We are looking for projects that use aspects of the Ensembl code (for example, the webcode, the genebuild pipeline, or comparative analyses).  If you want to be added to our list, please reply to this blog post, or email our helpdesk with your project name, url, and what aspect of the code you are using.

In addition to the projects on our powered by Ensembl page, we have heard from:

Let us know about your project!


This year the Human Genome Meeting has brought us to Dubai (in the United Arab Emirates) for a very interesting conference focusing on the genomics of human genetics. Ensembl is featured in one of the satellite events organised, The Open Door Workshop, offering us a unique opportunity to present the latest develoments in the project to participants from 12 countries (Australia, Brazil, India, Indonesia, Iran, Pakistan, Saudi Arabia, Slovenia, Spain, Sri Lanka, Sudan and obviously our host country UAE) with a broad range of interests ranging from clinical genomics to database management.

We have received very positive feedback on some of the latest goodies hidden in our favourite genome browser, such as the possibility of streaming BAM files to display NGS data alongside the Ensembl annotation (undoubtely we should be posting some tips on this very soon).

These are the Ensembl events for February:

10 Feb: Developers workshop at the Korea Genome Organization (KOGO) 2011 Winter Symposium, YongPyong Ski Resort, South Korea
11 Feb: Browser workshop at the Zentrum fuer Humangenetik und Laboratoriumsmedizin Dr. Klein und Dr. Rost, Martinsried, Germany
14 Feb: Developers workshop at Seoul National University, Seoul, South Korea
16 Feb: Developers workshop at the Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
17-18 Feb: Browser workshop at the University of Cambridge, Cambridge, UK
23-25 Feb: Ensembl module in the Bioinformatics Roadshow at the Research Centre for Biodiversity and Genetic Resources (CIBIO), Porto, Portugal

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Many thanks to the Ensembl browser users who have given us feedback in our recent survey entitled “Tell Us What You Think”! We learned some valuable points that are being addressed to improve our discoverability, functionality, and overall usability.

We heard back from scientists all over the world- the majority of you were in the UK, Netherlands, the US, and Germany. Represented fields include bioinformatics, basic research, clinical and genetics research, biotechnology and immunology. 50% of respondants work mainly with the computer, while the other half of you do at least some wet-lab biology. We even got responses from mainly wet-lab scientists (15% of respondants)- this is useful to us, as we strive to make Ensembl usable to the largest possible community.

So what did we learn? The use of BioMart and the Perl API by website-users has increased since our last survey a year and a half ago. We have more infrequent users, visiting our browser monthly or less often- though the majority of our users are Ensembl masters (frequent users). We believe that this represents the fact that an ever greater percentage of biological research involves at least some bioinformatics tools and hope this reflects a simpler, more straightforward website that does not need extensive study to use. Finally, 65% of our users take a genome-wide approach, while 20% focus on less than 10 genes.

So what did people like? Our tools are popular, especially the Variant Effect Predictor. The recent addition of sortable columns is also a hit. When you all were asked what other tools are desired, we were pleased to find that some (history) were already being implemented, while others exist, but seem to be hidden. On that note-

Those of you who asked for a record of recent actions in Ensembl, if you login (registration is free) a history of recent genes, transcripts, variations and locations you visit will appear in the tabs. Give it a try!

Many of you asked for tools and functionality that exist, such as CpG islands, (available as a track in Location view) a map of gene structure for all isoforms of a gene, and SyntenyView. To aid in the discoverability of these tools, our main search will be configured to also yield results from help pages. This should help people find what they’re looking for, without relying on browsing alone. Also, we will make more use of this blog by posting “Did You Know?” tips that will help you learn about functionalities of Ensembl and BioMart that may not be completely transparent. The archive (older) sites in particular don’t appear to be easy to find (the link is a small one, at the bottom of each Ensembl page), we address this in our FAQ section.

As for other requests for functionality we don’t yet have, these are being taken on board, and will hopefully lead to exciting new developments in the future.

Thanks again for your feedback!

The Ensembl Team

For about 3 weeks now researchers in the US have had their default Ensembl go to our US west mirror (uswest.ensembl.org) automatically – if you just go to www.ensembl.org you brower gets automatically redirected. The US joined Japan and Canada who we switched in late 2009.

From our perspective, this is all working fine; the usage of uswest has gone up, and IP tracking on that shows far more US IP addresses (so the redirect is working fine!). We get some 3,000 odd visits a day, with some 50,000 pages delivered from our uswest site – about 20% of our total hits. Brilliant.

What is slightly more surprising is that we’re not getting any queries on this. Given the usage, we think this means the default browser, content and other functionality must be working well (or Americans are very shy about complaining… but that doesn’t sound like a good description of all Americans…). But we’d also like to hear from American users – have you noticed ensembl “go faster?”. Are there any glitches?

Another issue we are unclear about is whether we should automatically shift other users on the Pacific Rim to automatically go to uswest – in terms of usage, the biggest country would be Australia, but New Zealand, Phillipines and other Pacific Rim countries would also be candidates. It’s quite hard for us to assess whether our Europe (Cambridge UK) based servers or US west servers are best for this – both latency and throughput changes on different routes, and the time zone shift makes things complex to assess systematically in an easy way.

So – feedback welcome – either on this post or by email to our helpdesk about what your experience is, either from the US or from the Pacific Rim.

From this little corner of the world Ensembl will be delivering an Interactive Workshop on Friday (October 23rd) from noon (12.00) in Room 315 in the Convention Center. If you want to attend, let us know as seating is restricted and we are allocating seats until the room is full. You must bring a laptop with a wireless card (and a fully charged battery).

Furthermore, you can also visit us on booth 432 where we will be happy to help you and get any feedback.

Who is using us?

During the long flight from London to Seoul, where I’m now giving workshops, I had time to do some analysis.

We have recently changed the way we analyse traffic on our website. Urchin Software allows us to pinpoint access to our site with more accuracy. (In a previous post, I showed data where some domains were excluded in the representation).

This month’s data (June 2009) is more comprehensive and can be shown with the following heatmap. Again, dark-coloured countries show more use than lightly shaded ones. We can now detect some low level traffic in the African continent missed in previous analyses.

Following a recent thread, I normalised these data taking into account population. (Did I mention how long the flight from London to Seoul actually is?) This puts the Netherlands as the country with the highest ratio of Ensembl users normalised by population, followed by Sweden, Switzerland, the United Kingdom, Finland, Belgium, Iceland, Germany, Denmark and Singapore (the first non European country in the list) pushing the United States (excluding traffic from the US mirror) to the 15th position.

On another matter, I’m glad to see that our user base in this country is well established. Apart from the obvious Seoul, we can also see access from Taejon, Kwangju, Taegu, Pusan, Inchon, Pohang and up to 29 locations in the country, and following these workshops we hope this will increase further.

As they say over here 안녕


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