Difference between revisions of "GBrowse DAS HOWTO"

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(New page: The Distributed Annotation System protocol (DAS; http://www.biodas.org) is a system for exchanging genomic annotations across the Internet. It works similarly to the idea of sharing the UR...)
 
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The Distributed Annotation System protocol (DAS; http://www.biodas.org) is a system for exchanging genomic annotations across the Internet. It works similarly to the idea of sharing the URLs of web-accessible GFF files, except that it is designed to support large data sets. When a client application needs to fetch just a subset of the data, such as a small piece of a chromosomal arm, the DAS protocol allows only the relevant annotations to be retrieved, rather than the whole data set.
 
The Distributed Annotation System protocol (DAS; http://www.biodas.org) is a system for exchanging genomic annotations across the Internet. It works similarly to the idea of sharing the URLs of web-accessible GFF files, except that it is designed to support large data sets. When a client application needs to fetch just a subset of the data, such as a small piece of a chromosomal arm, the DAS protocol allows only the relevant annotations to be retrieved, rather than the whole data set.
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== Installation ==
  
 
To take advantage of DAS functionality, you will have to install the Perl Bio::Das module. This is available from CPAN (the Comprehensive Perl Archive Network (http://www.cpan.org) or from the GMOD PPM repository. Unix users can install Bio::Das with this command:
 
To take advantage of DAS functionality, you will have to install the Perl Bio::Das module. This is available from CPAN (the Comprehensive Perl Archive Network (http://www.cpan.org) or from the GMOD PPM repository. Unix users can install Bio::Das with this command:
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  % perl -MCPAN -e 'install Bio::Das'
 
  % perl -MCPAN -e 'install Bio::Das'
 
  Windows users can use the PPM tool:
 
  Windows users can use the PPM tool:
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  C:\Windows> ppm
 
  C:\Windows> ppm
 
  ppm> install Bio::Das
 
  ppm> install Bio::Das
 
  ppm> quit
 
  ppm> quit
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You may need to issue the command "rep add gmod http://www.gmod.org/ggb/ppm" if PPM complains that it cannot find Bio::Das.
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== A Tutorial ==
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We start out with a short tutorial that illustrates how GBrowse DAS support works.
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When you installed GBrowse, the system also installed a series of tutorial files, the location of which you can find at http://localhost/gbrowse2. We will use the ''C. elegans core'' tutorial database as the basis for creating a DAS server.
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To start, find the elegans_core.conf configuration file in the tutorial '''conf''' directory and copy it to your GBrowse2 configuration directory (typically /etc/gbrowse2). Edit the master /etc/gbrowse2/GBrowse.conf configuration file to load this file by adding the following to the end (if it is not there already from previous tutorials):
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[elegans_core]
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description = Core C. elegans annotations
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path        = elegans_core.conf
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To enable the DAS server, add the following somewhere within the [GENERAL] section of the elegans_core.conf file:
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# DAS reference server
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das mapmaster      = SELF
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What this line is doing is to declare to the DAS system that our server is authoritative for the coordinates on the current C. elegans genome example. This is appropriate if you are starting out a genome for the first time. If, however, you want to annotate against an existing set of genome coordinates, you should replace SELF with the URL of the DAS reference server that serves that genome. For example release hg16 of the human genome at UCSC corresponds to DAS URL http://genome.cse.ucsc.edu/cgi-bin/das. A list of reference servers for various model organisms can be found at http://www.biodas.org.
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The next step is to go through the configured tracks and add a "das category" to each of them. DAS uses the idea of the "category" of a feature in order to filter sets of features by their purpose. Categories include:
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[[Category:MOD User Interfaces]]

Revision as of 21:11, 6 July 2010

The Distributed Annotation System protocol (DAS; http://www.biodas.org) is a system for exchanging genomic annotations across the Internet. It works similarly to the idea of sharing the URLs of web-accessible GFF files, except that it is designed to support large data sets. When a client application needs to fetch just a subset of the data, such as a small piece of a chromosomal arm, the DAS protocol allows only the relevant annotations to be retrieved, rather than the whole data set.

Installation

To take advantage of DAS functionality, you will have to install the Perl Bio::Das module. This is available from CPAN (the Comprehensive Perl Archive Network (http://www.cpan.org) or from the GMOD PPM repository. Unix users can install Bio::Das with this command:

% perl -MCPAN -e 'install Bio::Das'
Windows users can use the PPM tool:
C:\Windows> ppm
ppm> install Bio::Das
ppm> quit

You may need to issue the command "rep add gmod http://www.gmod.org/ggb/ppm" if PPM complains that it cannot find Bio::Das.

A Tutorial

We start out with a short tutorial that illustrates how GBrowse DAS support works.

When you installed GBrowse, the system also installed a series of tutorial files, the location of which you can find at http://localhost/gbrowse2. We will use the C. elegans core tutorial database as the basis for creating a DAS server.

To start, find the elegans_core.conf configuration file in the tutorial conf directory and copy it to your GBrowse2 configuration directory (typically /etc/gbrowse2). Edit the master /etc/gbrowse2/GBrowse.conf configuration file to load this file by adding the following to the end (if it is not there already from previous tutorials):

[elegans_core]
description = Core C. elegans annotations
path        = elegans_core.conf

To enable the DAS server, add the following somewhere within the [GENERAL] section of the elegans_core.conf file:

# DAS reference server
das mapmaster      = SELF

What this line is doing is to declare to the DAS system that our server is authoritative for the coordinates on the current C. elegans genome example. This is appropriate if you are starting out a genome for the first time. If, however, you want to annotate against an existing set of genome coordinates, you should replace SELF with the URL of the DAS reference server that serves that genome. For example release hg16 of the human genome at UCSC corresponds to DAS URL http://genome.cse.ucsc.edu/cgi-bin/das. A list of reference servers for various model organisms can be found at http://www.biodas.org.

The next step is to go through the configured tracks and add a "das category" to each of them. DAS uses the idea of the "category" of a feature in order to filter sets of features by their purpose. Categories include: