30 November, 2008

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}
    to turn off the top image on Location > Region in detail


    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


  • 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:
      - which attaches a DAS source to the session and selects the renderer
    For example:


    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!

29 November, 2008

Ensembl 51

The web team can finally let out a quick sigh of relief now that the long awaited new web code has finally emerged kicking and screaming out of the web team office...

It is obvious to see the "cosmetic" changes to the site:

  • the colours,
  • fonts,
  • layout,
  • the unified configuration
  • the reduction in page sizes.
On top of this there have been a large number of underlying technical improvements to the way the pages are put together.
  • Streamlining the JavaScript and css to make sure that the transfers to and from the server to your browser are as fast as possible; Using unobtrusive JavaScript throughout the new code so pages work with or without JavaScript or AJAX - althouth they are not quite as functional they still work!
  • Making the pages standards compliant to make them render in most browsers without issues (unless of course that browser is IE and there are lots of places where the "standards" approach fails)
  • Using an fast in memory cache (a modified version of memcached which allows for the use of tags) to reduce the load on our user database and to store and server temporary images, processed HTML etc.
  • Segregation of code into more modules to reduce the size of the very large modules we had (noticeably the breakdown of the Component modules into smaller chunks)
  • Configuration meta information contained in core databases making the site easier and more automatic to set up.
  • Optimisation of drawing and configuration code.
  • Transparent use of AJAX in many cases. Use of Perl's LWP::ParallelUserAgent where the user's browser doesn't support AJAX.
  • Further areas where the extensible plugin system is available - defining colours, configuring images.

19 November, 2008

Upcoming training events December

There are still a few more Ensembl training events before the end of the year.

Browser workshops:

UNAM, Mexico City, Mexico (1-2 Dec)
UNAM, Cuernavaca, Mexico (5 Dec) (+ departmental seminar 4 Dec)

Amsterdam, The Netherlands (19 Dec)

Developers workshop:

University of Cambridge, UK (1-3 Dec)

In addition, Ensembl will feature as part of the following courses:

Wellcome Trust Open Door Workshop 'Working with the Human Genome Sequence' (1-2 Dec, Hinxton, Cambridge, UK) and Genes en evolución, ecologia e conservación (8-9 Dec, La Paz, Baja California, Mexico)

For details of these workshops, please have a look at the complete list of Ensembl training events.

17 November, 2008

Accessing the Ensembl data with Perl

Do you know a bit of Perl? Ensembl hosts an API (Application Programmers Interface) which uses Object-Oriented Perl to extract data from Ensembl databases. This API is public and can be used for people to programmatically access the data in the Ensembl database. We understand that not everyone is used to Object-Oriented code, although people may have basic Perl skills and be interested in using our datasets. For that kind of bioinformaticist, I would recommend a recent short read in O'Reilly's Broadcast:

Beginners Introduction to Object-Oriented Programming with Perl - O'Reilly Broadcast

And for the more advanced readers, the classic reference book in OO-Perl would be Damian Conway's Object Oriented Perl, which a part from being very informative, has a really cool cover :-)

We are always trying to lower the barrier to entry for research communities interested in using the Ensembl database in programmatic ways that make use of all the complexity associated with the generation of our data. That's why our API is public and well-documented. You can learn about our API by attending on of our API workshops for free (e.g.: 1-3 December - Univ. Cambridge, UK). We are currently trying to smooth things out even more, working on ways to make it even easier to download all that's needed to use the API and have the example scripts running in your computer with the minimum number of steps. Keep tuned for news in this respect soon...