Difference between revisions of "DASworkshop200903"

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=DAS workshop March 9th-11th 2009 Genome Campus, Hinxton=
 
=DAS workshop March 9th-11th 2009 Genome Campus, Hinxton=
 
[[Image:Biosapiens_final.gif|frame|BioSapiens Network]]
 
[[Image:Biosapiens_final.gif|frame|BioSapiens Network]]
 +
 
==Day 1==
 
==Day 1==
  
 +
 +
{| class="wikitable" border="1"
 +
|- style="background:silver"
 +
! width="100px"|Time
 +
! Title
 +
! Speaker
 +
! Resources
 +
|-
 +
| 8:45 - 9:30
 +
| colspan="3" | Minibus/Taxis to pick attendees up from hotels and bring to Campus
 +
|- style="background:#ffdead;"
 +
| 9:30 - 10:00
 +
| colspan="3" | Coffee is served outside the training room
 +
|- style="background:#ffdead;"
 +
|-
 +
| 10:00 - 10:10
 +
| Welcome and Introduction to the Workshop
 +
| Jonathan Warren
 +
|
 +
|-
 +
| 10:10 - 11:10
 +
| DAS - Technical Introduction
 +
| Andy Jenkinson
 +
| [http://www.ebi.ac.uk/~aj/das_workshop_2009/DAS-Technical-Introduction.pptx Powerpoint 2008]<br/>
 +
[http://www.ebi.ac.uk/~aj/das_workshop_2009/DAS-Technical-Introduction.ppt Powerpoint 1997]<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
 +
| [http://www.biodas.org/wiki/DASworkshop200802:intro_tutorial#Finding_DAS_sources_.E2.80.93_the_DAS_Registry_Service_at_the_Sanger_Institute The Registry]
 +
|-
 +
| 11:30 - 12:15
 +
| Putting it all together
 +
| Rob Finn
 +
| [http://www.biodas.org/workshop_2009/20090309ClientSpecReview.ppt Powerpoint]<br/> [http://www.biodas.org/workshop_2009/20090309ClientSpecReview.pdf PDF]
 +
|- style="background:#ffdead;"
 +
| 12:15 - 13:15
 +
| colspan="3" | Lunch break
 +
|-
 +
| 13:15 - 15:10
 +
| 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
 +
| Java server: [http://www.dasregistry.org/DazzleTutorial.jsp Dazzle tutorial]<br/>
 +
Java client: [http://www.dasregistry.org/DasobertTutorial.jsp Dasobert tutorial]<br/>
 +
Perl server: [http://www.ebi.ac.uk/~aj/das_workshop_2009/proserver_tutorial.html Bio::Das::ProServer tutorial]<br/>
 +
Perl client: [http://www.ebi.ac.uk/~aj/das_workshop_2009/daslite_tutorial.html Bio::Das::Lite tutorial]<br/>
 +
|- style="background:#ffdead;"
 +
| 15:10 - 15:30
 +
| colspan="3"|Coffee break
 +
|-
 +
| 15:30 - 16:30
 +
| colspan="3" | Hands On Tutorial - continued
 +
|}
 +
 +
==Day 2==
  
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
Line 10: Line 67:
 
! Speaker
 
! Speaker
 
! Presentation
 
! Presentation
−
|-
+
|- style="background:#ffdead;"
 
| 09:30 - 10:00
 
| 09:30 - 10:00
−
| Arrival - Tea, Coffee.
+
| colspan="3" | Arrival - Tea, Coffee.
−
|
 
−
|
 
 
|-  
 
|-  
 
|10:00
 
|10:00
 
|Opening talk  
 
|Opening talk  
 
|Tim Hubbard
 
|Tim Hubbard
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/hubbard.ppt presentation]
 
|-
 
|-
 
|10:20
 
|10:20
 
|Collaborative Annotation tool (MaDAS)
 
|Collaborative Annotation tool (MaDAS)
 
|Victor de la Torre
 
|Victor de la Torre
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/MaDAS_victor_de_la_torre.pptx presentation]
 
|-
 
|-
 
|10:40
 
|10:40
 
|Jalview / VAMSAS
 
|Jalview / VAMSAS
 
|Jim Procter / Geoff Barton
 
|Jim Procter / Geoff Barton
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/Jalview_2009_DAS.pdf presentation]
 
|-
 
|-
 
|11:00
 
|11:00
 
|Pfam
 
|Pfam
 
|Rob Finn
 
|Rob Finn
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/20090309PfamDasWorkShop.ppt presentation]
 
|-
 
|-
 
|11:20
 
|11:20
 
|DASgenexp
 
|DASgenexp
 
|Bernat Gel
 
|Bernat Gel
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/DASGenExp3.ppt presentation]
 
|-
 
|-
 
|11:40
 
|11:40
 
|Dasty2
 
|Dasty2
 
|Rafael Jimenez
 
|Rafael Jimenez
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/rjimenez_dasworkshop2009_dasty2.ppt presentation]
 
|-
 
|-
 
|12:00
 
|12:00
 
|EMBOSS as an efficient DAS annotation source
 
|EMBOSS as an efficient DAS annotation source
 
|Peter Rice, Mahmut Uludag
 
|Peter Rice, Mahmut Uludag
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/DAS-Rice-Uludag.ppt presentation]
−
|-
+
|- style="background:#ffdead;"
 
