23 December, 2008

Upcoming Workshops (Jan 2009)

Happy Holidays, and Happy New Year from Ensembl!

The new year will start with some workshops given by our Outreach team on how to use our new interface (and the data behind the scenes!). We hope you have had time to explore and learn the layout! Remember to send any questions to our helpdesk.

Upcoming workshops in January, 2009:

11 Jan Ensembl Demo at the PAG XVII conference, San Diego, CA, USA
13-14 Ensembl 2-day browser workshop at the Universidad de Chile, Santiago, Chile
15-16 Modules in the EBI Bioinformatics Roadshow, UCLA, USA
19-20 Modules in the EBI Bioinformatics Roadshow, City of Hope, USA
22-23 Modules in the EBI Bioinformatics Roadshow, UCSF, USA
24 Browser course in the Computational Biology Workshop, Sultan Qaboos University, Muscat, Oman
26 Browser course in the 9th BioSapiens European School of Bioinformatics, Brussels, Belgium

That's all for now!

11 December, 2008

GeneTrees: how do I read them? And can I view alignments using Jalview?

If you have clicked on the GeneTree link in Ensembl (for example, the gene tree for IL2), you may have noticed that we have a new way of displaying large GeneTrees. This time, if you have a large gene family with lots of genes that you want to look at, you won't need to ask the Miami Dolphins to let you plug your laptop into their huge screen...

This new feature in EnsemblCompara is called collapsible subtrees and allows for more compact, summarized views of interesting gene families like PAX2/PAX5/PAX8:


If you check the legend at the bottom, you will see that "blue triangles" correspond to collapsed subtrees that have within-species paralogs of your gene. If you want to see all the within-species paralogs expanded, you can click on the option "View paralogs of current gene". You can even set that as a default if you want in the "Configure this page" options.

Jalview is a great way to view protein alignments in the tree. And were is my Jalview link now? Click on any internal node (square) in the tree, and be able to visualize the alignment (or subalignment) with the new Jalview applet by clicking on the Jalview link. You have to have Java installed though, or the link won't show. The two Jalview windows that pop up are one, the protein alignment and the other, the underlying TreeBeST tree. You can now use Jalview's sorting feature to sort your sequences according to the tree with: Calculate->Sort->By Tree Order->URL. Having the tree associated to the alignment allows for a more phylo-centric visualization of sequence conservation: if you click at a point in the tree, a red vertical line will appear that divides the alignment into different groups. If you choose Colour->Percentage Identity, the shades of blue will be relative to the subgroups in your tree (e.g., fish versus placental mammals). This is also useful to spot segments in the alignment that don't look that good, or gaps created in a subpart that can now be collapsed in the subalignment (Edit->Remove Empty Columns), or sequences that stand out as long branches in the alignment (View->Overview Window).

For even more tree funkiness, you can use PhyloWidget to visualize our NHX trees. Use our NHX tree ("Configure this page->Output for normal tree->NHX->Save and Close->Gene Tree(text)") to copy+paste the representation of the GeneTree into Phylowidget, with duplication/speciation events (red/blue), bootstrap values (greyscale) and taxonomy levels "View->Rendering->Show clade labels". Then use the "Zoom in/Zoom out" features, or clicking on an internal node, the "Tree Edit->collapse", and specially the "View->Branch lenghts [x]" and the "View->Layout->Options->Branch Scaling" options.

We hope these new features will help you in your research. We have some new ideas that we are currently testing to visualize even more phylogenetic information, and help make better judgement on the orthology and paralogy relationships in our EnsemblCompara GeneTrees. Stay tuned for more updates!

Ensembl 52

Hot on the heels of release 51 comes release 52 of Ensembl - the first revision of the new webcode... So what's new?

Web site:
  • Updated export: - Restored most of the functionality with the new Export wizard on Genes, Transcripts and Locations - to allow export of FASTA, EMBL, Genbank, GFF, TSV, Vista and PIP files.
  • Image export: - Restored an improved version of the image export functionality - all "Horizontal" generated images have and [Export image] button to allow the image to be exported in vector format (PDF, SVG, EPS) and scaled bitmap format (PNG x0.5, x1, x2, x5 and x10) to allow publication quality images to be exported.

    The vector formats PDF, SVG and EPS can all be imported into vector image editors to be manipulated as well.

04 December, 2008

Ensembl and Amazon Web Services

We're happy to announce that Ensembl is one of the launch partners for Amazon's "Public Data Sets" initiative, so the MySQL data and index files for the current release of Ensembl can be accessed from within Amazon's Elastic Compute Cloud (EC2) service. From the Amazon website:

AWS Hosted Public Data Sets provide a convenient way to share, access, and use public domain or non-proprietary data within your Amazon EC2 environment. Select public data sets are hosted on AWS for free as an Amazon EBS snapshot. Any Amazon EC2 customer can access this data by creating their own personal Amazon EBS volume from a publicly shared Amazon EBS public data set snapshot. They can then access, modify, and perform computation on these data sets directly using an Amazon EC2 instance and just pay for the compute and storage resources that they use.
Details of how to access the data can be found at http://aws.amazon.com/publicdatasets .

We have plans to make much more use of AWS in the future, stay tuned!