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Update tutorial describing what DAS is, and how to visualise and add DAS tracks in VectorBase.
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Karyn Mégy – May 2010 1
VectorBase http://www.vectorbase.org
DAS at VectorBase
Karyn Mégy���Update May 2010
Karyn Mégy – May 2010 2
VectorBase http://www.vectorbase.org
• In this tutorial you will find:
- A brief introduction to DAS > What is it? Why use it? What is the concept?
- A step by step guide on how to install a DAS track > Anopheles RNA-seq example
Karyn Mégy – May 2010 3
VectorBase http://www.vectorbase.org
Introduction
What is DAS? Why use DAS? What is the concept?
Karyn Mégy – May 2010 4
VectorBase http://www.vectorbase.org
• Developed by Robin Dowell, Sean Eddy and Lincoln Stein
• Specification of a protocol for requesting and returning sequence and annotation data
• Allows decentralised storage of sequence annotation and integration on demand basis by client-side software
• Simple storage protocol running over HTTP
…. see http://biodas.org for more details.
Distributed Annotation System
Karyn Mégy – May 2010 5
VectorBase http://www.vectorbase.org
• Annotation easier to share
• Annotation can be stored in a variety of formats
• Control over updating the data left to the original data provider
• Conflicting annotation permitted
Why DAS ?
Karyn Mégy – May 2010 6
VectorBase http://www.vectorbase.org
Client Reference server
Annotations ���- URL���- Upload a file
Reference Sequence on which
to align the annotations
Annotation server A ���E.g. manual annotation ��� @ VectorBase
Annotation server B ���E.g. ESTs clusters ��� @Mexico
Annotation server C ���E.g. RNA-seq data��� @ EBI
Reference server���@ VectorBase
Client���@ VectorBase
DAS concept
Karyn Mégy – May 2010 7
VectorBase http://www.vectorbase.org
• Client: an application (e.g. Apollo) or a website (e.g. VectorBase) requesting and displaying annotation for a region of a sequence
• Server: a reference server (provide the sequence) or an annotation server (provide the annotations) that has the sequences and/or annotation data stored in a flat file or a database
-> DAS server implementation • LDAS http://www.biodas.org/servers
- The lightweight DAS server using Perl, Apache and MySQL • DAZZLE http://www.derkholm/thomas/dazzle
- DAS server written in Java • ProServer http://www.sanger.ac.uk/proserver
- DAS server written in Perl
Client/Server
Karyn Mégy – May 2010 8
VectorBase http://www.vectorbase.org
How to set up a DAS track,
Example of the Anopheles RNA-seq data
Karyn Mégy – May 2010 9
VectorBase http://www.vectorbase.org
• From the Location, the Gene or the Transcript tabs, • Click on ‘Configure this page’,
then ‘Custom data’ • Or directly on ‘Manage your
data’
Setting up a DAS track
E.g.: http://www.vectorbase.org/Anopheles_gambiae/Location/View?r=2L:39221590-39222203
Karyn Mégy – May 2010 10
VectorBase http://www.vectorbase.org
Setting up a DAS track
• A window appears, • Select the ‘Custom Data’ tab
• Choose the data source: (1) Upload data, (2) or Attach a DAS source, (3) or Attach a URL, (4) Manage the data (i.e. the attached sources)
=> We are going to go through these 4 steps
Karyn Mégy – May 2010 11
VectorBase http://www.vectorbase.org
(1) Upload data
• Paste formatted information, E.g.2 afterwards
• OR upload a file stored locally on your computer, E.g.1 afterwards
• OR upload a file stored at a URL address,
Note: Accessing data via a URL can be slow if the file is large, but the data you see is always the same as the file on your server.
Karyn Mégy – May 2010 12
VectorBase http://www.vectorbase.org
(1) Upload data
• E.g.1: upload a file • Click on ’Browse’, • Select your file, • Then click on ‘Upload’
Karyn Mégy – May 2010 13
VectorBase http://www.vectorbase.org
(1) Upload data
• Here you see: • Notification of the file being uploaded, • Number of features uploaded, • Region where it has been uploaded.
• Click on “Close” or on the location link to go back to the genome browser
Karyn Mégy – May 2010 14
VectorBase http://www.vectorbase.org
(1) Upload data
• The track (color, shape, name) is configurable in the uploaded file
Karyn Mégy – May 2010 15
VectorBase http://www.vectorbase.org
(1) Upload data
• E.g.2: Paste the data • Copy/paste the data from
the following slide, • then process as exemple 1
Karyn Mégy – May 2010 16
VectorBase http://www.vectorbase.org
(1) Upload data
3L exonerate cDNA_match 41950563 41952426 99.05 + . ID=CDNA0001 3L exonerate match_part 41950563 41950679 99.05 + . ID=match001;Parent=CDNA0001;Target=BM592927.1 8 124 + 3L exonerate match_part 41951274 41951417 99.05 + . ID=match002;Parent=CDNA0001;Target=BM592927.1 125 268 + 3L exonerate match_part 41951956 41952426 99.05 + . ID=match003;Parent=CDNA0001;Target=BM592927.1 269 739 +
• Make sure there is a tabulation (NOT spaces) between each field!
