From jay at jays.net  Sat Mar  4 18:59:17 2006
From: jay at jays.net (Jay Hannah)
Date: Sat, 04 Mar 2006 17:59:17 -0600
Subject: [BioSQL-l] biosql-ERD - biodatabase table
Message-ID: <440A29D5.5080207@jays.net>

Greetings --

Does the biodatabase table intend to make virtual databases available inside a single mySQL database? In other words, if I have 500 sequences loaded into my mySQL database "VIRUS", does the biodatabase table intend to organize my 500 sequences into an arbitrary number of "databases" that I name? 

Or does it serve another purpose?

Thanks,

j
Omaha Perl Mongers
http://omaha.pm.org



From mjcipriano at lbl.gov  Tue Mar  7 12:39:44 2006
From: mjcipriano at lbl.gov (Michael Cipriano)
Date: Tue, 07 Mar 2006 09:39:44 -0800
Subject: [BioSQL-l] BioSQL and GBrowse
Message-ID: <1141753184.24737.27.camel@alien>

Hello,

I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
problem, so tell me if I should post this to the GBrowse list.

I have a BioSQL database with bacterial genome sequences loaded from
genbank files.  I can browse around the database just fine, but when I
try and use gbrowse_img, the image is messed up.

Take a look at these two links, they should show basicaly the same
thing, but the gbrowse_img link shows the features all piled up at the
left side of the image, and they are barely visible.


http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800

The weird thing is that I can sometimes get the images to work partialy,
but mostly on the most 5' end of the genome, in the low numbers. For
instance:

http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;

This shows more of the image in the gbrowse_img portion, but it is about
1kb off, so I think that the larger the position, the larger the stop
position is being displayed? This is purely conjecture, but it seems a
little weird. 

Here is part of my gbrowse conf file (below).  I will note that I have
installed many configurations of gbrowse, but this is my first one using
BioSQL. This does seem to be a biosql only problem, as the included
in-memory GFF database shows the correct image. 

Any help would be appreciated.

Thanks,
Michael Cipriano



Versions from the top of the files:

gbrowse_img:
$VERSION   = 1.64;
# $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $

gbrowse:
$VERSION   = 1.64;
$BIOGRAPHICS_VERSION   = 1.65;
# $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $


Here is the CDS stanza from gbrowse.

[CDS]
feature      = CDS
glyph        = transcript2
bgcolor      = turquoise
fgcolor      = black
height       = 10
connector    = solid
label        = sub {
        my $feature = shift;
        my @notes;
        if ($feature->primary_tag eq "CDS")
        {
                foreach (qw(product gene))
                {
                        next unless $feature->has_tag($_);
                        @notes = $feature->each_tag_value($_);
                        last;
                }
                return $notes[0];
        } else
        {
                return $feature->display_name;
        }
 }

description  = sub {
        my $feature = shift;
        my @notes;
        if ($feature->primary_tag eq "CDS")
        {
                foreach (qw(note))
                {
                        next unless $feature->has_tag($_);
                        @notes = $feature->each_tag_value($_);
                        last;
                }
                return unless @notes;
                substr($notes[0],30) = '...' if length $notes[0] > 30;
                return $notes[0];
        } else
        {
                my $description;
                foreach ($feature->all_tags)
                {
                        my @values = $feature->each_tag_value($_);
                        $description .= $_ eq 'note' ? "@values" :
"$_=@values; ";
                }
                $description =~ s/; $//; # get rid of last
                return $description;
        }
  }
link         = sub {
                        my $feature = shift;
                        my $pk = $feature->primary_key();
                        return
"/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
  }
key          = Predicted transcripts





From mjcipriano at lbl.gov  Wed Mar  8 13:07:53 2006
From: mjcipriano at lbl.gov (Michael Cipriano)
Date: Wed, 08 Mar 2006 10:07:53 -0800
Subject: [BioSQL-l] BioSQL and GBrowse
In-Reply-To: <1141753184.24737.27.camel@alien>
References: <1141753184.24737.27.camel@alien>
Message-ID: <1141841273.30883.0.camel@alien>


Ok, I installed the CVS version rather then the release version and
everything seems to be working now, so if anyone else gets this problem,
that is the simple solution.

