Hello all,

We are curious as to how our users are finding the current Ensembl web browser. We opened a survey in the current Ensembl (version 54). The survey will close in one week’s time (Friday, 5 June). Thank you to everyone who has already entered their feedback.

For users who have not yet replied to the survey, we ask that you spare 10 minutes or so of your time to do so. Please give us your thoughts and feedback by clicking on the link below:


The feedback centers on the web browser, specifically the new interface launched in Nov, 2008.

Many thanks for your time.

The Ensembl Team

Ensembl announces a workshop for developers that will take place in the Wellcome Trust Genome Campus in Hinxton (near Cambridge, UK) next September (14th-16th September), following the Genome Informatics meeting.

In this workshop we will be exploring Ensembl beyond the website. Participants will be expected to have experience in writing Perl programs and a background in object oriented programming techniques. Being familiar with databases (MySQL) and the Ensembl APIs would be an advantage.

Several Ensembl developers will present uses of our APIs (Application Programming Interfaces) as well as extensions of the Ensembl system. Note this is not a course about how to use the Ensembl APIs.

At the end of this course, attendees will:

• have a good understanding of Ensembl’s annotation pipeline;
• know how to customise a local installation of the Ensembl website;
• and have hands-on experience with the annotation pipeline.

In late 2008, the Ensembl Genomes project at the EBI will leverage the Ensembl system to create consistent genome annotation resources focused on a wide variety of eukaryote, as well as prokaryote genomes and thereby continue the activities of the current EBI Integr8 and Genome Reviews projects.

Thus, there will be a session where the new divisions of Ensembl will be introduced and previewed; the initial data content and future directions will be discussed.

There is no registration fee to attend this course, but you may need accommodation (or extending your stay in Hinxton Hall: info@wtconference.org.uk), if you could let us know you are planning to attend or wanted more information, please send an eMail to xose@ebi.ac.uk.

The Ensembl Team

In a previous post I promised to do some more genome browser screenshot counting. So, that is what I did last week at the XX International Congress of Genetics 2008 in Berlin. I limited myself to the second poster session of the conference that should have contained 675 posters. To my surprise a vast amount was missing though, so I estimate that the number I looked at was closer to somewhere between 400 and 500. Compared to the Barcelona conference the result was poor; I identified only 4 posters with Ensembl screenshots as well as 4 posters with UCSC Genome Browser screenshots and none with NCBI Map Viewer screenshots. So, based on the combined results from two genetics conferences, it seems that the Ensembl and UCSC browsers are about equally popular amongst poster-making geneticists.

However, I had expected more genome browser screenshots in general. What can be the reason for these low numbers? Is there no need for screenshots at all? Or can people not get what they need for their poster from Ensembl or UCSC? We are curious about your thoughts and views on this and are welcoming any suggestions for improvements to Ensembl that will make preparing figures for your poster (or publication) more of a breeze!

As you know, we are working on a new website design for the Ensembl 50 release. We are currently seeking ‘beta testers‘ who would be happy to take part in a survey and help us shape the look and feel of the new website.

If you could spare some time we would be very grateful if you could send an eMail to survey@ebi.ac.uk so we can add you to our list of testers.

We are looking forward to hearing from you.
The Ensembl Team

The past days I was in Barcelona at the European Human Genetics Conference 2008. After giving my presentation on Ensembl in one of the ‘Educational sessions’ and listening to numerous talks about GWAS (genome-wide association studies), I had a look at the posters. Under the impression that the UCSC Genome Browser is the preferred browser amongst (human) geneticists and with Ewan’s experience at the recent ‘Biology of Genomes’ meeting fresh in my mind, I decided to have a closer look at the posters in the Cytogenetics section. Out of 189 posters, I could positively identify 11 with Ensembl screenshots (mostly CytoView and ContigView, but also two times KaryoView), 8 with UCSC Genome Browser screenshots and none with NCBI Map Viewer screenshots. OK, I admit that I can recognise almost any pixel copied from our site and may have missed one or two UCSC screenshots, but all in all I thought this was a very encouraging result! Of course we should keep in mind that this was a European conference, mainly attended by European scientists …. I guess I have a bit more screenshot counting to do at the International Congress of Genetics 2008 in Berlin. So, let’s say Ensembl 11 – UCSC 8 is the score at half time …. next month I’ll report back with the final result!