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VectorBase
http://www.vectorbase.org




                            DAS at VectorBase	


                                 Karyn Mégy
                               Update May 2010 	





Karyn Mégy – May 2010                                1
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                                                    2
VectorBase
http://www.vectorbase.org




                                   Introduction	


                            What is DAS? Why use DAS?	

                                What is the concept?
                                                   	





Karyn Mégy – May 2010                                      3
VectorBase
http://www.vectorbase.org




                            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.
                                                                        	


Karyn Mégy – May 2010                                                          4
VectorBase
http://www.vectorbase.org




                                  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 	





Karyn Mégy – May 2010                                                          5
VectorBase
 http://www.vectorbase.org




                                            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	

 Karyn Mégy – May 2010                                                                             6
VectorBase
http://www.vectorbase.org




                                      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	

Karyn Mégy – May 2010                                                                     7
VectorBase
http://www.vectorbase.org




                                  How to set up a DAS track,
                                                           	


                            Example of the Anopheles RNA-seq data
                                                                	





Karyn Mégy – May 2010                                                 8
VectorBase
http://www.vectorbase.org




                            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 	

 Karyn Mégy – May 2010                                                         9
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                                                                 10
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                                                                      11
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                                                12
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                                                        13
VectorBase
http://www.vectorbase.org




                             (1) Upload data	





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





Karyn Mégy – May 2010                                                     14
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                                                 15
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                                                                                                                         16
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                                                                    17
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                                                           18
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                                                                         19
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                                                     20
VectorBase
  http://www.vectorbase.org




                              (2) Attach a DAS source	


                                             •  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? 	


   Karyn Mégy – May 2010                                                                   21
VectorBase
http://www.vectorbase.org




                            (2) Attach a DAS source	


                                                •  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 ! 	

 Karyn Mégy – May 2010                                                                   22
VectorBase
http://www.vectorbase.org




                            (2) Attach a DAS source	





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

   •  Close the window	



Karyn Mégy – May 2010                                                  23
VectorBase
http://www.vectorbase.org




                            (2) Attach a DAS source	





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




Karyn Mégy – May 2010                                    24
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                                                           25
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                                26
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                                                    27
VectorBase
http://www.vectorbase.org




                            (3) Attach a URL	





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





Karyn Mégy – May 2010                                                     28
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                                                           29
VectorBase
http://www.vectorbase.org




                            (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!	





Karyn Mégy – May 2010                                                   30
VectorBase
http://www.vectorbase.org




                            (4) Manage the data	




                                                     before	





                                                      after
                                                          	





Karyn Mégy – May 2010                                     31
VectorBase
http://www.vectorbase.org




                                  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/	





Karyn Mégy – May 2010                                                       32
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 	



Karyn Mégy – May 2010                                                      33

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Vb tutorial-das-update may2010

  • 1. VectorBase http://www.vectorbase.org DAS at VectorBase Karyn Mégy Update May 2010 Karyn Mégy – May 2010 1
  • 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 2
  • 3. VectorBase http://www.vectorbase.org Introduction What is DAS? Why use DAS? What is the concept? Karyn Mégy – May 2010 3
  • 4. VectorBase http://www.vectorbase.org 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. Karyn Mégy – May 2010 4
  • 5. VectorBase http://www.vectorbase.org 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 Karyn Mégy – May 2010 5
  • 6. VectorBase http://www.vectorbase.org 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 Karyn Mégy – May 2010 6
  • 7. VectorBase http://www.vectorbase.org 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 Karyn Mégy – May 2010 7
  • 8. VectorBase http://www.vectorbase.org How to set up a DAS track, Example of the Anopheles RNA-seq data Karyn Mégy – May 2010 8
  • 9. VectorBase http://www.vectorbase.org 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 Karyn Mégy – May 2010 9
  • 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 10
  • 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 11
  • 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 12
  • 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 13
  • 14. VectorBase http://www.vectorbase.org (1) Upload data •  The track (color, shape, name) is configurable in the uploaded file Karyn Mégy – May 2010 14
  • 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 15
  • 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 16
  • 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 17
  • 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 18
  • 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 19
  • 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 20
  • 21. VectorBase http://www.vectorbase.org (2) Attach a DAS source •  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? Karyn Mégy – May 2010 21
  • 22. VectorBase http://www.vectorbase.org (2) Attach a DAS source •  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 ! Karyn Mégy – May 2010 22
  • 23. VectorBase http://www.vectorbase.org (2) Attach a DAS source •  You should get a confirmation that the sources are attached, •  Close the window Karyn Mégy – May 2010 23
  • 24. VectorBase http://www.vectorbase.org (2) Attach a DAS source •  The DAS sources are attached! You can see them in the ‘Region in detail’ panel Karyn Mégy – May 2010 24
  • 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 25
  • 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 26
  • 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 27
  • 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 28
  • 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 29
  • 30. VectorBase http://www.vectorbase.org (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! Karyn Mégy – May 2010 30
  • 31. VectorBase http://www.vectorbase.org (4) Manage the data before after Karyn Mégy – May 2010 31
  • 32. VectorBase http://www.vectorbase.org 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/ Karyn Mégy – May 2010 32
  • 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 Karyn Mégy – May 2010 33