Difference between revisions of "DASworkshop200903"

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m (Reverted edits by Jw12 (Talk) to last version by Felix k)
(→‎Chromsome.java)
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==Day 3==
 
==Day 3==
 
[http://www.biodas.org/wiki/DASworkshop200903Day3 Day3page]
 
[http://www.biodas.org/wiki/DASworkshop200903Day3 Day3page]
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===Chromsome.java===
 
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<pre>
 
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package myplugins;
 
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import java.util.ArrayList;
 
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import java.util.Iterator;
 
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import org.biojava.servlets.dazzle.Segment;
 
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import org.biojava.servlets.dazzle.datasource.GFFFeature;
 
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/**
 
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* simple class for demo purposes that returns features from given
 
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segments of a chromosome
 
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* that has probably been specified in gff type format
 
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* @author jw12
 
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*
 
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*/
 
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public class Chromosome {
 
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      private String id="";
 
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      private int start=1;
 
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      private int end;
 
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      ArrayList features;
 
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      public Chromosome(String id, int end){
 
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        this.id=id;
 
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        this.end=end;
 
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        features =new ArrayList();
 
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      }
 
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      public void addFeature(GFFFeature feature){
 
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              this.features.add(feature);
 
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      }
 
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      public GFFFeature[] getFeatures(Segment seg){
 
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              System.out.println("seg in chromosome="+seg);
 
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              ArrayList featuresOnSegment=new ArrayList();
 
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              int start=seg.getStart();
 
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              int stop =seg.getStop();
 
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              //loop over arraylist of features and return a lis
 
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              Iterator it=features.iterator();
 
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            while(it.hasNext()){
 
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                      GFFFeature feature=(GFFFeature)it.next();
 
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                      int fStart=Integer.parseInt(feature.getStart());
 
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                      int fStop=Integer.parseInt(feature.getEnd());
 
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              //if between start and stop then include in returned list
 
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                      if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){
 
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                              featuresOnSegment.add(feature);
 
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                      }
 
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              }
 
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              return (GFFFeature[]) featuresOnSegment.toArray(new
 
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GFFFeature[featuresOnSegment.size()]);
 
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              //return new GFFFeature[0];
 
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      }
 
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}
 
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</pre>
 

Revision as of 06:44, 16 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 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

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