Re: A GBROWSE question

[Scott Cain-4]

Hello Juan Manuel,

I'm cc'ing this to the GBrowse mailing list, since there are a lot of
really smart, helpful people who read this list.

I think what you want to do is possible with the stackedplot glyph,
but I've never used it personally, so I don't know if there are any
gotchas in using it.  See the documentation locally with this command
line command:

  > perldoc Bio::Graphics::Glyph::stackedplot

or read it at cpan:

  http://search.cpan.org/~lds/Bio-Graphics-1.93/lib/Bio/Graphics/Glyph/stackedplot.pm

Scott


On Mon, Apr 13, 2009 at 3:31 PM, Juan Anzola <biojmal@...> wrote:

> Hello Scott, how are you?
>
> My name is Juan Anzola, I am a biologist interested in genomes and trying to
> use GBROWSE in my everyday work.
> I an sending you this email because there is something that I would like to
> do with GBROWSE, but I haven't been able to figure out how to do it.
>
> Here is the question:
> Is there any way I can create a GFF track with more than one type of
> quantitative information? I know how to create quantitative tracks with
> xyplot and I've been reading how to do it with the wiggle/BED format. But
> that is not exactly what I want to do. I want something similar to a STACKED
> XYPLOT with different boxes representing different types of data and the
> height of the boxes representing quantitative data. Is there any way to do
> this?
>
> Please take a look at the atached figure so you will understand what I mean.
> Thanks in advance for your help Scott.
>
> Regards,
>
> Juan Manuel
>
>
>
>
>
>
>
>
>
> --
> My Flickr Photos:
> http://www.flickr.com/photos/46611258@N00/sets/
>

--
------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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[Taner Z. Sen]

Hi guys,

I am using GBrowse 1.68, and  in my apache log, there are two consistent errors:

[Wed Apr 15 16:12:13 2009] [error] [client 66.249.67.5] Bio::Graphics::BrowserConfig=HASH(0xa62df8) at /usr/local/apache/gbrowse/lib/perl/Bio/Graphics/Browser.pm line 587

and

[Wed Apr 15 16:13:56 2009] [crit] (2)No such file or directory: mod_rewrite: could not init rewrite log lock in child

Any idea how I can get rid of these? What am I doing wrong?

Thanks,
Taner

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
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[Scott Cain-4]

Hi Taner,

Are  you sure you're using 1.68?  The BrowserConfig thing looks like a
debugging message that we left in the 1.69 release.  You can silence
it by commenting out line 587 in Browser.pm.

The other one looks like a config problem that I have no idea how to
debug but you can at least silence the error by setting
RewriteLogLevel 0 in your mod_rewrite section of your apache conf.

Scott

On Wed, Apr 15, 2009 at 5:16 PM, Taner Z. Sen <taner@...> wrote:

> Hi guys,
>
> I am using GBrowse 1.68, and  in my apache log, there are two consistent
> errors:
>
> [Wed Apr 15 16:12:13 2009] [error] [client 66.249.67.5]
> Bio::Graphics::BrowserConfig=HASH(0xa62df8) at
> /usr/local/apache/gbrowse/lib/perl/Bio/Graphics/Browser.pm line 587
>
> and
>
> [Wed Apr 15 16:13:56 2009] [crit] (2)No such file or directory: mod_rewrite:
> could not init rewrite log lock in child
>
> Any idea how I can get rid of these? What am I doing wrong?
>
> Thanks,
> Taner
>
>
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-ARS, MaizeGDB
> Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: [phone]
> Fax: [phone]
> taner@iastate. edu
> http://www.public.iastate.edu/~taner/

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

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[Taner Z. Sen]

Hmm.. Yep, it is 1.69.

Commenting out line 587 silenced the first error.

I got rid of the second error message by commenting out this line in the apache conf file (so it is an apache issue):
LoadModule rewrite_module         libexec/httpd/mod_rewrite.so

No rewriting is necessary in my case because there is no rerouting.

Thanks Scott.


