23 April, 2009

Ensembl Events in May 2009

For May we have the following Ensembl events:

29 April - 1 May: Ensembl Developers workshop at the University of Cambridge, Cambridge, UK
8 May: Browser workshop at Imperial College, London, UK
11-13 May: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence, Hinxton, UK
11-15 May: Ensembl module in the EBI hands-on training A walktrough EBI Bioinformatics Resources, Hinxton, UK
12-13 May: Ensembl module in the EBI roadshow at the Université Victor Segalen Bordeaux 2, Bordeaux, France
19-21 May: Ensembl module in the EBI roadshow at the Universidade de Santiago de Compostela, Santiago de Compostela, Spain
22 May: Browser workshop at the European Human Genetics Conference, Vienna, Austria
26 May: Ensembl Developers workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Ghent, Belgium
27-28 May: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands

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

20 April, 2009

Ensembl Genomes live!

Today the long-awaited Ensembl Genomes went live! This is a 'sister project' focusing on those species that aren't part of Ensembl, i.e. non-vertebrates. Please have a look at what the Ensembl Genomes team have to say about it themselves:

"We are delighted to announce the forthcoming release of Ensembl Bacteria, Ensembl Protists and Ensembl Metazoa, the first sites to be launched as part of the EBI's "Ensembl Genomes" project to extend the use of the Ensembl browser to non-vertebrate genomes.

These following site are available:


Additional sites for fungi and plants are in development and will be launched during the summer of this year.

In the Ensembl Genomes project, we are aiming to do two things: firstly to work with particular communities to support the bioinformatic analysis of genome-scale data; and secondly, to provide an integrative portal to data from species of scientific interest from across the taxonomic space. In pursuit of both these aims, we will re-use and extend the proven Ensembl software system, that has been developed by EBI and the Wellcome Trust Sanger Institute in the context of vertebrate genomics.

As with Ensembl, Ensembl Genomes will provide access to DNA and protein sequence, positional and functional annotation of protein-coding and non-protein coding genes, repeat analysis and other features and statistics. An interesting feature made available with the release of Ensembl Genomes is the inclusion of a multi-way comparative genomic analysis performed using a selection of species from bacteria to humans, and the production of gene trees showing the inferred ancestral relationships within deeply conserved protein families. Comparative resources are also provided at a narrower level (for example, DNA and protein-based analyses of individual bacterial clades). In partnership with collaborators, we are working on capturing gene expression, and population-scale variation data, in a number of contexts. More generally, we anticipate the ongoing enrichment of these resources through the integration of increasing quantities of high throughput data now becoming routinely available for all species.

Ensembl Genomes will provide access to data through the usual routes supported for vertebrate data; web-based browser, FTP site, programmatic API, DAS, and BioMart-style data warehouse; as well as text and sequence-based search.

We look forward to working with you as future producers and consumers of data. More information about the project is available at http://www.ensemblgenomes.org. We will be happy to receive any feedback you might wish to offer us at helpdesk@ensemblgenomes.org."

03 April, 2009

Ensembl Tips: Navigating the Browser

Though the overall response has been good, a few Ensembl users are finding it difficult to switch from the old interface to the new browser launched Nov, 2008. For those users, functionality has not been lost. You should still be able to do the same tasks as before in a faster interface.

We will post a series of tips to show you how to make the switch from the old interface to the new. If you still have trouble, please watch our video tutorial: Browsing Ensembl.

TIP: I want to use ExonView. Where is this now?

To view the full genomic sequences, exons and introns, go to any transcript. (Exons are transcript information. To see the exons page, go to a transcript tab, not the gene tab.) Click on the 'Exons' link under 'Sequence' at the left of any transcript page.

To show the full introns, click on 'Configure this page' at the left. Select 'Show full intronic sequence'. Click 'Save and Close' at the top right corner of the menu window.

Still can't find what you're looking for? Email us at helpdesk@ensembl.org.