Difference between revisions of "DASworkshop200802"

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=DAS workshop February 25th, 26th Genome Campus, Hinxton=
 
=DAS workshop February 25th, 26th Genome Campus, Hinxton=
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[[Image:Biosapiens_final.gif|frame|BioSapiens Network]]
 
==Day 1==
 
==Day 1==
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schedule see at
 
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[http://www.dasregistry.org/course.jsp http://www.dasregistry.org/course.jsp]
 
  
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==Day 2==
 
  
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{| class="wikitable" border="1"
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{| class="wikitable"
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|- style="background:silver"
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! width="100px"|Time
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! ProjectName
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! Speaker
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! Presentation
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|-
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| 09:30 - 10:00
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| Arrival - Tea, Coffee.
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|
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|
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|-
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|10:00
 +
|Opening talk
 +
|Tim Hubbard
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/hubbard.pdf presentation]
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|-
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|10:20
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|CNIO
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|Osvaldo Grana
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/grzibovska.pdf presentation]
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|-
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|10:40
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|Jalview / VAMSAS
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|Jim Procter / Geoff Barton
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/Jalview_DasDev2008.pdf presentation]
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|-
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|11:00
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|Pfam
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|Rob Finn
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|
 
|-
 
|-
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! time
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|11:20
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! title
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|UniProt / MyDAS
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! speaker
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|Phil Jones
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! resources
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jones.pdf presentation]
 
|-
 
|-
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| 9:15
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|11:40
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| das - technical info & Introduction
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|Dasty2
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| Phil Jones
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|Rafael Jimenez
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|
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jimenez.pdf presentation]
 
|-
 
|-
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|  
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|12:00
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| das - client demo ensembl, grouping, histogram
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|short demo: Dastard
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| Eugene Kulesha
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|Thomas Down
 
|
 
|
 
|-
 
|-
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| 1/2 hour
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|12:15-13:30
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| Dasty
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|Lunch break
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| Rafael Jimenez & co
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|
 
|
 
|
 
|-
 
|-
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|  
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|13:30
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| SPICE, mapping features on 3D, view alignments
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|Ensembl
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| Andreas Prlic
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|James Smith / Eugene Kulesha
 
|
 
|
 
|-
 
|-
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| 1/2 hour
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|13:50
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| Pepper
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|DAS registry, SPICE
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| Jose Ramon Macias
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|Andreas Prlic
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/prlic.pdf presentation]
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|-
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|14:10
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|DAS - writeback
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|Asja Grzibovska
 
|
 
|
 
|-
 
|-
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| Lunch break
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|14:30
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|Interaction DAS
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|Hagen Blankenburg / Mario Albrecht
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/blankenburg.pdf presentation]
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|-
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|14:50
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|PeppeR
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|Jose Ramon Macias
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/macias.pdf presentation]
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|-
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|15:10-15:30
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|coffee break
 
|
 
|
 
|
 
|
−
|
 
 
|-
 
|-
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|  
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|15:30
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| DAS - clients 
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|Annotation Pipeline
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| Perl - Eugene, Java - Andreas
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|Niall Haslam
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/DASworkshopNialHaslam.pdf  presentation]
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|-
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|15:50
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|Annotation type ontology
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|Gabby Reeves
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/reeves.pdf presentation]
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|-
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|16:10
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|Proserver
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|Roger Pettett / Andy Jenkinson
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jenkinson.pdf presentation]
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|-
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|16:30
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|BioMart & DAS
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|Syed Haider / Arek Kasprzyk
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/biomart.pdf presentation]
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|-
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|17:00
 +
|Open discussion
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|How to improve interopability, future extensions
 
|
 
|
 
|-
 
|-
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|
 
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| DAS - set up a server
 
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| Perl - Andy Jenkinson, Java - Andreas
 
 
|}
 
|}
  
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==Day 2==
  
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TODO: Prepare:
 