-Michael

On Tue, 2006-03-07 at 09:39 -0800, Michael Cipriano wrote:
> Hello,
> 
> I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
> problem, so tell me if I should post this to the GBrowse list.
> 
> I have a BioSQL database with bacterial genome sequences loaded from
> genbank files.  I can browse around the database just fine, but when I
> try and use gbrowse_img, the image is messed up.
> 
> Take a look at these two links, they should show basicaly the same
> thing, but the gbrowse_img link shows the features all piled up at the
> left side of the image, and they are barely visible.
> 
> 
> http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
> http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800
> 
> The weird thing is that I can sometimes get the images to work partialy,
> but mostly on the most 5' end of the genome, in the low numbers. For
> instance:
> 
> http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
> http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;
> 
> This shows more of the image in the gbrowse_img portion, but it is about
> 1kb off, so I think that the larger the position, the larger the stop
> position is being displayed? This is purely conjecture, but it seems a
> little weird. 
> 
> Here is part of my gbrowse conf file (below).  I will note that I have
> installed many configurations of gbrowse, but this is my first one using
> BioSQL. This does seem to be a biosql only problem, as the included
> in-memory GFF database shows the correct image. 
> 
> Any help would be appreciated.
> 
> Thanks,
> Michael Cipriano
> 
> 
> 
> Versions from the top of the files:
> 
> gbrowse_img:
> $VERSION   = 1.64;
> # $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $
> 
> gbrowse:
> $VERSION   = 1.64;
> $BIOGRAPHICS_VERSION   = 1.65;
> # $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $
> 
> 
> Here is the CDS stanza from gbrowse.
> 
> [CDS]
> feature      = CDS
> glyph        = transcript2
> bgcolor      = turquoise
> fgcolor      = black
> height       = 10
> connector    = solid
> label        = sub {
>         my $feature = shift;
>         my @notes;
>         if ($feature->primary_tag eq "CDS")
>         {
>                 foreach (qw(product gene))
>                 {
>                         next unless $feature->has_tag($_);
>                         @notes = $feature->each_tag_value($_);
>                         last;
>                 }
>                 return $notes[0];
>         } else
>         {
>                 return $feature->display_name;
>         }
>  }
> 
> description  = sub {
>         my $feature = shift;
>         my @notes;
>         if ($feature->primary_tag eq "CDS")
>         {
>                 foreach (qw(note))
>                 {
>                         next unless $feature->has_tag($_);
>                         @notes = $feature->each_tag_value($_);
>                         last;
>                 }
>                 return unless @notes;
>                 substr($notes[0],30) = '...' if length $notes[0] > 30;
>                 return $notes[0];
>         } else
>         {
>                 my $description;
>                 foreach ($feature->all_tags)
>                 {
>                         my @values = $feature->each_tag_value($_);
>                         $description .= $_ eq 'note' ? "@values" :
> "$_=@values; ";
>                 }
>                 $description =~ s/; $//; # get rid of last
>                 return $description;
>         }
>   }
> link         = sub {
>                         my $feature = shift;
>                         my $pk = $feature->primary_key();
>                         return
> "/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
>   }
> key          = Predicted transcripts
> 
> 
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l


From gad14 at cornell.edu  Mon Mar 13 16:24:30 2006
From: gad14 at cornell.edu (Genevieve DeClerck)
Date: Mon, 13 Mar 2006 16:24:30 -0500
Subject: [BioSQL-l] BioSQL and GBrowse
In-Reply-To: <1141841273.30883.0.camel@alien>
References: <1141753184.24737.27.camel@alien> <1141841273.30883.0.camel@alien>
Message-ID: <4415E30E.1020805@cornell.edu>

Hi,

I am trying to get GBrowse running with a biosql database but i'm having 
problems.

