Hello to our readers, I hope everyone is having a nice April. In the UK we are experiencing a long winter with some rain, but spring seems to be around the corner… as are these upcoming workshops…
Did you know? The EBI has released tutorial videos.
Have a look at the Ensembl browser videos for information and direction to some of its pages! Or, learn more about BioMart, a fast data mining tool.
Upcoming workshops- May
Browser workshop at the WHO in Cairo (12-13 May)
Module in the Open Door Workshop at the Sanger (12-14 May)
Ensembl in China: The Shanghai Center for Bioinformation Technology (14-16 May)
Ensembl in China: Center for Bioinformatics, Beijing (19-21 May)
Browser and API workshops at the GTPB in Oeiras, Portugal (27-30 May)
Presentation at the European Human Genetics Conference in Barcelona (30 May)
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.
We are looking forward to Ensembl release 49, which has been delayed to 13 March, 2008. This is a result of some downtime planned at the Wellcome Trust Sanger Institute. Users, beware! Ensembl will not be available from: Friday 7 March – Sunday 9 March
On the 13th March Ensembl version 49 will be available. Keep an eye out for:
Drosophila melanogaster (assembly BDGP 5.4)
Horse (first gene build)
Viral genes have been removed in multiple species. ncRNA updates will be ready for Pika and Mouse Lemur, and new variations from dbSNP 128 (mouse, chicken, cow, and zebrafish) and dbSNP 126 (rat) will be available. Have a look at the new pairwise alignments between human and horse genomes.
Upcoming Workshops – March
A series of talks and workshops are happening in March.
Browser Workshop (2-day course at the EBI) 5-7 March
Browser Workshop (part of a 2 day course, MRC London: EBI Roadshow) 11-12 March
Presentation at the Genomes to Systems 2008 conference in Manchester, 17-19 March
Interested in organising a course in Ensembl and BioMart? Contact our helpdesk.
-The Ensembl Outreach team
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.
Ensembl Workshops in January took us to the West Coast (USA) and the Netherlands. Workshops in February:
Browser workshop (Institute for Animal Health) Compton, UK 12 Feb
Browser workshop (EURATools, University of Edinburgh) Edinburgh, UK 12 Feb
Browser workshop (Cambridge University, Dept of Genetics) Cambridge, UK 28-29 Feb
Picture: Nijmegen, the Netherlands. The NBIC was the site of an Ensembl Browser workshop on 16 Jan, 2008
Interested in hosting a workshop? Contact us!
Happy New Year from Ensembl!
Our upcoming workshops this month are as follows:
Browser workshop (University of Nottingham) Nottigham, UK 8 Jan
Demo at the PAGXVI Conference, San Diego, CA, USA 13 Jan (8:00-11:20 AM)
* Tutorials for EBI resources presented at PAGXVI are here
Browser workshop (Netherlands Bioinformatics Center) Nijmegen, NL 16 Jan
Developers workshop: the core API (Netherlands Bioinformatics Center) Nijmegen, NL 17 Jan
Browser workshop (City of Hope) Duarte, CA, USA 18 Jan
Browser workshop (University of Oregon) Eugene, OR, USA 22 Jan
Browser workshop (University of California, San Francisco) San Francisco, CA, USA 24 Jan
Browser workshop (University of California, Santa Cruz) Santa Cruz, CA, USA 28 Jan
Browser workshop (University of California, Los Angeles) Los Angeles, CA, USA 30 Jan
Remember, the next Ensembl release is due 26 Feb, 2008.
Ensembl is pleased to announce a new release (version 48) due on 11 December. Featured in the release will be a new gene set for pika and the mouse lemur. These species will also be incorporated into homology calculations and alignments. Further upcoming features include variations from dbSNP128 for mouse and a new rat strain, RNB1 (from Japan). The human variation set will also feature updated data from Dr. Watson’s genome, along with updates from dbSNP128.
Did you know about our new human and mouse databases (since release 41)? The functional genomics database (funcgen) is a first step into the world of annotating promoter and enhancer elements detected in the ENCODE project. See these features in ContigView (‘Regulatory features’ under the ‘Features’ roll-down menu) or access the data with our API.
Finally, a new database integrating tissue expression data and presenting it on the rat genome will be available as EURATMart.
Upcoming Workshops in December:
Module in the Wellcome Trust Sanger Open Door Workshop, Montevideo, UY 4 Dec
Browser workshop (Universiti Kebangsaan Malaysia) Bangi, MY 4-5 Dec
Developers workshop (University of Cambridge) Cambridge, UK 17-19 Dec
Browser workshop (CNIO) Madrid, ES 18 Dec
The Barcelona Supercomputing Center, site of an EBI roadshow in November:
Ensembl released version 47. News highlights: New gene sets for mouse, human and C. elegans. A new mouse assembly (m37) is available with a new Ensembl gene set, also a new human gene set has been determined for assembly NCBI 36. WormBase 180 has been imported into the browser for C. elegans. A word of warning: the FTP site has been rearranged, so please check the site for the updated format. Click here for more release news.
New! An updated pig assembly and a new orangutan assembly in our Pre! site.
Upcoming workshops in November include:
Developers workshop at (CSHL, US) 30 Oct to 1 Nov
Browser workshop (UCL/Birkbeck College, UK) 5 Nov
Browser workshop (CSHL, US) 11, 12 Nov
Browser workshop (Erasmus MC, Rotterdam) 15,16 Nov
Browser workshop and EBI overview (UNAM, Mexico) 19-21 Nov
EBI Roadshow (Barcelona) 26-27 Nov
Have you seen our animated tutorials? Learn how to use BioMart to convert IDs here.