|12:15-13:30
 
|12:15-13:30
−
|Lunch break
+
| colspan="3" | Lunch break
−
|
 
−
|
 
 
|-
 
|-
 
|13:30
 
|13:30
 
|Ensembl
 
|Ensembl
 
|James Smith
 
|James Smith
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/2009-das-talk-smith.ppt presentation]
 
|-
 
|-
 
|13:50
 
|13:50
 
|Integration of info on gene expression and its temporal and spatial localization
 
|Integration of info on gene expression and its temporal and spatial localization
 
|Jose Ramon Macias
 
|Jose Ramon Macias
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/20090310_DAS_Workshop_DASxVO.ppt presentation]
 
|-
 
|-
 
|14:10
 
|14:10
 
|DAS - writeback
 
|DAS - writeback
 
|Gustavo Salazar
 
|Gustavo Salazar
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/DASwriteback.pdf presentation]
 
|-
 
|-
 
|14:30
 
|14:30
 
|Interaction DAS
 
|Interaction DAS
 
|Hagen Blankenburg
 
|Hagen Blankenburg
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/20090310_Blankenburg_DASMI.pdf presentation]
 
|-
 
|-
 
|14:50
 
|14:50
 
|DAS for ENCODE data coordination
 
|DAS for ENCODE data coordination
 
|Felix Kokocinski
 
|Felix Kokocinski
−
|
+
|[http://www.sanger.ac.uk/~fsk/DAS_workshop09.pdf pdf]
−
|-
+
|- style="background:#ffdead;"
 
|15:10-15:30
 
|15:10-15:30
−
|coffee break
+
| colspan="3" | coffee break
−
|
 
−
|
 
 
|-
 
|-
 
|15:30
 
|15:30
 
|A web resource for selecting epitopes for antibodies
 
|A web resource for selecting epitopes for antibodies
 
|Niall Haslam
 
|Niall Haslam
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/NiallHaslamDAS2009.pdf presentation]
 
|-
 
|-
 
|15:50
 
|15:50
 
|DAS Searches
 
|DAS Searches
 
|Andreas Prlic
 
|Andreas Prlic
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/DAS_searches_20090310.pdf presentation]
 
|-
 
|-
 
|16:10
 
|16:10
 
|A karyotype DAS client
 
|A karyotype DAS client
 
|Rafael Jimenez
 
|Rafael Jimenez
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/rjimenez_dasworkshop2009_KDC.ppt presentation]
 
|-
 
|-
 
|16:30
 
|16:30
 
|DASher, a standalone Java client for DAS protein sequence features
 
|DASher, a standalone Java client for DAS protein sequence features
 
|David Messina
 
|David Messina
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/Messina_DASconf09.keynote.zip presentation] [ftp://ftp.sanger.ac.uk/pub4/resources/software/das/Messina_DASconf09.pdf pdf]
 
|-
 
|-
 
|16:50
 
|16:50
 
|Data Federation - BioMart & DAS
 
|Data Federation - BioMart & DAS
 
|Syed Haider
 
|Syed Haider
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/BioMart_DAS_2009.ppt presentation]
 
|-
 
|-
 
|17:10
 
|17:10
 
|Trellis DAS2 framework- which includes the DAS1-->DAS2 proxy and alpha UCSC DAS2 server
 
|Trellis DAS2 framework- which includes the DAS1-->DAS2 proxy and alpha UCSC DAS2 server
 
|Gregg Helt
 
|Gregg Helt
−
|
+
|[ftp://ftp.sanger.ac.uk/pub4/resources/software/das/Trellis_Mar2009.pptx presentation]
 
|-
 
|-
 
|17:30
 
|17:30
Line 123: Line 174:
 
|}
 
|}
  
−
==Day 2==
+
==Day 3==
−
 
+
[http://www.biodas.org/wiki/DASworkshop200903Day3 Day3page]
−
 
 
−
{| class="wikitable" border="1"
 
−
|- style="background:silver"
 
−
! width="100px"|Time
 
−
! Title
 
−
! Speaker
 
−
! Resources
 
−
|-
 
−
| 09:15 - 10:00
 
−
| DAS - Technical Introduction
 
−
| 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
 
−
| DAS Introductory Tutorial - DAS servers and the DAS Registration Service
 
−
| Phil Jones
 
−
| [[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
 
−
| Dasty2
 
−
| Rafael Jimenez
 
−
|
 
−
|-
 
−
| 12:10 - 12:40
 
−
| SPICE, Mapping features on 3D, viewing alignments
 
−
| Andreas Prlic
 
−
| [[DASworkshop200802:spice| SPICE links]]
 
−
|- style="background:#ffdead;"
 
−
| 12:40 - 13:40
 
−
| colspan="3" | Lunch break
 
−
|-
 
−
| 13:40 - 14:10
 
−
| Pepper
 
−
| 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;"
 
−
| 15:10 - 15:30
 
−
| colspan="3"|Coffee break
 
−
|-
 
−
| 15:30 - 16:30
 
−
| DAS - Coding a Client.
 
−
| [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]
 
−
|}
 

Latest revision as of 16:54, 18 January 2011

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

BioSapiens Network

Day 1

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 Powerpoint 2008

Powerpoint 1997
PDF

11:10 - 11:30 The DAS Registration Service Jonathan Warren The Registry
11:30 - 12:15 Putting it all together Rob Finn Powerpoint
PDF
12:15 - 13:15 Lunch break
13:15 - 15:10 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 Java server: Dazzle tutorial

Java client: Dasobert tutorial
Perl server: Bio::Das::ProServer tutorial
Perl client: Bio::Das::Lite tutorial

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

Day 2

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

Day 3

Day3page

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