Here's what i'm working with:
GBrowse 1.64
Mysql database with fresh biosql-schema
bioperl 1.5.1 (CVS bioperl-live)
Perl 5.8.1
Mac OS X 10.3.9

At the moment, I can load in a web browser GBrowse db's that don't have 
a Biosql schema just fine. When I try to load my BioSQL database in 
Gbrowse I get the following in the web browser (printed with the nice 
blue, red, and black flavored GBrowse font/format):

----
An internal error has occurred

Could not open database.
Can't locate object method "new" via package "Bio::DB::Das::BioSQL" at 
/Library/Perl/5.8.1//darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm 
line 185.
----

And the following in my apache error log:

----
GBROWSE VERSION MISMATCH:
GBrowse version 1.64 requires a compatible version of the Bio::Graphics 
library.
You should either install BioPerl (the CVS live version) or reinstall 
GBrowse,
which will patch Bio::Graphics to the latest version.
gbrowse: trying to reload config, cache must be stale at 
/Library/Perl/5.8.1//darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm 
line 172.
Can't locate object method "new" via package "Bio::DB::Das::BioSQL" at 
/Library/Perl/5.8.1//darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm 
line 185.
----

 From what I've read in the docs, bioperl 1.5.1 should be the proper 
version to run with GBrowse 1.64. I also installed biosql and bioperl-db 
fresh. What does the error "gbrowse: trying to reload config, cache must 
be stale at" mean in relation to Util.pm? I've looked at the code in 
Util.pm -- the error seems related to the database adaptor...

My gbrowse .conf file is identical to the 06.biosql.conf file except for 
the first few lines (pasted below).
I used the load_seqdatabase.pl to load an abreviated version of 
NC_004578.gbk (p. syrinage dc3000 from ncbi refseq) into the biosql db.

---
my test_biosq.conf

[GENERAL]
description = test_biosql
db_adaptor  = Bio::DB::Das::BioSQL
db_args     = driver    mysql
	      dbname    test_biosql
	      namespace genbank
	      version 	1
	      host      localhost
	      user      nobody
	      pass     	""
	      port 3306

---

Any ideas or comments appreciated!

Thanks,
Genevieve



Michael Cipriano wrote:

> Ok, I installed the CVS version rather then the release version and
> everything seems to be working now, so if anyone else gets this problem,
> that is the simple solution.
> 
> -Michael
> 
> On Tue, 2006-03-07 at 09:39 -0800, Michael Cipriano wrote:
> 
>>Hello,
>>
>>I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
>>problem, so tell me if I should post this to the GBrowse list.
>>
>>I have a BioSQL database with bacterial genome sequences loaded from
>>genbank files.  I can browse around the database just fine, but when I
>>try and use gbrowse_img, the image is messed up.
>>
>>Take a look at these two links, they should show basicaly the same
>>thing, but the gbrowse_img link shows the features all piled up at the
>>left side of the image, and they are barely visible.
>>
>>
>>http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
>>http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800
>>
>>The weird thing is that I can sometimes get the images to work partialy,
>>but mostly on the most 5' end of the genome, in the low numbers. For
>>instance:
>>
>>http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
>>http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;
>>
>>This shows more of the image in the gbrowse_img portion, but it is about
>>1kb off, so I think that the larger the position, the larger the stop
>>position is being displayed? This is purely conjecture, but it seems a
>>little weird. 
>>
>>Here is part of my gbrowse conf file (below).  I will note that I have
>>installed many configurations of gbrowse, but this is my first one using
>>BioSQL. This does seem to be a biosql only problem, as the included
>>in-memory GFF database shows the correct image. 
>>
>>Any help would be appreciated.
>>
>>Thanks,
>>Michael Cipriano
>>
>>
>>
>>Versions from the top of the files:
>>
>>gbrowse_img:
>>$VERSION   = 1.64;
>># $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $
>>
>>gbrowse:
>>$VERSION   = 1.64;
>>$BIOGRAPHICS_VERSION   = 1.65;
>># $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $
>>
>>
>>Here is the CDS stanza from gbrowse.
>>
>>[CDS]
>>feature      = CDS
>>glyph        = transcript2
>>bgcolor      = turquoise
>>fgcolor      = black
>>height       = 10
>>connector    = solid
>>label        = sub {
>>        my $feature = shift;
>>        my @notes;
>>        if ($feature->primary_tag eq "CDS")
>>        {
>>                foreach (qw(product gene))
>>                {
>>                        next unless $feature->has_tag($_);
>>                        @notes = $feature->each_tag_value($_);
>>                        last;
>>                }
>>                return $notes[0];
>>        } else
>>        {
>>                return $feature->display_name;
>>        }
>> }
>>
>>description  = sub {
>>        my $feature = shift;
>>        my @notes;
>>        if ($feature->primary_tag eq "CDS")
>>        {
>>                foreach (qw(note))
>>                {
>>                        next unless $feature->has_tag($_);
>>                        @notes = $feature->each_tag_value($_);
>>                        last;
>>                }
>>                return unless @notes;
>>                substr($notes[0],30) = '...' if length $notes[0] > 30;
>>                return $notes[0];
>>        } else
>>        {
>>                my $description;
>>                foreach ($feature->all_tags)
>>                {
>>                        my @values = $feature->each_tag_value($_);
>>                        $description .= $_ eq 'note' ? "@values" :
>>"$_=@values; ";
>>                }
>>                $description =~ s/; $//; # get rid of last
>>                return $description;
>>        }
>>  }
>>link         = sub {
>>                        my $feature = shift;
>>                        my $pk = $feature->primary_key();
>>                        return
>>"/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
>>  }
>>key          = Predicted transcripts
>>
>>
>>
>>
>>_______________________________________________
>>BioSQL-l mailing list
>>BioSQL-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/biosql-l
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
> 


