by ·Comments Off on Upcoming training events September

After the Summer break we are getting up to speed again with our training events:

14-16 Sep: Ensembl User Meeting, Hinxton, UK

17-19 Sep: Browser workshops and presentations, Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands

22 Sep: Browser workshop, VIB Flanders Interuniversity Institute of Biotechnology, Antwerp, Belgium

We also have a complete list of all upcoming training events for the coming months available. Are we not coming to a location close to you? Why not host then an Ensembl workshop yourself? For more details, please contact Xose Fernandez.

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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!

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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!

by ·Comments Off on Ensembl US East Coast Tour

After a very successful Ensembl US West Coast Tour last month, the Ensembl Outreach team is presently looking into the possibility of organising a similar tour on the US East Coast in the second half of 2008. At the moment we are mainly thinking of 1-day browser workshops, but if there is interest in an API workshop we can of course also consider this.
The participating institutions would only have to pay the instructor’s expenses and would share the travel costs, but we would not otherwise charge for the workshops. People that are potentially interested in hosting a workshop can contact me for more details.

by ·Comments Off on California dreamin’

You might think that only our group and team leaders are traveling the globe, but also the members of the Ensembl outreach team (Xose Fernandez, Giulietta Spudich and myself) spend a fair amount of their time on the road (or in the air ….) to spread the word about Ensembl.

I myself, for example, just returned back in the UK from a 3-week “Ensembl US West Coast tour”. That means no more Margaritas, motels with ocean view or trendy LA restaurants for me for a while, but also no more lost luggage or cancelled or delayed flights (it’s not all glitz and glamour …. ).

My tour started with a visit to the Plant and Animal Genome XVI Conference in San Diego, where I gave a presentation on Ensembl and spent, together with other EBI colleagues, time in the EBI booth to promote our institute. After that I gave Ensembl browser workshops at City of Hope (see picture), the University of Oregon , UCSF, UCSC (where the audience mainly consisted of genome browser folks!), and UCLA. Numbers of participants ranged from around 15 till over 50 and in all places the workshop was very enthousiastically received. In fact, several of my hosts were already asking when we could repeat this ….

The principle aim of our workshops is of course to teach people how to get the most out of Ensembl, but apart from that it also is a really good way for us to stay in contact with our users. We can see what people exactly use Ensembl for, how they use it and what they like and dislike about it, so we always return back home with lots of new ideas and suggestions. One thing that, for instance, often strikes me is that most people are not aware of the existence of our data mining tool BioMart. However, after a short explanation and some hands-on exercises they find it almost without exception very useful! So, we still have some work to do to promote this very handy tool.

By the way, we not only offer browser workshops, but also workshops on the use of the various Ensembl Perl API’s. Keep an eye on this blog to see where and when the next workshops will be. Or, even better, host one at your own university or institute! For more information with regard to our workshops you can contact our helpdesk.