Difference between revisions of "DASworkshop200903"

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m (Reverted edits by Jw12 (Talk) to last version by Felix k)
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|Opening talk  
 
|Opening talk  
 
|Tim Hubbard
 
|Tim Hubbard
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/ ]]
+
|
 
|-
 
|-
 
|10:20
 
|10:20
 
|Collaborative Annotation tool (MaDAS)
 
|Collaborative Annotation tool (MaDAS)
 
|Victor de la Torre
 
|Victor de la Torre
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/MaDAS_victor_de_la_torre.pptx powerpoint]]
+
|
 
|-
 
|-
 
|10:40
 
|10:40
 
|Jalview / VAMSAS
 
|Jalview / VAMSAS
 
|Jim Procter / Geoff Barton
 
|Jim Procter / Geoff Barton
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/ ]]
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|
 
|-
 
|-
 
|11:00
 
|11:00
 
|Pfam
 
|Pfam
 
|Rob Finn
 
|Rob Finn
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/20090309PfamDasWorkShop.ppt] powerpoint]
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|
 
|-
 
|-
 
|11:20
 
|11:20
 
|DASgenexp
 
|DASgenexp
 
|Bernat Gel
 
|Bernat Gel
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/DASGenExp3.ppt] powerpoint]
+
|
 
|-
 
|-
 
|11:40
 
|11:40
 
|Dasty2
 
|Dasty2
 
|Rafael Jimenez
 
|Rafael Jimenez
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
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|
 
|-
 
|-
 
|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
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
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|
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|12:15-13:30
 
|12:15-13:30
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|Ensembl
 
|Ensembl
 
|James Smith
 
|James Smith
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/2009-das-talk-smith.ppt]]
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|
 
|-
 
|-
 
|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
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|14:10
 
|14:10
 
|DAS - writeback
 
|DAS - writeback
 
|Gustavo Salazar
 
|Gustavo Salazar
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|14:30
 
|14:30
 
|Interaction DAS
 
|Interaction DAS
 
|Hagen Blankenburg
 
|Hagen Blankenburg
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|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
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|15:50
 
|15:50
 
|DAS Searches
 
|DAS Searches
 
|Andreas Prlic
 
|Andreas Prlic
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|16:10
 
|16:10
 
|A karyotype DAS client
 
|A karyotype DAS client
 
|Rafael Jimenez
 
|Rafael Jimenez
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|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
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|16:50
 
|16:50
 
|Data Federation - BioMart & DAS
 
|Data Federation - BioMart & DAS
 
|Syed Haider
 
|Syed Haider
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|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
|[[http://www.sanger.ac.uk/Software/analysis/das/presentations/
+
|
 
|-
 
|-
 
|17:30
 
|17:30

Revision as of 11:39, 13 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

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];
       }
}