From darin.london at duke.edu  Tue Mar 28 09:42:45 2006
From: darin.london at duke.edu (Darin London)
Date: Tue, 28 Mar 2006 09:42:45 -0500
Subject: [BioSQL-l] Announcing BOSC 2006
Message-ID: <44294B65.4050207@duke.edu>

MEETING ANNOUNCEMENT & CALL FOR SPEAKERS

The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is
organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 14th
International Conference
on Intelligent Systems for Molecular Biology.  Please consult The Official
BOSC 2006 Website at

http://www.open-bio.org/wiki/BOSC_2006

for details and information. 

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB calendar
set up with all BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official
ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/


Thank You, and we look forward to seeing you all,
The BOSC Organizing Committee.

From jay at jays.net  Sat Mar  4 23:59:17 2006
From: jay at jays.net (Jay Hannah)
Date: Sat, 04 Mar 2006 17:59:17 -0600
Subject: [BioSQL-l] biosql-ERD - biodatabase table
Message-ID: <440A29D5.5080207@jays.net>

Greetings --

Does the biodatabase table intend to make virtual databases available inside a single mySQL database? In other words, if I have 500 sequences loaded into my mySQL database "VIRUS", does the biodatabase table intend to organize my 500 sequences into an arbitrary number of "databases" that I name? 

Or does it serve another purpose?

Thanks,

j
Omaha Perl Mongers
http://omaha.pm.org




From mjcipriano at lbl.gov  Tue Mar  7 17:39:44 2006
From: mjcipriano at lbl.gov (Michael Cipriano)
Date: Tue, 07 Mar 2006 09:39:44 -0800
Subject: [BioSQL-l] BioSQL and GBrowse
Message-ID: <1141753184.24737.27.camel@alien>

Hello,

I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
problem, so tell me if I should post this to the GBrowse list.

I have a BioSQL database with bacterial genome sequences loaded from
genbank files.  I can browse around the database just fine, but when I
try and use gbrowse_img, the image is messed up.

Take a look at these two links, they should show basicaly the same
thing, but the gbrowse_img link shows the features all piled up at the
left side of the image, and they are barely visible.


http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800

The weird thing is that I can sometimes get the images to work partialy,
but mostly on the most 5' end of the genome, in the low numbers. For
instance:

http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;

This shows more of the image in the gbrowse_img portion, but it is about
1kb off, so I think that the larger the position, the larger the stop
position is being displayed? This is purely conjecture, but it seems a
little weird. 

Here is part of my gbrowse conf file (below).  I will note that I have
installed many configurations of gbrowse, but this is my first one using
BioSQL. This does seem to be a biosql only problem, as the included
in-memory GFF database shows the correct image. 

Any help would be appreciated.

