Difference between revisions of "DASworkshop200903"

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(→‎Day 2)
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! Resources
 
! Resources
 
|-
 
|-
−
| 09:15 - 10:00
+
| 8:45 - 9:30
−
| DAS - Technical Introduction
+
| colspan="3" | Minibus/Taxis to pick attendees up from hotels and bring to Campus
−
| Phil Jones
+
|- style="background:#ffdead;"
−
| 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]
+
| 9:30 - 10:00
 +
| colspan="3" | Coffee is served outside the training room
 +
|- style="background:#ffdead;"
 
|-
 
|-
−
| 10:00 - 10:35
+
| 10:00 - 10:10
−
| DAS Introductory Tutorial - DAS servers and the DAS Registration Service
+
| Welcome and Introduction to the Workshop
−
| Phil Jones
+
| Jonathan Warren
−
| [[DASworkshop200802:intro_tutorial| Introductory Tutorial]]
 
−
|- 
 
−
| 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  
+
| 10:10 - 11:10
−
| Dasty2
+
| DAS - Technical Introduction
−
| Rafael Jimenez
+
| Andy Jenkinson
−
|
+
| Presentation:<br/>[http://www.ebi.ac.uk/~aj/das_workshop_2009/DAS-technical-introduction.ppt Powerpoint]<br/>[http://www.ebi.ac.uk/~aj/das_workshop_2009/DAS-technical-introduction.pdf PDF]
 +
|-
 +
| 11:10 - 11:30
 +
| The DAS Registration Service
 +
| Jonathan Warren
 +
|  
 
|-
 
|-
−
| 12:10 - 12:40
+
| 11:30 - 12:15
−
| SPICE, Mapping features on 3D, viewing alignments
+
| Hands On Tutorial - Setting up a DAS Server and creating a DAS Client. The room will be split into two groups: one for Java and one for Perl.
−
| Andreas Prlic
+
| Jonathan Warren and Andy Jenkinson
−
| [[DASworkshop200802:spice| SPICE links]]
+
| [http://www.ebi.ac.uk/~aj/das_workshop_2009/daslite_tutorial.html Bio::Das::ProServer server tutorial]<br/>
 +
[http://www.ebi.ac.uk/~aj/das_workshop_2009/daslite_tutorial.html Bio::Das::Lite client tutorial]<br/>
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
−
| 12:40 - 13:40
+
| 12:15 - 13:15
 
| colspan="3" | Lunch break
 
| colspan="3" | Lunch break
 
|-
 
|-
−
| 13:40 - 14:10
+
| 13:15 - 15:10
−
| Pepper
+
| colspan="3" | Hands On Tutorial - continued
−
| Jose Ramon Macias
 
−
| [http://biocomp.cnb.csic.es/das 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. 
 
−
| [http://www.sanger.ac.uk/Software/analysis/proserver Proserver]: Andy Jenkinson<br/>
 
−
[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 - Coding a Client.
+
| colspan="3" | Hands On Tutorial - continued
−
| [http://search.cpan.org/~rpettett/Bio-Das-Lite/ Bio::Das::Lite] (Perl) - Andy Jenkinson<br/>
 
−
[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]
 
 
|}
 
|}

Revision as of 12:16, 4 March 2009

DAS workshop March 9th-11th 2009 Genome Campus, Hinxton

BioSapiens Network

Day 1

Time ProjectName Speaker Presentation
09:30 - 10:00 Arrival - Tea, Coffee.
10:00 Opening talk Tim Hubbard
10:20 Collaborative Annotation tool (MaDAS) Victor de la Torre
10:40 Jalview / VAMSAS Jim Procter / Geoff Barton
11:00 Pfam Rob Finn
11:20 DASgenexp Bernat Gel
11:40 Dasty2 Rafael Jimenez
12:00 EMBOSS as an efficient DAS annotation source Peter Rice, Mahmut Uludag
12:15-13:30 Lunch break
13:30 Ensembl James Smith
13:50 Integration of info on gene expression and its temporal and spatial localization Jose Ramon Macias
14:10 DAS - writeback Gustavo Salazar
14:30 Interaction DAS Hagen Blankenburg
14:50 DAS for ENCODE data coordination Felix Kokocinski
15:10-15:30 coffee break
15:30 A web resource for selecting epitopes for antibodies Niall Haslam
15:50 DAS Searches Andreas Prlic
16:10 A karyotype DAS client Rafael Jimenez
16:30 DASher, a standalone Java client for DAS protein sequence features David Messina
16:50 Data Federation - BioMart & DAS Syed Haider
17:10 Trellis DAS2 framework- which includes the DAS1-->DAS2 proxy and alpha UCSC DAS2 server Gregg Helt
17:30 Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups

Day 2

Time Title Speaker Resources
8:45 - 9:30 Minibus/Taxis to pick attendees up from hotels and bring 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 - 11:10 DAS - Technical Introduction Andy Jenkinson Presentation:
Powerpoint
PDF
11:10 - 11:30 The DAS Registration Service Jonathan Warren
11:30 - 12:15 Hands On Tutorial - Setting up a DAS Server and creating a DAS Client. The room will be split into two groups: one for Java and one for Perl. Jonathan Warren and Andy Jenkinson Bio::Das::ProServer server tutorial

Bio::Das::Lite client tutorial

12:15 - 13:15 Lunch break
13:15 - 15:10 Hands On Tutorial - continued
15:10 - 15:30 Coffee break
15:30 - 16:30 Hands On Tutorial - continued
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