At 09:38 PM 4/15/2009, Scott Cain wrote:

Hi Taner,

Are  you sure you're using 1.68?  The BrowserConfig thing looks like a
debugging message that we left in the 1.69 release.  You can silence
it by commenting out line 587 in Browser.pm.

The other one looks like a config problem that I have no idea how to
debug but you can at least silence the error by setting
RewriteLogLevel 0 in your mod_rewrite section of your apache conf.

Scott

On Wed, Apr 15, 2009 at 5:16 PM, Taner Z. Sen <taner@...> wrote:
> Hi guys,
>
> I am using GBrowse 1.68, and  in my apache log, there are two consistent
> errors:
>
> [Wed Apr 15 16:12:13 2009] [error] [client 66.249.67.5]
> Bio::Graphics::BrowserConfig=HASH(0xa62df8) at
> /usr/local/apache/gbrowse/lib/perl/Bio/Graphics/Browser.pm line 587
>
> and
>
> [Wed Apr 15 16:13:56 2009] [crit] (2)No such file or directory: mod_rewrite:
> could not init rewrite log lock in child
>
> Any idea how I can get rid of these? What am I doing wrong?
>
> Thanks,
> Taner
>
>
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-ARS, MaizeGDB
> Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: [phone]
> Fax: [phone]
> taner@iastate. edu
> http://www.public.iastate.edu/~taner/



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

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
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[Smithies, Russell]

Congratulations to Ram Podicheti, Rajesh Gollapudi and Qunfeng Dong for getting WebGBrowse published in "Bioinformatics"
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp239v1?papetoc 
It looked like a very useful tool when it was presented at the GMOD meeting after PAG.


Russell Smithies

Bioinformatics Applications Developer
T [phone]
E  russell.smithies@...

Invermay  Research Centre
Puddle Alley,
Mosgiel,
New Zealand
T  [phone]  
F  [phone] 
www.agresearch.co.nz




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[Taner Z. Sen]

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,
Taner

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
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[Lincoln Stein-3]

Hi Taner,

I'm not quite understanding the scenario here. When the glyphs are appearing as lines, what is the DAS server and what is the DAS viewer?

Thanks,

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,
Taner

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

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[Taner Z. Sen]

Hi Lincoln,

Sorry for being vague.

This is how we generated the problem:

1) Go to the MaizeGDB Genome Browser ( http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/)

2) Put the following link in the "Add Remote Annotation URL" http://beta.plantgdb.org/ZmGDB/cgi-bin/das/ZmGDB_v157_yrgate/ , click update

3) Go to this region: http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/?name=Chr1%3A255723499..255726899

The last track shows the remote annotation track. This track is supposed to show gene models with introns/exons with boxes and lines connecting them. Here is the stylesheet they use:
http://beta.plantgdb.org/ZmGDB/cgi-bin/das/DSN/stylesheet

Let me know if you want more info.

Thanks,
Taner


At 02:30 PM 4/21/2009, Lincoln Stein wrote:

Hi Taner,

I'm not quite understanding the scenario here. When the glyphs are appearing as lines, what is the DAS server and what is the DAS viewer?

Thanks,

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,

Taner

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
------------------------------------------------------------------------------
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[Lincoln Stein-3]

Hi Taner,

What version of gbrowse are you using? What version is plantgdb using?

Hi Taner,

I think that what you're seeing is a change in how the stylesheets are interpreted by the client (your instance of gbrowse). It may have been fixed in the CVS version of GBrowse (the upcoming 1.70 release), but I'll have to check.

Lincoln

On Wed, Apr 22, 2009 at 10:12 AM, Taner Z. Sen <taner@...> wrote:

Hi Lincoln,

Sorry for being vague.

This is how we generated the problem:

1) Go to the MaizeGDB Genome Browser ( http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/)

2) Put the following link in the "Add Remote Annotation URL" http://beta.plantgdb.org/ZmGDB/cgi-bin/das/ZmGDB_v157_yrgate/ , click update

3) Go to this region: http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/?name=Chr1%3A255723499..255726899

The last track shows the remote annotation track. This track is supposed to show gene models with introns/exons with boxes and lines connecting them. Here is the stylesheet they use:
http://beta.plantgdb.org/ZmGDB/cgi-bin/das/DSN/stylesheet

Let me know if you want more info.

