Following our recent post updating you with feedback from our recent user survey, I wanted to share with you the following data. I’ve been data mining our web logs to get a picture of worldwide access to Ensembl (this is page impressions) and I put them on a heat map representing access to our browser (this doesn’t include either BioMart or direct access of our public databases). I filtered out commercial IP addresses (i.e. all those .com, and .net) to simplify the analysis. Countries are shaded according to how much they accessed the Ensembl browser in the month of May. Dark countries use the Ensembl browser more, light countries, less. And this is what you get:

Heat map May 2009

Can you see your country here? If not, consider running a browser workshop in order to join our wide community of Ensembl users!

This map should help us to monitor the success of our workshops (at this moment I’m writing this from Venezuela which hopefully should appear in future heat maps!) Although there are still some gaps in the map, we are happy to see that Ensembl is used globally and our efforts are recompensed. Training leads to more in depth understanding of how to use the browser, and we think our worldwide workshops are helpful in using Ensembl to guide and enhance research.

Greetings from Venezuela, or as you would say here… ¡Hasta la próxima


Dear all,

Thanks to all of you who participated in our Ensembl browser survey, which closed at well over 150 respondents. We appreciate hearing from users worldwide, and our responses came from Europe, the Americas, Asia, India, New Zealand and Australia.

We will be able to move forward based on the feedback, in order to make the browser smoother and easier to use.

Some of the things we learned.

How often do you use Ensembl?

The majority of our users (83%) access the Ensembl browser multiple times per week. (See pie chart above). A similar survey run by Ensembl in 2007 reflected a much lower figure: only 32% of users browsed as frequently, with the majority of respondents accessing the browser once a month or less. Genome browsers appear to have moved from being tentative, browse-for-interest curiousities to comprehensive resources that can be integrated into daily research.

We were pleased to see our users are accessing many types of Ensembl data, from transcripts to variations to comparative genomics. Most respondents found the tabs in our new interface to be intuitive, so we won’t change those! Many users scroll through views using the buttons on each page, so again, we will keep those in place.

More of you are finding the Pre! and Archive! sites helpful. And 65% of users voted that the most important aspect was good information.

Things we will work on?

In addition to custom data and user upload advances, we are focusing on graphical display of our comparative data. These improvements are already in our pipeline. We did get some new ideas from the survey, for example, some of our respondents could not find the Pre! or Archive! pages. We will think about how to make these links more obvious.

Speed of the browser could be faster. We will keep you posted on the Ensembl mirror on the US west coast.

Finally, more users are finding our help pages and videos, including a new YouTube channel. and we will be constantly adding to the tutorials page. If you have ideas about videos or tutorials you would like to see, please send your comments to our helpdesk. We find it immensely helpful to hear feedback from our user community.

Thanks again for the view of Ensembl from our users! We will be polling again next year.

The Ensembl Team

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:, if you could let us know you are planning to attend or wanted more information, please send an eMail to

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 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!