Difference between revisions of "DASworkshop200903"

From BioDAS
Jump to: navigation, search
(New page: =DAS workshop March 9th-11th 2009 Genome Campus, Hinxton= frame|BioSapiens Network ==Day 1== {| class="wikitable" border="1" |- style="background:silver" !...)
 
Line 19: Line 19:
 
|Opening talk  
 
|Opening talk  
 
|Tim Hubbard
 
|Tim Hubbard
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/hubbard.pdf presentation]
+
|
 
|-
 
|-
 
|10:20
 
|10:20
−
|CNIO
+
|Collaborative Annotation tool (MaDAS)
−
|Osvaldo Grana
+
|Victor de la Torre
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/grzibovska.pdf presentation]
+
|
 
|-
 
|-
 
|10:40
 
|10:40
 
|Jalview / VAMSAS
 
|Jalview / VAMSAS
 
|Jim Procter / Geoff Barton
 
|Jim Procter / Geoff Barton
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/Jalview_DasDev2008.pdf presentation]
+
|
 
|-
 
|-
 
|11:00
 
|11:00
Line 37: Line 37:
 
|-
 
|-
 
|11:20
 
|11:20
−
|UniProt / MyDAS
+
|DASgenexp
−
|Phil Jones
+
|Bernat Gel
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jones.pdf presentation]
+
|
 
|-
 
|-
 
|11:40
 
|11:40
 
|Dasty2
 
|Dasty2
 
|Rafael Jimenez
 
|Rafael Jimenez
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jimenez.pdf presentation]
+
|
 
|-
 
|-
 
|12:00
 
|12:00
−
|short demo: Dastard
+
|EMBOSS as an efficient DAS annotation source
−
|Thomas Down
+
|Peter Rice, Mahmut Uludag
 
|
 
|
 
|-
 
|-
Line 58: Line 58:
 
|13:30
 
|13:30
 
|Ensembl
 
|Ensembl
−
|James Smith / Eugene Kulesha
+
|James Smith
 
|
 
|
 
|-
 
|-
 
|13:50
 
|13:50
−
|DAS registry, SPICE
+
|Integration of info on gene expression and its temporal and spatial localization
−
|Andreas Prlic
+
|Jose Ramon Macias
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/prlic.pdf presentation]
+
|
 
|-
 
|-
 
|14:10
 
|14:10
 
|DAS - writeback
 
|DAS - writeback
−
|Asja Grzibovska
+
|Gustavo Salazar
 
|
 
|
 
|-
 
|-
 
|14:30
 
|14:30
 
|Interaction DAS
 
|Interaction DAS
−
|Hagen Blankenburg / Mario Albrecht
+
|Hagen Blankenburg
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/blankenburg.pdf presentation]
+
|
 
|-
 
|-
 
|14:50
 
|14:50
−
|PeppeR
+
|DAS for ENCODE data coordination
−
|Jose Ramon Macias
+
|Felix Kokocinski
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/macias.pdf presentation]
+
|
 
|-
 
|-
 
|15:10-15:30
 
|15:10-15:30
Line 87: Line 87:
 
|-
 
|-
 
|15:30
 
|15:30
−
|Annotation Pipeline
+
|A web resource for selecting epitopes for antibodies
 
|Niall Haslam
 
|Niall Haslam
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/DASworkshopNialHaslam.pdf  presentation]
+
|
 
|-
 
|-
 
|15:50
 
|15:50
−
|Annotation type ontology
+
|DAS Searches
−
|Gabby Reeves
+
|Andreas Prlic
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/reeves.pdf presentation]
+
|
 
|-
 
|-
 
|16:10
 
|16:10
−
|Proserver
+
|A karyotype DAS client
−
|Roger Pettett / Andy Jenkinson
+
|Rafael Jimenez
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/jenkinson.pdf presentation]
+
|
 
|-
 
|-
 
|16:30
 
|16:30
−
|BioMart & DAS
+
|DASher, a standalone Java client for DAS protein sequence features
−
|Syed Haider / Arek Kasprzyk
+
|David Messina
−
|[http://www.sanger.ac.uk/Users/ap3/dasworkshop200802/biomart.pdf presentation]
+
|
 
|-
 
|-
−
|17:00
+
|16:50
−
|Open discussion
+
|Data Federation - BioMart & DAS
−
|How to improve interopability, future extensions
+
|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
 +
|
 
|
 
|
 
|-
 
|-

Revision as of 11:35, 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
Retrieved from "http://biodas.open-bio.org/w/index.php?title=DASworkshop200903&oldid=733"