Linking in to Ensembl...

Due to the changes in the web interface there have been a number of changes to the URLs for pages. In most cases the web code catches these changes but there are a number of requests which due to the nature of the site have changed:

• Configuring the way a page is rendered;
  
• Changing the way tracks are rendered;
• Adding DAS sources via a web-address and not via the web interface;
• Attach UCSC style external resources.

These are now all attached in a similar - systematic way:

• To change global page settings: add a paramter config=key=value{,key=val}
  e.g. to turn off the top image on Location > Region in detail
  
  http://www.ensembl.org/Homo_sapiens/Location/View?r=1:1000-2000;config=view_top=off
  
  e.g. to link directly to the Exon Intron markup panel (Transcript > Exons) and to show full introns and only 60bp flanking sequence AND turn the display to be 60bp wide
  
  http://www.ensembl.org/Homo_sapiens/Transcript/Exons?t=ENST00000309255;config=flanking=60,seq_cols=60,fullseq=yes
  
  

• To change configuration for an individual panel add a parameter refering to the panel (this will be documented shortly on the website) e.g. For Location > Region in detail the two panels are contigviewtopcontigviewbottom, for Location > Region overview it is cytoview. This is again a comma separated list, where the left hand side of each "=" is the name of the track, and the right hand side is the name of the "renderer" to use - the latter depends on the type of track. Additionally the left hand side can be used to integrate external data: Notes:
  
  • Track names are now systematically named so will have changed from the values you may have been used to using - again we will shortly publish a list of these, but examples are: transcript_core_ensembl - the ensembl genes from the ensembl database.
  • Renderers depend on the type of track, but e.g. for transcripts you have the option of "transcript_label", "transcript_nolabel", "collapsed_label" and "collapsed_nolabel", for alignment features (and also url attached data at the moment) "normal", "half_height", "stack", "unlimited" and "ungrouped", for DAS tracks "labels" (show labels if configured by the source) or "nolabels" - hide labels.
  • At the moment two special parameters can be used:
    das:http://www.mydas.source/das/my_data=render
    - which attaches a DAS source to the session and selects the renderer
    url:http://www.myweb.server/my_data.format=render
  For example:
  
  http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000012048;config=panel_top=off;contigviewbottom=das:http://www.ensembl.org/das/Homo_sapiens.NCBI36.transcript=nolabels,transcript_core_ensembl=collapsed_nolabel
  
  Turns on a das source (in this case the Ensembl transcripts) and collapses the standard ensembl track down to a single line per Gene AND also turns off the top panel!