DASworkshop200903

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Revision as of 10:29, 9 March 2009 by Jw12 (talk) (Chromsome.java)
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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];
       }
}