VG2 In The News...


  1. November 2, 2004: New-and-improved bVG2!
  2. November 1, 2004, hopefully last today: New-and-improved beta VG2!
  3. November 1, 2004, later: New-and-improved betaVG2!
  4. November 1, 2004: New-and-improved betaVG2!
  5. October 29, 2004: New-and-improved betaVG2!
  6. October 28, 2004: ATTENTION VG2 USERS: BETA vg2 update
  7. October 21, 2004: New-and-improved betaVG2!
  8. October 15, 2004: ALPHA VG2

November 2, 2004: New-and-improved bVG2!

Hello VG2 Users,

  This version removes the Zoom: slider bar, since the current VG2 does not support 'zoom' 
function components.  If there's enough requests for 'zoom' functionality, perhaps it will make a comeback at a later date.

Thanks,
   Eben Calhoun
    

November 1, 2004, hopefully last today: New-and-improved beta VG2!

Hello VG2 Users,

  Yet another version of beta VG2 has been released.  This version correctly aligns the LDGram and 
BlockGram with one another.

Thanks,
  Eben Calhoun
    

November 1, 2004, later: New-and-improved betaVG2!

Hello VG2 Users,

  Yet another version of beta VG2 has been released.  This version exports PNG, SVG and JPEG files to 
the correct directory on the Macintosh.  Check-it-out if you use a Mac.

Thanks,
  Eben Calhoun
    

November 1, 2004: New-and-improved betaVG2!

Hello VG2 Users,

  Today I have released a new *BETA* version of VG2.  This one has some minor 
bugfixes with regards to correctly outputting JPEG and PNG files, eliminating 
the space between the BlockGram and LDGram, LDGram alignment with respect to 
BlockGram and removal of some diagnostic console messages.

Thanks,
  Eben Calhoun
    

October 29, 2004: New-and-improved betaVG2!

Hello VG2 Users,

  Today I have released a new *BETA* version of VG2.  This one has some minor 
bugfixes with regards to correct display of long sample names, minor component 
alignment adjustments and display of the entire Blockgram.

Thanks,
   Eben Calhoun
    

October 28, 2004: ATTENTION VG2 USERS: BETA vg2 update

Hello VG2 Users,

  Today I have released a new *BETA* version of VG2 for you to try out.  
Essentially, this version is the same as last week's *BETA* version, plus a few
 bugfixes.  This version does not export to JPG, PNG or SVG-format files yet.

  If one feels daring, please try it out and let me know about any bugs one 
might encounter.  I've put in a request to have this software installed, and it
 should show-up before too long.  And if one doesn't feel daring, the original,
 old 'betavg2' will be available at 'betavg2classic'.

  In the future, all VG2 updates will be posted on the:

http://nick-lab.gs.washington.edu/

web page under the 'VG2 INFO / UPDATES'  link.  This way one will be able to 
view all prior VG2 update messages at the same time, and not be inundated with 
VG2 update email messages.

Thanks,
   Eben Calhoun
    

October 21, 2004 New-and-improved betaVG2!

	From: 	  ecalhoun@gs.washington.edu
	Subject: 	New-and-improved betaVG2!
	Date: 	October 21, 2004 3:50:37 PM PDT
	To: 	  nick-talk@gs.washington.edu

Hello VG2 Users,

  Today I have released a new *BETA* version of VG2 for you to try out.  
Essentially, this version is the same as last week's *ALPHA* version, plus it 
has the capability to print.  This version does not export to JPG, PNG or 
SVG-format files yet.

  If you feel daring, please try it out and let me know about any bugs you may 
encounter.  I've put in a request to have this software installed, and it 
should show-up before too long.  And if you aren't feeling daring, the old 
'betavg2' will be available at 'betavg2classic'.

  One final note, if you did not use *ALPHA* VG2 yet, you will need to follow 
the directions in the *ALPHA* VG2 email regarding configuration of the 
databases before you will be able to connect to databases in *BETA* VG2.

Thanks,
   Eben Calhoun
    

October 15, 2004: ALPHA VG2

From:   ecalhoun@gs.washington.edu
Subject: INFO for VG2 USERS
Date: October 15, 2004 11:44:46 AM PDT
To:   nick-talk@gs.washington.edu

Hello VG2 users,

I have built a new, *ALPHA* VG2 for your perusal.  Please note that this 
version does not support printing nor file exportation.  Otherwise it should 
get you where you need to go.  I submitted a request to the system 
administrators have the files installed, so they ought to show-up before too 
long.

To run *ALPHA* VG2, just type 'alphavg2'.

One item to mention is that this VG2 has a new means of connection to the 
database.  Database code is no longer hard-coded into the software and is now 
kept in a Preferences database.  One will need to define one's database 
connections in order to connect to pgatmp or egptmp.  This only needs to be 
done the 1st time one runs the more recent versions of VG2.  Afterwards, only 
new project databases will have to be added via this menu.  The reasoning 
behind this is to allow external users to be able to integrate VG2 with their 
databases, whose schemas are different than Nickerson lab databases.

This is done as follows:

1. Open the 'Edit' -> 'Properties' menu.

2. Click on the 'Databases' tab.

3. Click on the 'New' button.

4. Fill-out each box with the exact following text:

Nickname:

PGATMP

JDBC URL:

jdbc:postgresql://superfriends.gs.washington.edu:5432/pgatmp

JDBC Driver:

org.postgresql.Driver

Single Site Query:

SELECT consensus_seq_start, contig_name, chromat_name, chromat_start FROM 
@$@TABLENAME@$@ WHERE consensus_seq_start = @$@VARIATION@$@ AND chromat_name 
LIKE '%@$@SAMPLENAME@$@%' ORDER BY consensus_seq_start, chromat_name

Batch Sites Query:

SELECT consensus_seq_start, contig_name, chromat_name, chromat_start FROM 
@$@TABLENAME@$@ WHERE consensus_seq_start = @$@VARIATION@$@ AND 
(allele1 != '@$@COMMONALLELE@$@' OR allele2 != '@$@COMMONALLELE@$@') ORDER BY 
consensus_seq_start, chromat_name

5. Click the 'OK' button.  One now has a connection to PGATMP defined.

6. Click on the 'New' button.

7. Fill-out each box with the exact following text:

Nickname:

EGPTMP

JDBC URL:

jdbc:postgresql://superfriends.gs.washington.edu:5433/egptmp

JDBC Driver:

org.postgresql.Driver

Single Site Query:

SELECT consensus_seq_start, contig_name, chromat_name, chromat_start FROM 
@$@TABLENAME@$@ WHERE consensus_seq_start = @$@VARIATION@$@ AND chromat_name 
LIKE '%@$@SAMPLENAME@$@%' ORDER BY consensus_seq_start, chromat_name

Batch Sites Query:

SELECT consensus_seq_start, contig_name, chromat_name, chromat_start FROM 
@$@TABLENAME@$@ WHERE consensus_seq_start = @$@VARIATION@$@ AND 
(allele1 != '@$@COMMONALLELE@$@' OR allele2 != '@$@COMMONALLELE@$@') ORDER BY 
consensus_seq_start, chromat_name

8. Click the 'OK' button.  One now has a connection to EGPTMP defined.

9. Now click on the 'Display' tab.

10. Click the 'Choose' to select one's Consed executable file. ( probably 
going to be /afs/nick.gs.washington.edu/genome/bin_linux_ia32/consed )

11. Click the 'OK' button.  One should now be back at the main VG2 screen.

Thanks,
   Eben Calhoun