Thanks,
Michael Cipriano



Versions from the top of the files:

gbrowse_img:
$VERSION   = 1.64;
# $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $

gbrowse:
$VERSION   = 1.64;
$BIOGRAPHICS_VERSION   = 1.65;
# $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $


Here is the CDS stanza from gbrowse.

[CDS]
feature      = CDS
glyph        = transcript2
bgcolor      = turquoise
fgcolor      = black
height       = 10
connector    = solid
label        = sub {
        my $feature = shift;
        my @notes;
        if ($feature->primary_tag eq "CDS")
        {
                foreach (qw(product gene))
                {
                        next unless $feature->has_tag($_);
                        @notes = $feature->each_tag_value($_);
                        last;
                }
                return $notes[0];
        } else
        {
                return $feature->display_name;
        }
 }

description  = sub {
        my $feature = shift;
        my @notes;
        if ($feature->primary_tag eq "CDS")
        {
                foreach (qw(note))
                {
                        next unless $feature->has_tag($_);
                        @notes = $feature->each_tag_value($_);
                        last;
                }
                return unless @notes;
                substr($notes[0],30) = '...' if length $notes[0] > 30;
                return $notes[0];
        } else
        {
                my $description;
                foreach ($feature->all_tags)
                {
                        my @values = $feature->each_tag_value($_);
                        $description .= $_ eq 'note' ? "@values" :
"$_=@values; ";
                }
                $description =~ s/; $//; # get rid of last
                return $description;
        }
  }
link         = sub {
                        my $feature = shift;
                        my $pk = $feature->primary_key();
                        return
"/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
  }
key          = Predicted transcripts






From mjcipriano at lbl.gov  Wed Mar  8 18:07:53 2006
From: mjcipriano at lbl.gov (Michael Cipriano)
Date: Wed, 08 Mar 2006 10:07:53 -0800
Subject: [BioSQL-l] BioSQL and GBrowse
In-Reply-To: <1141753184.24737.27.camel@alien>
References: <1141753184.24737.27.camel@alien>
Message-ID: <1141841273.30883.0.camel@alien>


Ok, I installed the CVS version rather then the release version and
everything seems to be working now, so if anyone else gets this problem,
that is the simple solution.

-Michael

On Tue, 2006-03-07 at 09:39 -0800, Michael Cipriano wrote:
> Hello,
> 
> I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
> problem, so tell me if I should post this to the GBrowse list.
> 
> I have a BioSQL database with bacterial genome sequences loaded from
> genbank files.  I can browse around the database just fine, but when I
> try and use gbrowse_img, the image is messed up.
> 
> Take a look at these two links, they should show basicaly the same
> thing, but the gbrowse_img link shows the features all piled up at the
> left side of the image, and they are barely visible.
> 
> 
> http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
> http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800
> 
> The weird thing is that I can sometimes get the images to work partialy,
> but mostly on the most 5' end of the genome, in the low numbers. For
> instance:
> 
> http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
> http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;
> 
> This shows more of the image in the gbrowse_img portion, but it is about
> 1kb off, so I think that the larger the position, the larger the stop
> position is being displayed? This is purely conjecture, but it seems a
> little weird. 
> 
> Here is part of my gbrowse conf file (below).  I will note that I have
> installed many configurations of gbrowse, but this is my first one using
> BioSQL. This does seem to be a biosql only problem, as the included
> in-memory GFF database shows the correct image. 
> 
> Any help would be appreciated.
> 
> Thanks,
> Michael Cipriano
> 
> 
> 
> Versions from the top of the files:
> 
> gbrowse_img:
> $VERSION   = 1.64;
> # $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $
> 
> gbrowse:
> $VERSION   = 1.64;
> $BIOGRAPHICS_VERSION   = 1.65;
> # $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $
> 
> 
> Here is the CDS stanza from gbrowse.
> 
> [CDS]
> feature      = CDS
> glyph        = transcript2
> bgcolor      = turquoise
> fgcolor      = black
> height       = 10
> connector    = solid
> label        = sub {
>         my $feature = shift;
>         my @notes;
>         if ($feature->primary_tag eq "CDS")
>         {
>                 foreach (qw(product gene))
>                 {
>                         next unless $feature->has_tag($_);
>                         @notes = $feature->each_tag_value($_);
>                         last;
>                 }
>                 return $notes[0];
>         } else
>         {
>                 return $feature->display_name;
>         }
>  }
> 
> description  = sub {
>         my $feature = shift;
>         my @notes;
>         if ($feature->primary_tag eq "CDS")
>         {
>                 foreach (qw(note))
>                 {
>                         next unless $feature->has_tag($_);
>                         @notes = $feature->each_tag_value($_);
>                         last;
>                 }
>                 return unless @notes;
>                 substr($notes[0],30) = '...' if length $notes[0] > 30;
>                 return $notes[0];
>         } else
>         {
>                 my $description;
>                 foreach ($feature->all_tags)
>                 {
>                         my @values = $feature->each_tag_value($_);
>                         $description .= $_ eq 'note' ? "@values" :
> "$_=@values; ";
>                 }
>                 $description =~ s/; $//; # get rid of last
>                 return $description;
>         }
>   }
> link         = sub {
>                         my $feature = shift;
>                         my $pk = $feature->primary_key();
>                         return
> "/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
>   }
> key          = Predicted transcripts
> 
> 
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l



