Difference between revisions of "DASworkshop200903"

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(Day 3)
(Chromsome.java)
Line 193: Line 193:
 
  */
 
  */
 
public class Chromosome {
 
public class Chromosome {
 
 
       private String id="";
 
       private String id="";
 
       private int start=1;
 
       private int start=1;
 
       private int end;
 
       private int end;
 
       ArrayList features;
 
       ArrayList features;
 
 
       public Chromosome(String id, int end){
 
       public Chromosome(String id, int end){
 
         this.id=id;
 
         this.id=id;
 
         this.end=end;
 
         this.end=end;
 
         features =new ArrayList();
 
         features =new ArrayList();
 
 
       }
 
       }
 
 
       public void addFeature(GFFFeature feature){
 
       public void addFeature(GFFFeature feature){
 
               this.features.add(feature);
 
               this.features.add(feature);
 
       }
 
       }
 
 
       public GFFFeature[] getFeatures(Segment seg){
 
       public GFFFeature[] getFeatures(Segment seg){
 
               System.out.println("seg in chromosome="+seg);
 
               System.out.println("seg in chromosome="+seg);
Line 217: Line 212:
 
               //loop over arraylist of features and return a lis
 
               //loop over arraylist of features and return a lis
 
               Iterator it=features.iterator();
 
               Iterator it=features.iterator();
 
+
            while(it.hasNext()){
              while(it.hasNext()){
 
 
                       GFFFeature feature=(GFFFeature)it.next();
 
                       GFFFeature feature=(GFFFeature)it.next();
 
                       int fStart=Integer.parseInt(feature.getStart());
 
                       int fStart=Integer.parseInt(feature.getStart());
Line 225: Line 219:
 
                       if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){
 
                       if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){
 
                               featuresOnSegment.add(feature);
 
                               featuresOnSegment.add(feature);
 
 
                       }
 
                       }
 
               }
 
               }
Line 231: Line 224:
 
GFFFeature[featuresOnSegment.size()]);
 
GFFFeature[featuresOnSegment.size()]);
 
               //return new GFFFeature[0];
 
               //return new GFFFeature[0];
 
 
       }
 
       }
 
 
 
}
 
}

Revision as of 14:26, 9 March 2009

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
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
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 3

Day3page

Chromsome.java

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];
      }

}