Thanks,
Taner

At 02:30 PM 4/21/2009, Lincoln Stein wrote:

Hi Taner,

I'm not quite understanding the scenario here. When the glyphs are appearing as lines, what is the DAS server and what is the DAS viewer?

Thanks,

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,

Taner

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------

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around Java (TM) technology - register by April 22, and save

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300 plus technical and hands-on sessions. Register today.

Use priority code J9JMT32. http://p.sf.net/sfu/p

_______________________________________________

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
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around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
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[Taner Z. Sen]

Hi Lincoln

I am using GBrowse 1.69, PlantGDB has its own browser (xGDB) and they have written custom perl script that provide XML output based on DAS/1 standard.

GBrowse 1.70 might have solved the problem, but only if the problem is on the GBrowse side. Do you think it is a GBrowse issue and not a problem with their code?

Thanks.

At 12:56 PM 4/22/2009, Lincoln Stein wrote:

Hi Taner,

What version of gbrowse are you using? What version is plantgdb using?

Hi Taner,

I think that what you're seeing is a change in how the stylesheets are interpreted by the client (your instance of gbrowse). It may have been fixed in the CVS version of GBrowse (the upcoming 1.70 release), but I'll have to check.

Lincoln

On Wed, Apr 22, 2009 at 10:12 AM, Taner Z. Sen <taner@...> wrote:

Hi Lincoln,

Sorry for being vague.

This is how we generated the problem:

1) Go to the MaizeGDB Genome Browser ( http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/)

2) Put the following link in the "Add Remote Annotation URL" http://beta.plantgdb.org/ZmGDB/cgi-bin/das/ZmGDB_v157_yrgate/ , click update

3) Go to this region: http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/?name=Chr1%3A255723499..255726899

The last track shows the remote annotation track. This track is supposed to show gene models with introns/exons with boxes and lines connecting them. Here is the stylesheet they use:

http://beta.plantgdb.org/ZmGDB/cgi-bin/das/DSN/stylesheet

Let me know if you want more info.

Thanks,

Taner

At 02:30 PM 4/21/2009, Lincoln Stein wrote:

Hi Taner,

I'm not quite understanding the scenario here. When the glyphs are appearing as lines, what is the DAS server and what is the DAS viewer?

Thanks,

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,

Taner

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------

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around Java (TM) technology - register by April 22, and save

$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.

300 plus technical and hands-on sessions. Register today.

Use priority code J9JMT32. http://p.sf.net/sfu/p

_______________________________________________

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--

Lincoln D. Stein

Director, Informatics and Biocomputing Platform

Ontario Institute for Cancer Research

101 College St., Suite 800

Toronto, ON, Canada M5G0A3

416 673-8514

Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
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[Lincoln Stein-3]

Hi Taner,

I've looked into it further and am pretty sure that it is not a problem with either PlantGDB or GBrowse. It is an issue with the Bio::Das library, which has not been updated to reflect the latest DAS/1.6 standard.

There is currently no one maintaining Bio::Das except myself, and I have a grant due at the end of next week. If you can wait three weeks I think I can make a release that will fix the problem.

Lincoln

On Wed, Apr 22, 2009 at 2:56 PM, Taner Z. Sen <taner@...> wrote:

Hi Lincoln

I am using GBrowse 1.69, PlantGDB has its own browser (xGDB) and they have written custom perl script that provide XML output based on DAS/1 standard.

GBrowse 1.70 might have solved the problem, but only if the problem is on the GBrowse side. Do you think it is a GBrowse issue and not a problem with their code?

Thanks.

At 12:56 PM 4/22/2009, Lincoln Stein wrote:

Hi Taner,

What version of gbrowse are you using? What version is plantgdb using?

