Difference between revisions of "DASworkshop200903"

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(New page: =DAS workshop March 9th-11th 2009 Genome Campus, Hinxton= frame|BioSapiens Network ==Day 1== {| class="wikitable" border="1" |- style="background:silver" !...)
 
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|Opening talk  
 
|Opening talk  
 
|Tim Hubbard
 
|Tim Hubbard
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/hubbard.pdf presentation]
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|10:20
 
|10:20
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|CNIO
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|Collaborative Annotation tool (MaDAS)
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|Osvaldo Grana
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|Victor de la Torre
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/grzibovska.pdf presentation]
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|10:40
 
|10:40
 
|Jalview / VAMSAS
 
|Jalview / VAMSAS
 
|Jim Procter / Geoff Barton
 
|Jim Procter / Geoff Barton
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/Jalview_DasDev2008.pdf presentation]
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|11:00
 
|11:00
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|11:20
 
|11:20
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|UniProt / MyDAS
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|DASgenexp
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|Phil Jones
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|Bernat Gel
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jones.pdf presentation]
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|11:40
 
|11:40
 
|Dasty2
 
|Dasty2
 
|Rafael Jimenez
 
|Rafael Jimenez
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jimenez.pdf presentation]
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|12:00
 
|12:00
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|short demo: Dastard
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|EMBOSS as an efficient DAS annotation source
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|Thomas Down
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|Peter Rice, Mahmut Uludag
 
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|13:30
 
|13:30
 
|Ensembl
 
|Ensembl
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|James Smith / Eugene Kulesha
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|James Smith
 
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|13:50
 
|13:50
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|DAS registry, SPICE
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|Integration of info on gene expression and its temporal and spatial localization
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|Andreas Prlic
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|Jose Ramon Macias
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/prlic.pdf presentation]
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|14:10
 
|14:10
 
|DAS - writeback
 
|DAS - writeback
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|Asja Grzibovska
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|Gustavo Salazar
 
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|14:30
 
|14:30
 
|Interaction DAS
 
|Interaction DAS
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|Hagen Blankenburg / Mario Albrecht
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|Hagen Blankenburg
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/blankenburg.pdf presentation]
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|14:50
 
|14:50
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|PeppeR
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|DAS for ENCODE data coordination
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|Jose Ramon Macias
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|Felix Kokocinski
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/macias.pdf presentation]
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|15:10-15:30
 
|15:10-15:30
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|15:30
 
|15:30
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|Annotation Pipeline
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|A web resource for selecting epitopes for antibodies
 
|Niall Haslam
 
|Niall Haslam
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/DASworkshopNialHaslam.pdf  presentation]
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|15:50
 
|15:50
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|Annotation type ontology
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|DAS Searches
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|Gabby Reeves
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|Andreas Prlic
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/reeves.pdf presentation]
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|16:10
 
|16:10
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|Proserver
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|A karyotype DAS client
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|Roger Pettett / Andy Jenkinson
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|Rafael Jimenez
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jenkinson.pdf presentation]
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|16:30
 
|16:30
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|BioMart & DAS
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|DASher, a standalone Java client for DAS protein sequence features
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|Syed Haider / Arek Kasprzyk
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|David Messina
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|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/biomart.pdf presentation]
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|17:00
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|16:50
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|Open discussion
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|Data Federation - BioMart & DAS
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|How to improve interopability, future extensions
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|Syed Haider
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|17:10
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|Trellis DAS2 framework- which includes the DAS1-->DAS2 proxy and alpha UCSC DAS2 server
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|Gregg Helt
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|17:30
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|Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups
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Revision as of 07:35, 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
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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