DASworkshop200903

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	[[1]]
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	pdf
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];
       }
}