Re: DAS-configured gbrowse sites

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: (515) 294-5326

Fax: (515) 294-8280

taner@... taner@...

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

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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: (515) 294-5326

Fax: (515) 294-8280

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: (515) 294-5326
Fax: (515) 294-8280
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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