Vb tutorial-das-update may2010

VectorBase
http://www.vectorbase.org

DAS at VectorBase

Karyn Mégy
Update May 2010

Karyn Mégy – May 2010 1

VectorBase

•  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


VectorBase

Introduction

What is DAS? Why use DAS?

What is the concept?


VectorBase

Distributed Annotation System

•  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.


VectorBase

Why DAS ?

•  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


VectorBase

DAS concept

Annotation server A Annotation server B Annotation server C
E.g. manual annotation E.g. ESTs clusters E.g. RNA-seq data
@ VectorBase

@Mexico

@ EBI

Annotations
- URL
- Upload a ﬁle

Reference

Sequence on which

to align the annotations

Client

Client Reference server
Reference server

@ VectorBase

@ VectorBase


VectorBase

Client/Server

•  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


VectorBase

How to set up a DAS track,

Example of the Anopheles RNA-seq data


VectorBase

Setting up a DAS track

•  From the Location, the Gene or
the Transcript tabs,

•  Click on ‘Conﬁgure this page’,
then ‘Custom data’

•  Or directly on ‘Manage your
data’

E.g.:

http://www.vectorbase.org/Anopheles_gambiae/Location/View?r=2L:39221590-39222203


VectorBase


•  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


VectorBase

(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.


VectorBase

(1) Upload data

•  E.g.1: upload a ﬁle

•  Click on ’Browse’,

•  Select your ﬁle,

•  Then click on ‘Upload’


VectorBase

(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


VectorBase

(1) Upload data

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


VectorBase

(1) Upload data

•  E.g.2: Paste the data

•  Copy/paste the data from
the following slide,

•  then process as exemple 1


VectorBase

(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 +


3L

exonerate

match_part

41951956

41952426

99.05 +


•  Make sure there is a tabulation (NOT spaces) between each ﬁeld!


VectorBase

(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


VectorBase


•  Chose the data source:

(1) Upload data,

(2) Attach a DAS source,

(3) Attach a URL,

(4) Manage the data



VectorBase

(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


VectorBase


•  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


VectorBase


•  Select the source:

•  DAS registry

•  Other DAS server

(e.g. one you have installed locally)

•  Then click on the ‘Next’ button
E.g. of DAS server:

Be Patient
http://www.ebi.ac.uk/das-srv/ensemblgenomes/das

! It takes a few sec. to upload !

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


VectorBase


•  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 !


VectorBase


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

•  Close the window


VectorBase


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


VectorBase



(1) Upload data,


(3) Attach a URL,

(4) Manage the data



VectorBase

(3) Attach a URL

•  Paste the URL,

•  Give a name to the track (optional),

•  Then click on ‘next’


VectorBase

(3) Attach a URL

•  A message informs you know it is (successfully) attached

•  Click on ‘Close’ to go back to the genome browser


VectorBase

(3) Attach a URL

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


VectorBase



(1) Upload data,


(3) Attach a URL,

(4) Manage the data



VectorBase

(4) Manage the data

•  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!


VectorBase

(4) Manage the data

before

after


VectorBase

More about DAS
(specially to set up a DAS server)

•  Ensembl documentation:
http://www.ensembl.org/info/docs/das/das_server.html

•  Sanger documentation:

http://www.sanger.ac.uk/resources/software/das/


VectorBase

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


Vb tutorial-das-update may2010

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