easydas/wiki/tutorialDASWorkshop2011 Creating DAS sources from GFF files supplied using easyDAS] (Bernat), Viewing DAS sources using Dalliance (Thomas) [http://www.biodalliance.org/people/thomas/dalliance-for-das-workshop.pdf PDF]-or- Dasty3 (Jose) [http://www.ebi.ac.uk/~ljgarcia/Presentations/Tutorials/DASTY3_DASWorkshop_2011.pdf PDF]
 
|-
 
|-
−
| 11:40 - 12:15
+
| 11:25 - 12:15
−
| The DAS Registry and registering your source
+
| Hands-on programming tutorial: Creating a custom DAS source
−
| Jonathan Warren
+
| Gustavo, Andy
−
|[http://www.biodas.org/wiki/RegistryTutorial2010 RegistryTutorial2010]
+
| [http://www.biotnet.org/training-materials/das-servers 10 minute introduction to DAS servers], [http://code.google.com/p/mydas/wiki/Tutorials MyDAS] -or- [http://www.biotnet.org/training-materials/bio-das-proserver-tutorial ProServer]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
| 12:15 - 13:15  
 
| 12:15 - 13:15  
 
| colspan="3" | Lunch break
 
| colspan="3" | Lunch break
 
|-
 
|-
−
| 13:15 - 14:15
+
| 13:15 - 14:50
 
| Tutorial - DAS servers continued
 
| Tutorial - DAS servers continued
−
| Andy Jenkinson, Rafael Jimenez, Gustavo Salazar
+
| Andy Jenkinson and 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]
+
| Perl(ProServer) and Java(MyDAS)
 
|-
 
|-
−
|14:15 - 14:35
+
|14:50 - 15:10
−
|DAS clients - Putting it all together
+
| Hands on Tutorial The DAS registry: Short introduction talk then hands on tutorial
−
|Rob Finn
+
| Jonathan Warren
−
| [http://www.biodas.org/workshop_2009/20090309ClientSpecReview.ppt 2009 Powerpoint]<br/>[http://www.biodas.org/workshop_2009/20090309ClientSpecReview.pdf 2009 PDF]
+
| [http://www.biotnet.org/training-materials/short-das-registry-tutorial-basic-knowledge DAS Registry Tutorial]  
−
|-
 
−
|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;"
 
|-style="background:#ffdead;"
 
| 15:10 - 15:30
 
| 15:10 - 15:30
 
| colspan="3" | Cofee Break
 
| colspan="3" | Cofee Break
 
|-
 
|-
−
| 15:30 - 17:00
+
| 15:30 - 17:15
−
| colspan="3" | Hands On Tutorial - continued
+
| Hands-on programming tutorial: DAS client libraries, 10 minute introduction
−
|-  style="background:#ffdead;"
+
| Andy, Rafael, Leyla, Jose, Bernat
−
|17:15
+
| [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
−
| colspan="3" |Departure from Campus to Cambridge Leisure Park at circa 17:15 hrs.
+
|-   
 +
|17:30
 +
| colspan="3" |Departure from Campus to Cambridge Travel Lodge and Leisure Park at circa 17:30 hrs.
 +
|- style="background:#ffdead;"
 +
|19:00
 +
|Dinner at [http://www.browns-restaurants.co.uk/menu-cambridge.php Browns] [http://maps.google.co.uk/maps?f=d&source=s_d&saddr=Travelodge,+Clifton+Way,+Cambridge&daddr=23+Trumpington+St,+Cambridge+CB2+1+(Browns+Restaurant)&hl=en&geocode=FdNbHAMdAhcCACErVS-6-2CqXg%3BFZ9_HAMdXNoBACE-peCSwSHlsA&mra=ls&dirflg=w&sll=52.194166,0.129647&sspn=0.012233,0.035534&ie=UTF8&ll=52.194166,0.129647&spn=0.012233,0.035534&z=15 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==
 
==Day 2==
−
 
+
Preliminary schedule where the order and content may still change considerably.
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
 
|- style="background:silver"
 
|- style="background:silver"
Line 92: Line 96:
 
|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.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.scivee.tv/node/28151 Video]
 
|-
 
|-
 
|10:40
 
|10:40
−
|Dealing with Personal Genomes using DAS
+
|DAS search
−
|Manuel Corpas
+
|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.scivee.tv/node/28152 Video]
 
|-
 
|-
 
|11:00
 
|11:00
−
|
+
|Short break
 
|
 
|
 
|[]
 
|[]
Line 112: Line 116:
 
|easyDAS: a hosted solution for DAS server creation
 
|easyDAS: a hosted solution for DAS server creation
 
|Bernat Gel
 
|Bernat Gel
−
|[http://www.biodas.org/workshop_2010/bernat_easydas.ppt PPT]
+
|[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.biodas.org/workshop_2010/warren_registry.ppt 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
−
|
+
|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://www.scivee.tv/node/28130 Video]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|12:15-13:30
 
|12:15-13:30
Line 128: Line 132:
 
|-
 
|-
 
|13:30
 
|13:30
−
|
+
|EBI Search
−
|
+
|Andy Jenkinson
−
|[]
+
|[http://www.ebi.ac.uk/~aj/das_workshop_2011/EBI-Search.pptx PPTX][http://www.scivee.tv/node/28153 Video]
 
|-
 
|-
 
|13:50
 
|13:50
−
|
+
|Dealing with Personal Genomes using DAS
−
|
+
|Manuel Corpas
 
|[]
 
|[]
 
|-
 
|-
 
|14:10
 
|14:10
−
|jsDAS: A javascript DAS client library
+
|Dasty update
−
|Jose Villaveces (and Bernat Gel)
+
|Jose Villaveces
−
|[http://www.biodas.org/workshop_2010/jose_jsdas.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
−
|
+
|Peter Rice, Mahmut Uludag
−
|[]
+
|[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
−
|
+
|James Procter
−
|[], []
+
|[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
Line 156: Line 160:
 
|-
 
|-
 
|15:30
 
|15:30
−
|<del>Text Mining DAS source</del>
+
|Setting up a BAM based DAS source in GBrowse experience.
−
|<del>Maximilian Haussler</del>
+
|Frank Schwach
−
|
+
|[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
−
|
+
|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.scivee.tv/node/28136 Video]
 
|-
 
|-
 
|16:10
 
|16:10
−
|
+
|Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups
 
|
 
|
 
|[]
 
|[]
 
|-
 
|-
 
|16:30
 
|16:30
−
|Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups
+
|
 
|
 
|
 
|
 
|
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|17:10
 
|17:10
 
|Bus Leaves for Cambridge Travel Lodge
 
|Bus Leaves for Cambridge Travel Lodge
−
|
 
−
|
 
−
|- style="background:#ffdead;"
 
−
|19:00
 
−
|Dinner at [http://restaurantalimentum.co.uk/index.php Alimentum] The Private Dining Room 7.00 pm for 7.30 pm sit down.
 
−
|
 
−
|
 
 
|-
 
|-
 
|}
 
|}
  
 
==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
 
  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.
 
Start at 10am
 
Start at 10am
−
  Departure 16:00 hrs form campus to Travellodge 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:===
 
−
 
−
[http://www.doodle.com/cvb5btwmrzz9avgh doodle poll for expressing interest in topics]
 

Latest revision as of 06:40, 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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