Difference between revisions of "DASworkshop200802"

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[[Image:Biosapiens_final.gif|frame|BioSapiens Network]]
 
[[Image:Biosapiens_final.gif|frame|BioSapiens Network]]
 
==Day 1==
 
==Day 1==
−
schedule see at
+
 
−
  [http://www.dasregistry.org/course.jsp http://www.dasregistry.org/course.jsp]
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 +
{| class="wikitable" border="1"
 +
|- style="background:silver"
 +
! width="100px"|Time
 +
! ProjectName
 +
! Speaker
 +
! Presentation
 +
|-
 +
| 09:30 - 10:00
 +
| Arrival - Tea, Coffee.
 +
|
 +
|
 +
|-
 +
|10:00
 +
|Opening talk
 +
|Tim Hubbard
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/hubbard.pdf presentation]
 +
|-
 +
|10:20
 +
|CNIO
 +
|Osvaldo Grana
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/grzibovska.pdf presentation]
 +
|-
 +
|10:40
 +
|Jalview / VAMSAS
 +
|Jim Procter / Geoff Barton
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/Jalview_DasDev2008.pdf presentation]
 +
|-
 +
|11:00
 +
|Pfam
 +
|Rob Finn
 +
|
 +
|-
 +
|11:20
 +
|UniProt / MyDAS
 +
|Phil Jones
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jones.pdf presentation]
 +
|-
 +
|11:40
 +
|Dasty2
 +
|Rafael Jimenez
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jimenez.pdf 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
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/prlic.pdf presentation]
 +
|-
 +
|14:10
 +
|DAS - writeback
 +
|Asja Grzibovska
 +
|
 +
|-
 +
|14:30
 +
|Interaction DAS
 +
|Hagen Blankenburg / Mario Albrecht
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/blankenburg.pdf presentation]
 +
|-
 +
|14:50
 +
|PeppeR
 +
|Jose Ramon Macias
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/macias.pdf presentation]
 +
|-
 +
|15:10-15:30
 +
|coffee break
 +
|
 +
|
 +
|-
 +
|15:30
 +
|Annotation Pipeline
 +
|Niall Haslam
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/DASworkshopNialHaslam.pdf presentation]
 +
|-
 +
|15:50
 +
|Annotation type ontology
 +
|Gabby Reeves
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/reeves.pdf presentation]
 +
|-
 +
|16:10
 +
|Proserver
 +
|Roger Pettett / Andy Jenkinson
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jenkinson.pdf presentation]
 +
|-
 +
|16:30
 +
|BioMart & DAS
 +
|Syed Haider / Arek Kasprzyk
 +
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/biomart.pdf presentation]
 +
|-
 +
|17:00
 +
|Open discussion
 +
|How to improve interopability, future extensions
 +
|
 +
|-
 +
|}
  
 
==Day 2==
 
==Day 2==
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|-
 
|-
 
| 09:15 - 10:00
 
| 09:15 - 10:00
−
| das - technical info & Introduction  
+
| DAS - Technical Introduction  
 
| Phil Jones  
 
| Phil Jones  
−
|
+
| 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]
 
|-
 
|-
 
| 10:00 - 10:35
 
| 10:00 - 10:35
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|-   
 
|-   
 
| 10:35 - 11:15
 
| 10:35 - 11:15
−
| das - client demo ensembl, grouping, histogram
+
| DAS - Client Demonstration: Ensembl, grouping and histograms
 
| Eugene Kulesha
 
| Eugene Kulesha
 
|
 
|
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|-
 
|-
 
| 11:40 - 12:10  
 
| 11:40 - 12:10  
−
| Dasty
+
| Dasty2
−
| Rafael Jimenez & co
+
| Rafael Jimenez
 
|
 
|
 
|-
 
|-
 
| 12:10 - 12:40
 
| 12:10 - 12:40
−
| SPICE, mapping features on 3D, view alignments
+
| SPICE, Mapping features on 3D, viewing alignments
 
| Andreas Prlic
 
| Andreas Prlic
 
| [[DASworkshop200802:spice| SPICE links]]
 
| [[DASworkshop200802:spice| SPICE links]]
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| Pepper
 
| Pepper
 
| Jose Ramon Macias
 
| Jose Ramon Macias
−
|
+
| [http://biocomp.cnb.csic.es/das http://biocomp.cnb.csic.es/das]
 
|-
 
|-
 
| 14:10 - 15:10
 
| 14:10 - 15:10
−
| DAS: set up a server
+
| 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, [http://www.biojava.org/wiki/Dazzle Dazzle]: Andreas
+
| [http://www.sanger.ac.uk/Software/analysis/proserver Proserver]: Andy Jenkinson<br/>
−
| [http://www.biojava.org/wiki/Dazzle:plugins use existing Dazzle plugins], [http://www.biojava.org/wiki/Dazzle:writeplugin how to write a new plugin]
+
[http://www.biojava.org/wiki/Dazzle Dazzle]: Andreas Prlic
 +
| [http://www.ebi.ac.uk/~aj/das_workshop_2008/proserver_tutorial.html ProServer: writing a SourceAdaptor]<br/>
 +
[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;"
 
|- style="background:#ffdead;"
 
| 15:10 - 15:30
 
| 15:10 - 15:30
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|-
 
|-
 
| 15:30 - 16:30  
 
| 15:30 - 16:30  
−
| DAS - client 
+
| DAS - Coding a Client.
−
| Bio::Das::Lite (Perl) - Andy,  Dasobert (Java) - Andreas
+
| [http://search.cpan.org/~rpettett/Bio-Das-Lite/ Bio::Das::Lite] (Perl) - Andy Jenkinson<br/>
−
| [http://www.spice-3d.org/dasobert/ Dasobert]
+
[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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