Hi Taner,

I think that what you're seeing is a change in how the stylesheets are interpreted by the client (your instance of gbrowse). It may have been fixed in the CVS version of GBrowse (the upcoming 1.70 release), but I'll have to check.

Lincoln

On Wed, Apr 22, 2009 at 10:12 AM, Taner Z. Sen <taner@...> wrote:

Hi Lincoln,

Sorry for being vague.

This is how we generated the problem:

1) Go to the MaizeGDB Genome Browser ( http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/)

2) Put the following link in the "Add Remote Annotation URL" http://beta.plantgdb.org/ZmGDB/cgi-bin/das/ZmGDB_v157_yrgate/ , click update

3) Go to this region: http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/?name=Chr1%3A255723499..255726899

The last track shows the remote annotation track. This track is supposed to show gene models with introns/exons with boxes and lines connecting them. Here is the stylesheet they use:

http://beta.plantgdb.org/ZmGDB/cgi-bin/das/DSN/stylesheet

Let me know if you want more info.

Thanks,

Taner

At 02:30 PM 4/21/2009, Lincoln Stein wrote:

Hi Taner,

I'm not quite understanding the scenario here. When the glyphs are appearing as lines, what is the DAS server and what is the DAS viewer?

Thanks,

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,

Taner

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------

Stay on top of everything new and different, both inside and

around Java (TM) technology - register by April 22, and save

$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.

300 plus technical and hands-on sessions. Register today.

Use priority code J9JMT32. http://p.sf.net/sfu/p

_______________________________________________

Gmod-gbrowse mailing list

Gmod-gbrowse@...

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

Lincoln D. Stein

Director, Informatics and Biocomputing Platform

Ontario Institute for Cancer Research

101 College St., Suite 800

Toronto, ON, Canada M5G0A3

416 673-8514

Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
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[Taner Z. Sen]

Hi Lincoln,

Thank you for looking into this issue. Yes, we can definitely wait for a few weeks.

Thanks again.
Taner


At 02:50 PM 4/22/2009, Lincoln Stein wrote:

Hi Taner,

I've looked into it further and am pretty sure that it is not a problem with either PlantGDB or GBrowse. It is an issue with the Bio::Das library, which has not been updated to reflect the latest DAS/1.6 standard.

There is currently no one maintaining Bio::Das except myself, and I have a grant due at the end of next week. If you can wait three weeks I think I can make a release that will fix the problem.

Lincoln

On Wed, Apr 22, 2009 at 2:56 PM, Taner Z. Sen <taner@...> wrote:

Hi Lincoln

I am using GBrowse 1.69, PlantGDB has its own browser (xGDB) and they have written custom perl script that provide XML output based on DAS/1 standard.

GBrowse 1.70 might have solved the problem, but only if the problem is on the GBrowse side. Do you think it is a GBrowse issue and not a problem with their code?

Thanks.

At 12:56 PM 4/22/2009, Lincoln Stein wrote:

Hi Taner,

What version of gbrowse are you using? What version is plantgdb using?

Hi Taner,

I think that what you're seeing is a change in how the stylesheets are interpreted by the client (your instance of gbrowse). It may have been fixed in the CVS version of GBrowse (the upcoming 1.70 release), but I'll have to check.

Lincoln

On Wed, Apr 22, 2009 at 10:12 AM, Taner Z. Sen <taner@...> wrote:

Hi Lincoln,

Sorry for being vague.

This is how we generated the problem:

1) Go to the MaizeGDB Genome Browser ( http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/)

2) Put the following link in the "Add Remote Annotation URL" http://beta.plantgdb.org/ZmGDB/cgi-bin/das/ZmGDB_v157_yrgate/ , click update

3) Go to this region: http://chimera.gdcb.iastate.edu/gbrowse/cgi-bin/gbrowse/maize/?name=Chr1%3A255723499..255726899

The last track shows the remote annotation track. This track is supposed to show gene models with introns/exons with boxes and lines connecting them. Here is the stylesheet they use:

http://beta.plantgdb.org/ZmGDB/cgi-bin/das/DSN/stylesheet

Let me know if you want more info.

