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.

GWAS Data in Ensembl

Ensembl has begun to incorporate data from genome-wide association studies. These data are being added in coordination with the European Genotype Archive, a new database resource at the EBI designed to provide a permanent archive for human variation data that is not available for unlimited public release because of ethical or individual privacy restrictions. The European Genotype Archive has recently launched with the raw data from the Wellcome Trust Case Control Consortium (WTCCC. 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661-678). In the future the EGA will provide additional array-based genotype data as well as data from re-sequencing and CNV studies. The EGA will also contain phenotype data.

Ensembl is incorporating summary data from genome-wide association studies represented in the EGA. The data generally represent the p-value for each of the tested SNP (Single Nucleotide Polymorphism) associated with the given phenotype.

The WTCCC summary data is now available on Ensembl as DAS tracks selectable from the "DAS Sources" menu from the CytoView and ContigView pages. The following menu items provide access to data from biopolar disorder (BD), coronary artery disease (CAD), cardiovascular disease (CD), hypertension (HT), type 1 diabetes (T1D), type 2 diabetes (T2D):

WTCCC BD
WTCCC CAD
WTCCC CD
WTCCC HT
WTCCC T1D
WTCCC T2D

In future releases, GWAS data will be integrated into the Ensembl variation databases.

We will be adding additional data to both Ensembl and the European Genotype Archive as the data become available. We hope you find these new data resources useful.

Glitches in Ensembl

Ensembl is currently migrating to new hardware in conjunction to the development of new webcode for the next release (due in late September). During this period, and due to some technical issues, there might be some downtime of our website. We apologise for any problems this may cause and we are working to minimise its impact in Ensembl.

The Ensembl Team

Ensembl in China

The Ensembl team has recently run a series of workshops in China:

In Shanghai we were at Tongji University for a workshop organised by the Shanghai Center for Bioinformation Technology, and

In Beijing, we were hosted by Professor Jingchu Luo from the Center of Bioinformatics at Peking University where we also delivered some lectures in the Applied Bioinformatics Course.

Following this experience and due to the success of the tour, we are planning to go back to China. So if you were interested in hosting a workshop or you have a collaboration with a Chinese group who might be interested in knowing more about Ensembl, please contact us to discuss dates. We are trying to coordinate our next trip with different hosts.

The Ensembl Team

Ensembl User Meeting

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