From gad14 at cornell.edu  Mon Mar 13 21:24:30 2006
From: gad14 at cornell.edu (Genevieve DeClerck)
Date: Mon, 13 Mar 2006 16:24:30 -0500
Subject: [BioSQL-l] BioSQL and GBrowse
In-Reply-To: <1141841273.30883.0.camel@alien>
References: <1141753184.24737.27.camel@alien> <1141841273.30883.0.camel@alien>
Message-ID: <4415E30E.1020805@cornell.edu>

Hi,

I am trying to get GBrowse running with a biosql database but i'm having 
problems.

Here's what i'm working with:
GBrowse 1.64
Mysql database with fresh biosql-schema
bioperl 1.5.1 (CVS bioperl-live)
Perl 5.8.1
Mac OS X 10.3.9

At the moment, I can load in a web browser GBrowse db's that don't have 
a Biosql schema just fine. When I try to load my BioSQL database in 
Gbrowse I get the following in the web browser (printed with the nice 
blue, red, and black flavored GBrowse font/format):

----
An internal error has occurred

Could not open database.
Can't locate object method "new" via package "Bio::DB::Das::BioSQL" at 
/Library/Perl/5.8.1//darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm 
line 185.
----

And the following in my apache error log:

----
GBROWSE VERSION MISMATCH:
GBrowse version 1.64 requires a compatible version of the Bio::Graphics 
library.
You should either install BioPerl (the CVS live version) or reinstall 
GBrowse,
which will patch Bio::Graphics to the latest version.
gbrowse: trying to reload config, cache must be stale at 
/Library/Perl/5.8.1//darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm 
line 172.
Can't locate object method "new" via package "Bio::DB::Das::BioSQL" at 
/Library/Perl/5.8.1//darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm 
line 185.
----

 From what I've read in the docs, bioperl 1.5.1 should be the proper 
version to run with GBrowse 1.64. I also installed biosql and bioperl-db 
fresh. What does the error "gbrowse: trying to reload config, cache must 
be stale at" mean in relation to Util.pm? I've looked at the code in 
Util.pm -- the error seems related to the database adaptor...

My gbrowse .conf file is identical to the 06.biosql.conf file except for 
the first few lines (pasted below).
I used the load_seqdatabase.pl to load an abreviated version of 
NC_004578.gbk (p. syrinage dc3000 from ncbi refseq) into the biosql db.

---
my test_biosq.conf

[GENERAL]
description = test_biosql
db_adaptor  = Bio::DB::Das::BioSQL
db_args     = driver    mysql
	      dbname    test_biosql
	      namespace genbank
	      version 	1
	      host      localhost
	      user      nobody
	      pass     	""
	      port 3306

---

Any ideas or comments appreciated!

Thanks,
Genevieve



Michael Cipriano wrote:

> Ok, I installed the CVS version rather then the release version and
> everything seems to be working now, so if anyone else gets this problem,
> that is the simple solution.
> 
> -Michael
> 
> On Tue, 2006-03-07 at 09:39 -0800, Michael Cipriano wrote:
> 
>>Hello,
>>
>>I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
>>problem, so tell me if I should post this to the GBrowse list.
>>
>>I have a BioSQL database with bacterial genome sequences loaded from
>>genbank files.  I can browse around the database just fine, but when I
>>try and use gbrowse_img, the image is messed up.
>>
>>Take a look at these two links, they should show basicaly the same
>>thing, but the gbrowse_img link shows the features all piled up at the
>>left side of the image, and they are barely visible.
>>
>>
>>http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
>>http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800
>>
>>The weird thing is that I can sometimes get the images to work partialy,
>>but mostly on the most 5' end of the genome, in the low numbers. For
>>instance:
>>
>>http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
>>http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;
>>
>>This shows more of the image in the gbrowse_img portion, but it is about
>>1kb off, so I think that the larger the position, the larger the stop
>>position is being displayed? This is purely conjecture, but it seems a
>>little weird. 
>>
>>Here is part of my gbrowse conf file (below).  I will note that I have
>>installed many configurations of gbrowse, but this is my first one using
>>BioSQL. This does seem to be a biosql only problem, as the included
>>in-memory GFF database shows the correct image. 
>>
>>Any help would be appreciated.
>>
>>Thanks,
>>Michael Cipriano
>>
>>
>>
>>Versions from the top of the files:
>>
>>gbrowse_img:
>>$VERSION   = 1.64;
>># $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $
>>
>>gbrowse:
>>$VERSION   = 1.64;
>>$BIOGRAPHICS_VERSION   = 1.65;
>># $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $
>>
>>
>>Here is the CDS stanza from gbrowse.
>>
>>[CDS]
>>feature      = CDS
>>glyph        = transcript2
>>bgcolor      = turquoise
>>fgcolor      = black
>>height       = 10
>>connector    = solid
>>label        = sub {
>>        my $feature = shift;
>>        my @notes;
>>        if ($feature->primary_tag eq "CDS")
>>        {
>>                foreach (qw(product gene))
>>                {
>>                        next unless $feature->has_tag($_);
>>                        @notes = $feature->each_tag_value($_);
>>                        last;
>>                }
>>                return $notes[0];
>>        } else
>>        {
>>                return $feature->display_name;
>>        }
>> }
>>
>>description  = sub {
>>        my $feature = shift;
>>        my @notes;
>>        if ($feature->primary_tag eq "CDS")
>>        {
>>                foreach (qw(note))
>>                {
>>                        next unless $feature->has_tag($_);
>>                        @notes = $feature->each_tag_value($_);
>>                        last;
>>                }
>>                return unless @notes;
>>                substr($notes[0],30) = '...' if length $notes[0] > 30;
>>                return $notes[0];
>>        } else
>>        {
>>                my $description;
>>                foreach ($feature->all_tags)
>>                {
>>                        my @values = $feature->each_tag_value($_);
>>                        $description .= $_ eq 'note' ? "@values" :
>>"$_=@values; ";
>>                }
>>                $description =~ s/; $//; # get rid of last
>>                return $description;
>>        }
>>  }
>>link         = sub {
>>                        my $feature = shift;
>>                        my $pk = $feature->primary_key();
>>                        return
>>"/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
>>  }
>>key          = Predicted transcripts
>>
>>
>>
>>
>>_______________________________________________
>>BioSQL-l mailing list
>>BioSQL-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/biosql-l
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
> 



From darin.london at duke.edu  Tue Mar 28 14:42:45 2006
From: darin.london at duke.edu (Darin London)
Date: Tue, 28 Mar 2006 09:42:45 -0500
Subject: [BioSQL-l] Announcing BOSC 2006
Message-ID: <44294B65.4050207@duke.edu>

MEETING ANNOUNCEMENT & CALL FOR SPEAKERS

The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is
organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 14th
International Conference
on Intelligent Systems for Molecular Biology.  Please consult The Official
BOSC 2006 Website at

http://www.open-bio.org/wiki/BOSC_2006

for details and information. 

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB calendar
set up with all BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official
ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/


Thank You, and we look forward to seeing you all,
The BOSC Organizing Committee.