  
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Bookmarks for important urls
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{| class="wikitable" border="1"
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find common examples for the demos - [all] exchange by email
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|- style="background:silver"
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suggestions: P53, BRCA1
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! width="100px"|Time
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! Title
 +
! Speaker
 +
! Resources
 +
|-
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| 09:15 - 10:00
 +
| DAS - Technical Introduction
 +
| Phil Jones
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| Presentation:<br/>[http://www.ebi.ac.uk/~pjones/DAS2008/DAS-technical-introduction.ppt Powerpoint]<br/>[http://www.ebi.ac.uk/~pjones/DAS2008/DAS-technical-introduction.odp Open Document Format]<br/>[http://www.ebi.ac.uk/~pjones/DAS2008/DAS-technical-introduction.pdf PDF]
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|-
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| 10:00 - 10:35
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| DAS Introductory Tutorial - DAS servers and the DAS Registration Service
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| Phil Jones
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| [[DASworkshop200802:intro_tutorial| Introductory Tutorial]]
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|- 
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| 10:35 - 11:15
 +
| DAS - Client Demonstration: Ensembl, grouping and histograms
 +
| Eugene Kulesha
 +
|
 +
|- style="background:#ffdead;"
 +
| 11:15 - 11:40
 +
| colspan="3" | Coffee break
 +
|-
 +
| 11:40 - 12:10
 +
| Dasty2
 +
| Rafael Jimenez
 +
|
 +
|-
 +
| 12:10 - 12:40
 +
| SPICE, Mapping features on 3D, viewing alignments
 +
| Andreas Prlic
 +
| [[DASworkshop200802:spice| SPICE links]]
 +
|- style="background:#ffdead;"
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| 12:40 - 13:40
 +
| colspan="3" | Lunch break
 +
|-
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| 13:40 - 14:10
 +
| Pepper
 +
| Jose Ramon Macias
 +
| [http://biocomp.cnb.csic.es/das http://biocomp.cnb.csic.es/das]
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|-
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| 14:10 - 15:10
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| DAS: Setting Up Your Own Server.  In this section the group will split into two tracks - one for Perl programmers and one for Java programmers. 
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| [http://www.sanger.ac.uk/Software/analysis/proserver Proserver]: Andy Jenkinson<br/>
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[http://www.biojava.org/wiki/Dazzle Dazzle]: Andreas Prlic
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| [http://www.ebi.ac.uk/~aj/das_workshop_2008/proserver_tutorial.html ProServer: writing a SourceAdaptor]<br/>
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[http://www.biojava.org/wiki/Dazzle:plugins Dazzle: using existing plugins]<br/>
 +
[http://www.biojava.org/wiki/Dazzle:writeplugin Dazzle: writing a plugin]<br/>
 +
[http://www.ebi.ac.uk/~pjones/DAS2008/chr21.gff Chromosome 21 GFF File]
 +
|- style="background:#ffdead;"
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| 15:10 - 15:30
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| colspan="3"|Coffee break
 +
|-
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| 15:30 - 16:30
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| DAS - Coding a Client.
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| [http://search.cpan.org/~rpettett/Bio-Das-Lite/ Bio::Das::Lite] (Perl) - Andy Jenkinson<br/>
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[http://www.spice-3d.org/dasobert/ Dasobert] (Java) - Andreas Prlic
 +
| [http://www.ebi.ac.uk/~aj/das_workshop_2008/daslite_tutorial.html Bio::Das::Lite tutorial]
 +
|}

Latest revision as of 11:02, 16 January 2009

DAS workshop February 25th, 26th Genome Campus, Hinxton

BioSapiens Network

Day 1

Time ProjectName Speaker Presentation
09:30 - 10:00 Arrival - Tea, Coffee.
10:00 Opening talk Tim Hubbard presentation
10:20 CNIO Osvaldo Grana presentation
10:40 Jalview / VAMSAS Jim Procter / Geoff Barton presentation
11:00 Pfam Rob Finn
11:20 UniProt / MyDAS Phil Jones presentation
11:40 Dasty2 Rafael Jimenez presentation
12:00 short demo: Dastard Thomas Down
12:15-13:30 Lunch break
13:30 Ensembl James Smith / Eugene Kulesha
13:50 DAS registry, SPICE Andreas Prlic presentation
14:10 DAS - writeback Asja Grzibovska
14:30 Interaction DAS Hagen Blankenburg / Mario Albrecht presentation
14:50 PeppeR Jose Ramon Macias presentation
15:10-15:30 coffee break
15:30 Annotation Pipeline Niall Haslam presentation
15:50 Annotation type ontology Gabby Reeves presentation
16:10 Proserver Roger Pettett / Andy Jenkinson presentation
16:30 BioMart & DAS Syed Haider / Arek Kasprzyk presentation
17:00 Open discussion How to improve interopability, future extensions

Day 2

Time Title Speaker Resources
09:15 - 10:00 DAS - Technical Introduction Phil Jones Presentation:
Powerpoint
Open Document Format
PDF
10:00 - 10:35 DAS Introductory Tutorial - DAS servers and the DAS Registration Service Phil Jones Introductory Tutorial
10:35 - 11:15 DAS - Client Demonstration: Ensembl, grouping and histograms Eugene Kulesha
11:15 - 11:40 Coffee break
11:40 - 12:10 Dasty2 Rafael Jimenez
12:10 - 12:40 SPICE, Mapping features on 3D, viewing alignments Andreas Prlic SPICE links
12:40 - 13:40 Lunch break
13:40 - 14:10 Pepper Jose Ramon Macias http://biocomp.cnb.csic.es/das
14:10 - 15:10 DAS: Setting Up Your Own Server. In this section the group will split into two tracks - one for Perl programmers and one for Java programmers. Proserver: Andy Jenkinson

Dazzle: Andreas Prlic

ProServer: writing a SourceAdaptor

Dazzle: using existing plugins
Dazzle: writing a plugin
Chromosome 21 GFF File

15:10 - 15:30 Coffee break
15:30 - 16:30 DAS - Coding a Client. Bio::Das::Lite (Perl) - Andy Jenkinson

Dasobert (Java) - Andreas Prlic

Bio::Das::Lite tutorial
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