Thanks,

Taner

At 02:30 PM 4/21/2009, Lincoln Stein wrote:

Hi Taner,

I'm not quite understanding the scenario here. When the glyphs are appearing as lines, what is the DAS server and what is the DAS viewer?

Thanks,

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,

Taner

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------

Stay on top of everything new and different, both inside and

around Java (TM) technology - register by April 22, and save

$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.

300 plus technical and hands-on sessions. Register today.

Use priority code J9JMT32. http://p.sf.net/sfu/p

_______________________________________________

Gmod-gbrowse mailing list

Gmod-gbrowse@...

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

Lincoln D. Stein

Director, Informatics and Biocomputing Platform

Ontario Institute for Cancer Research

101 College St., Suite 800

Toronto, ON, Canada M5G0A3

416 673-8514

Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

--

Lincoln D. Stein

Director, Informatics and Biocomputing Platform

Ontario Institute for Cancer Research

101 College St., Suite 800

Toronto, ON, Canada M5G0A3

416 673-8514

Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Lincoln Stein-3]

Hi Taner,

I've got the client side now working with DAS version 1.6, so you should be able to view PlantGDB tracks with correctly rendered genes and alignments. You will need to download and install the following from CPAN:

Bio::Das version 1.11
Bio::Graphics version 1.96

You may also wish to update your das script so that it emits better version 1.6 (although the version you have works pretty well as it is). To do this, you will need to CVS update the GBrowse "stable" branch.

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,
Taner

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
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[Taner Z. Sen]

Thanks Lincoln!  Will work on it.

At 05:06 PM 6/4/2009, Lincoln Stein wrote:

Hi Taner,

I've got the client side now working with DAS version 1.6, so you should be able to view PlantGDB tracks with correctly rendered genes and alignments. You will need to download and install the following from CPAN:

Bio::Das version 1.11
Bio::Graphics version 1.96

You may also wish to update your das script so that it emits better version 1.6 (although the version you have works pretty well as it is). To do this, you will need to CVS update the GBrowse "stable" branch.

Lincoln

On Tue, Apr 21, 2009 at 1:44 PM, Taner Z. Sen <taner@...> wrote:

Hi,

I am trying to create a DAS track in our GBrowse generated by another group. When the other group creates a track using "Remote annotations" in our site, the glyphs appear as lines. But if I upload a DAS track using "Remote annotations" from somewhere else (e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation), the tracks and glyphs look fine. So that led me to believe that our GBrowse is well configured for DAS. But then, if the other group uses Ensembl-based browser, their tracks appear fine there... 

So there is a configuration problem either on our side, on their side, or both. To resolve the issue, I need GBrowse sites that is well-configured for DAS so that the other group can test their DAS servers. Do you know any such GBrowse sites?

If you have other comments, please let me know.

Thanks,

Taner

Taner Z. Sen, Ph.D.

Computational Biologist, USDA-ARS, MaizeGDB

Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology

Iowa State University

1025 Crop Genome Informatics Lab

Ames, IA 50011

Phone: [phone]

Fax: [phone]

taner@... taner@...

http://www.public.iastate.edu/~taner/

------------------------------------------------------------------------------

Stay on top of everything new and different, both inside and

around Java (TM) technology - register by April 22, and save

$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.

300 plus technical and hands-on sessions. Register today.

Use priority code J9JMT32. http://p.sf.net/sfu/p

_______________________________________________

Gmod-gbrowse mailing list

Gmod-gbrowse@...

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@... >

Taner Z. Sen, Ph.D.
Computational Biologist, USDA-ARS, MaizeGDB
Collab. Assist. Prof., Dept. of Genetics, Development and Cell Biology
Iowa State University
1025 Crop Genome Informatics Lab
Ames, IA 50011
Phone: [phone]
Fax: [phone]
taner@... taner@...
http://www.public.iastate.edu/~taner/
------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse