[Gmod-gbrowse] gbrowse configuration help

Discussion:

Irina Garanina

2016-09-12 14:29:32 UTC

Dear somebody,

I tried to create my own database, but I have an error Can't call method
"new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description = mycoplasma
database = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

#################################
# database definitions
#################################

[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k

[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise

Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta

chr

seq...

and gff3 file mycoplasma.gff3:

##gff-version 3
##Note: See http://song.sourceforge.net

# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + . Name=parA
chr GI gene 3160 4546 . + . Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf

Please, help me

Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia

Scott Cain

2016-09-12 14:54:41 UTC

Permalink

Hi Irina,

The problem is here:

chr GI chromosome 1 985433 . . .
Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing
where your features are located) needs to have the same name in column 1 as
you declare in column 9, so it should look like this instead:

CP006916.3 GI chromosome 1 985433 . . .
Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1
(assume there is only one chromosome).

Scott

Post by Irina Garanina
Dear somebody,
I tried to create my own database, but I have an error Can't call method
"new" on an undefined value
I tested my browser in volvox and yeast databases and it worked well
[GENERAL]
description = mycoplasma
database = mycoplasma
initial landmark = chr:1..1800
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
Submitter
autocomplete = 1
default tracks = Genes
# examples to show in the introduction
examples = chr
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta

chr

seq...
##gff-version 3
##Note: See http://song.sourceforge.net
# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + . Name=parA
chr GI gene 3160 4546 . + . Name=dnaA
[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf
Please, help me
Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia
------------------------------------------------------------
------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2016-09-12 15:30:25 UTC

Permalink

Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.
Follow the Preferences link, hit the "Update appearance", and then try
navigating to another section of the genome. If you still see that
message, look at the apache error log to see what error message it is
giving, and if that is not helpful to you, send it to the list and we'll
take a look.

Scott

Scott,
thank you for your answer
chr GI chromosome 1 985433 . . .
Name=chr
chr GI gene 1891 2680 . + . Name=parA
chr GI gene 3160 4546 . + . Name=dnaA
and I still see the same error
Irina

Post by Scott Cain
Hi Irina,
chr GI chromosome 1 985433 . . .
Name=CP006916.3
The line where you specify the "reference sequence" (that is, the thing
where your features are located) needs to have the same name in column 1 as
CP006916.3 GI chromosome 1 985433 . .
. Name=CP006916.3
and the other lines in the GFF file should have the same thing in column
1 (assume there is only one chromosome).
Scott
On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <

Post by Irina Garanina
Dear somebody,
I tried to create my own database, but I have an error Can't call
method "new" on an undefined value
I tested my browser in volvox and yeast databases and it worked well
[GENERAL]
description = mycoplasma
database = mycoplasma
initial landmark = chr:1..1800
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
Submitter
autocomplete = 1
default tracks = Genes
# examples to show in the introduction
examples = chr
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
Then in directory /data5/bio/gbrowse2/mycoplasma I created

chr

seq...
##gff-version 3
##Note: See http://song.sourceforge.net
# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf
Please, help me
Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia
------------------------------------------------------------
------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2016-09-12 16:12:08 UTC

Permalink

Ah, I see, you have a line that looks like this:

database = mycoplasma

which means that there should be a database defined in the config with the
name "mycoplasma", but the databases defined look like this:

[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

where one of those should be like "[mycoplasma:database]" and in fact,
since they are the same thing, you only need one. In the example config,
there are two because it demonstrates that you can have more than one
database configured, but you don't need to. Just be sure to change any
references in track configurations to use the database named "mycoplasma"
instead of annotations or scaffolds.

Scott

Scott,
if I trying to navigate to another section of the genome I get another
error Can't call method "get_feature_by_name" on an undefined value
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database
defined for general at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database
defined for general at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database
defined for general at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value in concatenation (.) or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database
defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database
defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_
perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-
thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.

Post by Scott Cain
Hi Irina,
Please keep the GBrowse mailing list cc'ed in your replies.
Most likely what you're seeing is a result of caching in the web
browser. Follow the Preferences link, hit the "Update appearance", and
then try navigating to another section of the genome. If you still see
that message, look at the apache error log to see what error message it is
giving, and if that is not helpful to you, send it to the list and we'll
take a look.
Scott
On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <

Scott,
thank you for your answer
chr GI chromosome 1 985433 . . .
Name=chr
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
and I still see the same error
Irina

Post by Scott Cain
Hi Irina,
chr GI chromosome 1 985433 . . .
Name=CP006916.3
The line where you specify the "reference sequence" (that is, the thing
where your features are located) needs to have the same name in column 1 as
CP006916.3 GI chromosome 1 985433 . .
. Name=CP006916.3
and the other lines in the GFF file should have the same thing in
column 1 (assume there is only one chromosome).
Scott
On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <

Post by Irina Garanina
Dear somebody,
I tried to create my own database, but I have an error Can't call
method "new" on an undefined value
I tested my browser in volvox and yeast databases and it worked well
[GENERAL]
description = mycoplasma
database = mycoplasma
initial landmark = chr:1..1800
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper
TrackDumper Submitter
autocomplete = 1
default tracks = Genes
# examples to show in the introduction
examples = chr
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
Then in directory /data5/bio/gbrowse2/mycoplasma I created

chr

seq...
##gff-version 3
##Note: See http://song.sourceforge.net
# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf
Please, help me
Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia
------------------------------------------------------------
------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2016-09-12 17:09:50 UTC

Permalink

Hi Irina,

Please keep the GBrowse mailing list cc'ed on your replies (ie, "reply
all").

Any time you make a change to the configuration file, be sure to use the
"update appearance" button, and if you're using fastcgi, be sure to restart
apache first too.

Another suggestion is that you take the example configuration and make
changes very incrementally, like only changing the name of the database and
making sure it still works, and then changing the name of the GFF file
(without changing the contents), and then changing the contents of the GFF
file, etc. That way you'll be able to tell what is causing the problem
when it comes up.

Scott

It can be some problem with database name
but I think I have another problem in logs, I changed database name and
deleted the second annotation database and error in log did not changed

Post by Irina Garanina
database = mycoplasma
which means that there should be a database defined in the config with
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
where one of those should be like "[mycoplasma:database]" and in fact,
since they are the same thing, you only need one. In the example config,
there are two because it demonstrates that you can have more than one
database configured, but you don't need to. Just be sure to change any
references in track configurations to use the database named "mycoplasma"
instead of annotations or scaffolds.
Scott
On Mon, Sep 12, 2016 at 12:05 PM, Irina Garanina <

Scott,
if I trying to navigate to another section of the genome I get another
error Can't call method "get_feature_by_name" on an undefined value
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value in concatenation (.) or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for plugin:RestrictionAnnotator at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for plugin:RestrictionAnnotator at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.

Scott,
thank you for your answer
chr GI chromosome 1 985433 . . .
Name=chr
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
and I still see the same error
Irina

Post by Scott Cain
Hi Irina,
chr GI chromosome 1 985433 . . .
Name=CP006916.3
The line where you specify the "reference sequence" (that is, the
thing where your features are located) needs to have the same name in
CP006916.3 GI chromosome 1 985433 . .
. Name=CP006916.3
and the other lines in the GFF file should have the same thing in
column 1 (assume there is only one chromosome).
Scott
On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <

Post by Irina Garanina
Dear somebody,
I tried to create my own database, but I have an error Can't call
method "new" on an undefined value
I tested my browser in volvox and yeast databases and it worked well
[GENERAL]
description = mycoplasma
database = mycoplasma
initial landmark = chr:1..1800
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper
TrackDumper Submitter
autocomplete = 1
default tracks = Genes
# examples to show in the introduction
examples = chr
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
Then in directory /data5/bio/gbrowse2/mycoplasma I created

chr

seq...
##gff-version 3
##Note: See http://song.sourceforge.net
# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf
Please, help me
Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia
------------------------------------------------------------
------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Irina Garanina

2016-09-13 13:11:01 UTC

Permalink

Sorry, Scott, for cc

I tried to make changes incrementally: if I used text from volvox.conf
without changes in file mycoplasma.conf and volvox data, respectively, it
still did not worked, worked only in case I used volvox.conf itself in
GBbrowse.conf like:

[mycoplasma]
description = Mycoplasma gallisepticum
path = volvox.conf

also do not work if I changed the name of directory with gff3 file

if I change file volvox.conf like this, it works, but I can't see the
tracks and can't navigate:

[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma

Post by Scott Cain
Hi Irina,
Please keep the GBrowse mailing list cc'ed on your replies (ie, "reply
all").
Any time you make a change to the configuration file, be sure to use the
"update appearance" button, and if you're using fastcgi, be sure to restart
apache first too.
Another suggestion is that you take the example configuration and make
changes very incrementally, like only changing the name of the database and
making sure it still works, and then changing the name of the GFF file
(without changing the contents), and then changing the contents of the GFF
file, etc. That way you'll be able to tell what is causing the problem
when it comes up.
Scott
On Mon, Sep 12, 2016 at 12:24 PM, Irina Garanina <

It can be some problem with database name
but I think I have another problem in logs, I changed database name and
deleted the second annotation database and error in log did not changed

Scott,
if I trying to navigate to another section of the genome I get another
error Can't call method "get_feature_by_name" on an undefined value
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value in concatenation (.) or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for plugin:RestrictionAnnotator at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for plugin:RestrictionAnnotator at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open
database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.

Scott,
thank you for your answer
chr GI chromosome 1 985433 . . .
Name=chr
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
and I still see the same error
Irina

Post by Scott Cain
Hi Irina,
chr GI chromosome 1 985433 . . .
Name=CP006916.3
The line where you specify the "reference sequence" (that is, the
thing where your features are located) needs to have the same name in
CP006916.3 GI chromosome 1 985433 . .
. Name=CP006916.3
and the other lines in the GFF file should have the same thing in
column 1 (assume there is only one chromosome).
Scott
On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <

Post by Irina Garanina
Dear somebody,
I tried to create my own database, but I have an error Can't call
method "new" on an undefined value
I tested my browser in volvox and yeast databases and it worked well
[GENERAL]
description = mycoplasma
database = mycoplasma
initial landmark = chr:1..1800
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper
TrackDumper Submitter
autocomplete = 1
default tracks = Genes
# examples to show in the introduction
examples = chr
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
Then in directory /data5/bio/gbrowse2/mycoplasma I created

chr

seq...
##gff-version 3
##Note: See http://song.sourceforge.net
# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf
Please, help me
Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia
------------------------------------------------------------
------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2016-09-13 15:19:22 UTC

Permalink

And when you make that change (changing the path and file name for the
database), what is the error in the error log? This is why you make small,
incremental changes, so that when things go wrong, you can isolate what
happened and know from the error message what to do. My guess is that
there is an error in the log about file or directory permissions.

Scott

Post by Irina Garanina
Sorry, Scott, for cc
I tried to make changes incrementally: if I used text from volvox.conf
without changes in file mycoplasma.conf and volvox data, respectively, it
still did not worked, worked only in case I used volvox.conf itself in
[mycoplasma]
description = Mycoplasma gallisepticum
path = volvox.conf
also do not work if I changed the name of directory with gff3 file
if I change file volvox.conf like this, it works, but I can't see the
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma

It can be some problem with database name
but I think I have another problem in logs, I changed database name and
deleted the second annotation database and error in log did not changed

Scott,
if I trying to navigate to another section of the genome I get another
error Can't call method "get_feature_by_name" on an undefined value
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not
open database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not
open database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for general at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not
open database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $db in hash element at /srv/common/lib/perl5/site_per
l/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value in concatenation (.) or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for plugin:RestrictionAnnotator at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of
uninitialized value $symbolic_db_name in join or string at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown
database defined for plugin:RestrictionAnnotator at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not
open database: Can't call method "new" on an undefined value at
/srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-
multi/Bio/Graphics/Browser2/DataBase.pm line 44.

Scott,
thank you for your answer
chr GI chromosome 1 985433 . . .
Name=chr
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
and I still see the same error
Irina

Post by Scott Cain
Hi Irina,
chr GI chromosome 1 985433 . . .
Name=CP006916.3
The line where you specify the "reference sequence" (that is, the
thing where your features are located) needs to have the same name in
CP006916.3 GI chromosome 1 985433 . .
. Name=CP006916.3
and the other lines in the GFF file should have the same thing in
column 1 (assume there is only one chromosome).
Scott
On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <

Post by Irina Garanina
Dear somebody,
I tried to create my own database, but I have an error Can't call
method "new" on an undefined value
I tested my browser in volvox and yeast databases and it worked well
[GENERAL]
description = mycoplasma
database = mycoplasma
initial landmark = chr:1..1800
# bring in the special Submitter plugin for the rubber-band select menu
plugins = FastaDumper RestrictionAnnotator SequenceDumper
TrackDumper Submitter
autocomplete = 1
default tracks = Genes
# examples to show in the introduction
examples = chr
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k
[Genes]
feature = gene
glyph = segments
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
Then in directory /data5/bio/gbrowse2/mycoplasma I created

chr

seq...
##gff-version 3
##Note: See http://song.sourceforge.net
# file: mycoplasma.gff3
chr GI chromosome 1 985433 . . .
Name=CP006916.3
chr GI gene 1891 2680 . + .
Name=parA
chr GI gene 3160 4546 . + .
Name=dnaA
[mycoplasma]
description = Mycoplasma gallisepticum S6
path = mycoplasma.conf
Please, help me
Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia
------------------------------------------------------------
------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research