Difference between revisions of "DASworkshop200903"

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| Putting it all together
 
| Putting it all together
 
| Rob Finn
 
| Rob Finn
−
|  
+
| [http://www.biodas.org/workshop_2009/20090309ClientSpecReview.ppt Powerpoint]<br/> [http://www.biodas.org/workshop_2009/20090309ClientSpecReview.pdf PDF]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
| 12:15 - 13:15  
 
| 12:15 - 13:15  
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|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;"
 
|- style="background:#ffdead;"
 
|12:15-13:30
 
|12:15-13:30
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|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
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|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
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==Day 3==
 
==Day 3==
 
[http://www.biodas.org/wiki/DASworkshop200903Day3 Day3page]
 
[http://www.biodas.org/wiki/DASworkshop200903Day3 Day3page]
−
===Chromsome.java===
 
−
<pre>
 
−
package myplugins;
 
−
 
−
import java.util.ArrayList;
 
−
import java.util.Iterator;
 
−
 
−
import org.biojava.servlets.dazzle.Segment;
 
−
import org.biojava.servlets.dazzle.datasource.GFFFeature;
 
−
 
−
/**
 
−
* simple class for demo purposes that returns features from given
 
−
segments of a chromosome
 
−
* that has probably been specified in gff type format
 
−
* @author jw12
 
−
*
 
−
*/
 
−
public class Chromosome {
 
−
      private String id="";
 
−
      private int start=1;
 
−
      private int end;
 
−
      ArrayList features;
 
−
      public Chromosome(String id, int end){
 
−
        this.id=id;
 
−
        this.end=end;
 
−
        features =new ArrayList();
 
−
      }
 
−
      public void addFeature(GFFFeature feature){
 
−
              this.features.add(feature);
 
−
      }
 
−
      public GFFFeature[] getFeatures(Segment seg){
 
−
              System.out.println("seg in chromosome="+seg);
 
−
              ArrayList featuresOnSegment=new ArrayList();
 
−
              int start=seg.getStart();
 
−
              int stop =seg.getStop();
 
−
              //loop over arraylist of features and return a lis
 
−
              Iterator it=features.iterator();
 
−
            while(it.hasNext()){
 
−
                      GFFFeature feature=(GFFFeature)it.next();
 
−
                      int fStart=Integer.parseInt(feature.getStart());
 
−
                      int fStop=Integer.parseInt(feature.getEnd());
 
−
              //if between start and stop then include in returned list
 
−
                      if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){
 
−
                              featuresOnSegment.add(feature);
 
−
                      }
 
−
              }
 
−
              return (GFFFeature[]) featuresOnSegment.toArray(new
 
−
GFFFeature[featuresOnSegment.size()]);
 
−
              //return new GFFFeature[0];
 
−
      }
 
−
}
 
−
</pre>
 

Latest revision as of 12:54, 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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