31 October, 2008

Ensembl at the IMGC

Ensembl is attending the 22nd International Mammalian Genome Conference taking place in Prague (Czech Republic) from 2-5 November 2008. This meeting starts with three bioinformatics workshops on Sunday (2nd November) at the Institute of Molecular Genetics (AS CR). One of these workshops will focus on Ensembl, discussing new developments and featuring a preview of our new interface. We will be starting a 9:00 (Seminar Room 3.102, in the third floor). You can download the workshop materials here (exercises and tutorials). As part of our commitment with the EURATools consortium, we'll be focusing on rat genomics, but if you work with any other species annotated in Ensembl, you are welcome.
See you in Prague!

30 October, 2008

Upcoming training events November

Only 3 continents to cover this time, but November will be even busier for the Ensembl trainers than October ....

Ensembl will feature as part of the following courses:

'Computational & Comparative Genomics' (5-11 Nov, Cold Spring Harbor Laboratory, New York, US)
Wellcome Trust Open Door Workshop 'Working with the Human Genome Sequence (10-12 Nov, Wellcome Trust Genome Campus, Hinxton, UK)
Hands-on training at EBI 'Programmatic access in Java: webservices & work flows' (24-27 Nov, Wellcome Trust Genome Campus, Hinxton, UK)

Browser workshops will be given at the following locations:

Prague, Czech Republic (2 Nov)
Madrid, Spain (5 Nov)
Newcastle, UK (13 Nov)
Cambridge, UK (13-14 Nov)
Naples, Italy (19 Nov)

North America:
Cambridge, Massachusetts, US (12 Nov & 14 Nov)
Boston, Massachusetts, US (13 Nov)

Kuala Lumpur, Malaysia (24-25 Nov)
Sabah, Malaysia (27-28 Nov)

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

14 October, 2008

Power outage

Ensembl is currently down due to a power outage in the data centre at the Sanger Institute last night. Power has been restored, but it will take some time to restore all of the services.

We are working to get things up and running and expect that Ensembl will be back mid to late morning UK time.

03 October, 2008

Ensembl 51 development

New design
You will already have seen a number of emails about the upcoming Ensembl 51 release - the web team are working hard to tidy up the loose ends of the release! We have got most of the major views ready, and just working on some of the views you may have never found before. As a taster I'm posting a few screen shots from our development site, the first shows the new page layout for graphical display of genomic regions (the old contigview). You will see many of the new design decisions in this screen shot:

  • There are more views per object as we have broken up the large single pages into smaller components;
  • Tabs for the different focus objects - in this case Gene and Location. Transcript and Variation feature are the other tabs available;
  • A tree of all information available about the focus feature on the left hand side;
  • Left/right pagination buttons to allow you to navigate between all the information we have about the focus object.
  • "General" and "local" tools areas
Under the hood!

There have been a large number of changes under the hood of the web-site. Notable changes have been:
  • Use of modified version of memcached to store and retrieve cached images, static and dynamic content, user settings;
  • Re-writing the configuration code to automagically detect the contents of the databases and try and display the content appropriately;
  • Breaking up of the component code into separate modules;
  • Removing the need for a script per view - by using "routeing" style URL parsing to work out what objects are to be rendered and how... e.g. /Gene/Compara_Tree/Text displays the text version of a gene's homology tree.
  • More and easier to configure renderers for drawing code.
  • A strive for standards compliance in both XHTML and CSS; which should allow us to support more easily modern web browsers. We will be actively supporting Firefox 3+, Internet Explorer 7+ and Safari 3+ (and other similar browsers), while trying to make sure that the site is still workable in other browsers (at the site appears to work in Opera 9.25+)
New configuration panel

All configuration of the site and individual views has been moved to a common "Configuration dialog" box.
  • The old "yellow menus" are replaced by a more expansive and easier to navigate tree of features. Important now there are nearly 200 individual tracks in the Human Location view page.
  • There are more choices to display some tracks - rather than just turning them on and off, you can decide how you wish them to be displayed.
  • Configuration for other pages are loaded in a similar way.
  • The site has a common site-wide image width setting.
  • The configuration panel is also where you will: manage your accounts, upload data, attach DAS and URL based data
Different renderers

For different data types we now support different renderers - not just collapsed and expanded.
For example:
  • For genomic alignments we support, the ungrouped features (all on one line), normal grouped and bumped features at both full and half-height, and now also "stacked" features - "2 pixel" high glyphs.
We hope when you see the new interface that you will find it more intuitive, more discoverable and faster to use and most importantly more productive for the research work that you are doing.

Incredible !ndia

The Ensembl team has been involved in several activities in Hyderabad (India) during the last few days, making the most of the latest HUGO's 13th Human Genome (HGM2008).

A satellite workshop has been organised within the Open Door Workshop framework at the Centre for Cellular and Molecular Biology (CCMB). Over 40 scientists from different countries had the opportunity to learn about different resources freely available on the Internet, providing us with useful feedback.

Following our presence in the HGM2008 in the EBI booth we had the opportunity to make several contacts that hopefully should allow us to organise a series of workshops around India next year. If you were interested to know more about this, or query about possibilities to host one of our workshops, you can contact us.

Greetings from India भारत से नमस्ते