Ensembl Events in April 2010 - Ensembl goes Down Under

When we show during workshops a map of the world with the places that have been visited by the Ensembl Outreach team, people are often surprised that we never have been to Australia yet. Well, coming month this is going to change as two of my colleagues will travel to Down Under for a whole series of workshops:

12 Apr: Browser workshop at the University of Melbourne
15-16 Apr: Browser workshop at the University of Adelaide, Adelaide
21-22 Apr: Browser module in the PANDA workshop at the University of New South Wales, Sydney
23 Apr: Developers workshop at the University of New South Wales, Sydney
27-28 Apr: Browser module in the PANDA workshop at the University of Queensland / Griffith University, Brisbane
29 Apr: Developers workshop at the University of Queensland / Griffith University, Brisbane
29-30 Apr: Browser workshop at the Australian National University, Canberra

Aside from that there are many more Ensembl events in other parts of the world this month:

7-9 Apr: Browser module in the EBI Bioinformatics Roadshow at the University of Florence, Florence, Italy
15-16 Apr: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
19 Apr: Browser workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Leuven, Belgium
20 Apr: Browser workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Ghent, Belgium
20-21 Apr: Browser module in the EBI Bioinformatics Roadshow at the Dana-Farber Cancer Institute, Boston, MA, US *postponed to 3,4 May*
21 Apr: Developers workshop at the Hubrecht Institute, Utrecht, The Netherlands
22-23 Apr: Browser module in the EBI Bioinformatics Roadshow at the Harvard School of Public Health, Boston, MA, US *postponed to 3,4 May*
26-27 Apr: Browser module in the EBI Bioinformatics Roadshow at Northwestern University, Chicago, IL, US
28-30 Apr: Developers workshop at the University of Cambridge, Cambridge, UK
29-30 Apr: Browser module in the EBI Bioinformatics Roadshow at the University of Pennsylvania, Philadelphia, PA, US

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

Genomics and Transcriptomics in Mexico

As part of the EBI Roadshow training programme, Ensembl teamed up with ArrayExpress to run workshops for students, postdocs, and professors at ITESM, UNAM, and CIBNOR in these bioinformatic tools. The response was very positive. Feedback from 86 participants includes comments such as:

"I am an undergraduate student, and know little about bioinformatics. In the future, I will be able to use EBI as my primary resource."

"It is a really good opportunity to now get all these tools, to help facilitate understanding and analysis of scientific data"

"An excellent course, and very useful tools!"

Ensembl and ArrayExpress were ranked by 99% of participants as being useful to their work. Not only are people made more aware of individual projects through these workshops, EBI resources are publicised. 31% of our participants were unaware of EBI resources before the workshop, which contrasts to 95% responding that after this workshop, they would most likely use EBI resources. 88% of participants would like more training in these resources and others; specifically mentioned were ontologies, proteomics, and genome sequencing as topics to learn more about. This reflects a need for bioinformatics courses in the life sciences in that part of the world, if not in all the world.

And finally, an after-effect of the workshops was to prove that there is a lot of interest in bioinformatics. This from our host at CIBNOR:

"CIBNOR is in a growing stage, we have a project for an Innovation and Technology Park and I am trying to convince people about the need for a Bioinformatics Unit. I am sure that things like this course will help us a lot."

We greatly enjoyed training in Mexico, because of all the keen interest, energy, and the evenings on the sand dunes. We took the course into the field, discovering a pufferfish and spine on the beach, in honor of vertebrate genomes!

Orthologues on the trees

We have added a little trick for orthology-lovers. Starting from the orthologues page, you can choose to switch to the GeneTree. This will highlight the orthologue of interest, as well as the ancestral node that relates both genes.

Another useful feature added in Ensembl 57 is the possibility to display a set of genes (up to 10) using the Multi-Species view. Click on an internal node and select the "Jump to Multi-species view" option. This will show each of these genes in their respective genomic location, with genomic alignments when available.

New avian and new fish mutliple alignments

Ensembl 57 includes the turkey genome, the third bird in Ensembl. We are now providing a 3-way avian multiple alignments (chicken, turkey and zebra finch) together with GERP constraint analysis. The image shows amniote and bird constrained elements on the chicken genome.

We have also added a new set of fish multiple alignments (stickleback, medaka, takifugu, tetraodon and zebrafish). GERP constraint analysis is available on fish genomes as well.

Gene Trees now have intron ticks.

The gene tree images now have little intron "ticks" on them showing how the intron position is placed relative to the protein sequence. An example is shown above. Each tick is a little black line on each side of the green protein bars, on the right. As intron positions have been remarkably stable on the "chordate" side of the metazoan tree (ie, the deutrosomes), one should expect that the introns line up - if they do, it is good evidence that the alignment is right.

There are some interesting things. Ensembl models small frameshifts to create open reading frames around erroneous data as tiny introns. In this code you cannot distinguish these two classes of introns, but as these errors normally come in patches, a run of intron ticks unique to a genome is probably a set of errors (an example is in Gorilla). I've enjoyed browsing around some of my favourite genes to check out that the introns make sense.

There is some more to go here. The fact that the intron ticks disappear on collapsed nodes is a bit frustrating - it would be nice to see "consensus" intron positions (though this is a bit complex to execute underneath).

Ensembl browser workshop at ESHG 2010

The Ensembl Outreach team is pleased to offer a 1-day Ensembl browser workshop as a satellite to the European Human Genetics Conference 2010 that is held from 12-15 June in Gothenburg, Sweden. The workshop will be held on Friday 11 June at Gothenburg University and is free of charge for conference participants. Places are limited to 30 participants. More details can be found here.