Vb tutorial-das-update may2010

Karyn Mégy – May 2010 1

VectorBase http://www.vectorbase.org

DAS at VectorBase

Karyn Mégy��Update May 2010



•  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



Introduction

What is DAS? Why use DAS? What is the concept?



•  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



•  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 ?



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



•  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



How to set up a DAS track,

Example of the Anopheles RNA-seq data



•  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




•  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



(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.



(1) Upload data

•  E.g.1: upload a file •  Click on ’Browse’, •  Select your file, •  Then click on ‘Upload’



(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



(1) Upload data

•  The track (color, shape, name) is configurable in the uploaded file



(1) Upload data

•  E.g.2: Paste the data •  Copy/paste the data from

the following slide, •  then process as exemple 1



(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!



(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




•  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)



(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




•  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��



•  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 !


Note: have you noticed the yellow ‘Tip’ box?

E.g. of DAS server:��http://www.ebi.ac.uk/das-srv/ensemblgenomes/das



•  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 !


Note: List ALL the sources in the DAS registry, not all are linked to VectorBase species !



•  You should get a confirmation that the sources are attached, •  Close the window




•  The DAS sources are attached! ��You can see them in the ‘Region in detail’ panel








(3) Attach a URL

•  Paste the URL, •  Give a name to the track (optional), •  Then click on ‘next’



(3) Attach a URL

•  A message informs you know it is (successfully) attached •  Click on ‘Close’ to go back to the genome browser



(3) Attach a URL

•  The track (color, shape, name) is configurable in the uploaded file







•  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



before

(4) Manage the data

after



•  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)



Questions?

•  E-mail VectorBase at [email protected]

•  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

Technology

Vb tutorial-das-update may2010