Karyn Mégy – May 2010 17
VectorBase http://www.vectorbase.org
(1) Upload data
• Be aware that the file for uploading needs to be in a specific format! Supported formats are:
• GFF & GTF • PSL • BED • BedGraph • WIG
• See help pages to get an exemple of these formats ���(E.g. http://vectorbase.ensemblgenomes.org/info/website/upload/index.html)
• Useful link for a GFF3 description: http://song.sourceforge.net/gff3.shtml
Karyn Mégy – May 2010 18
VectorBase http://www.vectorbase.org
Setting up a DAS track
• Chose the data source: (1) Upload data, (2) Attach a DAS source, (3) Attach a URL, (4) Manage the data (i.e. the attached sources)
Karyn Mégy – May 2010 19
VectorBase http://www.vectorbase.org
(2) Attach a DAS source
• To visualise data by attaching a DAS source, the source has to be available on a DAS server or in the DAS registry: ���
VectorBase DAS server for functional genomics (EBI): http://funcgen.vectorbase.org/ExpressionData/das
EnsemblGenomes DAS server (EBI): ���http://www.ebi.ac.uk/das-srv/ensemblgenomes/das
DAS registry: http://www.dasregistry.org/ http://www.dasregistry.org/showProjectDetails.jsp?project_id=90
Karyn Mégy – May 2010 20
VectorBase http://www.vectorbase.org
(2) Attach a DAS source
• List of DAS sources available for VectorBase on the Help Wiki: http://www.vectorbase.org/Help/DAS_track_list
• At the moment, most are for Anopheles gambiae and Aedes aegypti���
Karyn Mégy – May 2010 21
VectorBase http://www.vectorbase.org
• Select the source: • DAS registry • Other DAS server (e.g. one you have installed locally)���
• Then click on the ‘Next’ button ��� Be Patient ���
! It takes a few sec. to upload !
(2) Attach a DAS source
Note: have you noticed the yellow ‘Tip’ box?
E.g. of DAS server:���http://www.ebi.ac.uk/das-srv/ensemblgenomes/das
Karyn Mégy – May 2010 22
VectorBase http://www.vectorbase.org
• A list of DAS sources appears, select the one(s) you’re interested in,
• Click on the ‘Next’ button
Be Patient���! It takes a few sec. to upload !
(2) Attach a DAS source
Note: List ALL the sources in the DAS registry, not all are linked to VectorBase species !
Karyn Mégy – May 2010 23
VectorBase http://www.vectorbase.org
• You should get a confirmation that the sources are attached, • Close the window
(2) Attach a DAS source
Karyn Mégy – May 2010 24
VectorBase http://www.vectorbase.org
• The DAS sources are attached! ���You can see them in the ‘Region in detail’ panel
(2) Attach a DAS source
Karyn Mégy – May 2010 25
VectorBase http://www.vectorbase.org
Setting up a DAS track
• Chose the data source: (1) Upload data, (2) Attach a DAS source, (3) Attach a URL, (4) Manage the data (i.e. the attached sources)
Karyn Mégy – May 2010 26
VectorBase http://www.vectorbase.org
(3) Attach a URL
• Paste the URL, • Give a name to the track (optional), • Then click on ‘next’
Karyn Mégy – May 2010 27
VectorBase http://www.vectorbase.org
(3) Attach a URL
• A message informs you know it is (successfully) attached • Click on ‘Close’ to go back to the genome browser
Karyn Mégy – May 2010 28
VectorBase http://www.vectorbase.org
(3) Attach a URL
• The track (color, shape, name) is configurable in the uploaded file
Karyn Mégy – May 2010 29
VectorBase http://www.vectorbase.org
Setting up a DAS track
• Chose the data source: (1) Upload data, (2) Attach a DAS source, (3) Attach a URL, (4) Manage the data (i.e. the attached sources)
Karyn Mégy – May 2010 30
VectorBase http://www.vectorbase.org
• Click on the DAS source you want to remove,
• It’s gone from the list,
• Click on ‘Close’, • It’s gone from the web browser!
(4) Manage the data
Karyn Mégy – May 2010 31
VectorBase http://www.vectorbase.org
before
(4) Manage the data
after
Karyn Mégy – May 2010 32
VectorBase http://www.vectorbase.org
• Ensembl documentation:���http://www.ensembl.org/info/docs/das/das_server.html
• Sanger documentation: http://www.sanger.ac.uk/resources/software/das/
More about DAS ���(specially to set up a DAS server)
Karyn Mégy – May 2010 33
VectorBase http://www.vectorbase.org
Questions?
• E-mail VectorBase at info@vectorbase.org
• Post a question on the forum��� http://www.vectorbase.org/sections/Forum/index.php
• Check out the FAQs ��� http://www.vectorbase.org/Help/Help:Contents
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