1. GBrowse-related work at ApiDB
Haiming Wang
ApiDB Bioinformatics Resource Center
Dr. Jessica Kissinger Group
GMOD Nov 2007

2. Same database schema – GUS
Multi-species – comparative analysis
Graphical for protein data

3. Database adaptor vs GFF
Pros:
Live interactive with database
Flexible with database schema – GUS, Chado
Support complex data type, e.g. synteny, protein data
Cons:
Relatively slow – database tuning + bulkSubfeatures
Familiar with SQL

4. Database Adaptor for GBrowse
Based on the Chado adaptor
Separate queries into a separate config file
Segment->Feature->SubFeature
[GENERAL]
description = PlasmoDB Release 5.3
db_adaptor = DAS::GUS
database = dbi:Oracle:sid=crypto;host=rad.rcc.uga.edu;port=1521
user = gususer
pass = pass
db_args = -sqlfile =>$ENV{DOC_ROOT}.'/gbrowse.conf/plasmodb.xml'

5. features
segment

6. PBrowse

7. Synteny Browser - SynView
Steve Fisher will present it in details later

8. Track Customization

9. init_code = sub hover {
use HTML::Template;
my ($name, $data)
my $tmpl = HTML::Template=>new(filename=>$ENV{ROOT}.'/gbrowse/hover.tmpl');
$tmpl->param(DATA => [ map > 1 ? (KEY=>$_->[0],
VALUE => $_->[1]):(SINGLE =>
my $str = $tmpl->output;
$str =~ s/'/\\'/g;
return qq{" onMouseOver="$cmd;return escape('$str')}; }
link_target = sub { my $f = shift;
my $name = $f->name;
my $start = $f->start;
my $stop = $f->stop;
my ($freq) = $f->get_tag_values('RawCount');
my ($tag) = $f->get_tag_values('Sequence');
[ 'Location:' => "$start..$stop" ];
[ 'Sequence:' => $tag ];
[ 'Library:' => $lib ];
[ 'Frequency:' => $freq];
return hover( "Sage Tag - Temp ID $name",

10. Future Works Performance tuning – SQL, bulksubfeatures, AJAX tooltips
Unification with web inferface WDK
All projects share same gbrowse configuration
Be able to divide the .conf and .xml files into sub files
Be able to include/exclude based on project
Re-using sql and perl across tracks, e.g. duplicate code