22 December, 2010

Ensembl UK shutdown - 8/9th January 2011

Owing to problems with our data centre cooling system, the Sanger network will be offline from around 4.30pm on Friday 7th January until the evening of Sunday 9th January (UK time).

This means that all UK-based Ensembl sites, including www.ensembl.org, archives and pre site, will be unavailable from late Friday afternoon until Monday morning.

However, you can still browse the genome using our US (Ensembl west & east) and Asia mirror sites. Services that depend on machines based in the UK, i.e. BLAST/BLAT and user logins, will be disabled during this time.

In the case of bacteria, fungi, metazoa, plants, and protists at www.ensemblgenomes.org, no mirror site is as of yet available. Those services will not be running over the weekend.

Please accept our apologies for any inconvenience caused. A reminder will be sent out to the announce@ensembl.org mailing list, and on our Twitter feed, nearer the time.

21 December, 2010

Seasons Greetings and Upcoming Features

Happy holidays from Ensembl! Here in Hinxton, we are planning new developments for the new year (what else would we do with all this snow!) Some of the highlights planned for early next year include:

  • The first gene set for turkey in Ensembl, and inclusion of turkey into pairwise (between two species) whole-genome alignments and multiple species alignments (including a new 3-way avian alignment).
  • Inclusion (merge) of manual curation of the zebra-fish genome by the HAVANA group into the Ensembl gene set.
  • Update to dbSNP 132 for variations in the human genome.
  • Sea Urchin (Strongylocentrotus purpuratus) and Honey Bee (Apis mellifera) genomes in the Ensembl Metazoa site. See other upcoming species to Ensembl genomes here.
Don't forget, an overview of upcoming annotation to Ensembl is on our roadmap.

For those of you going on holiday soon, enjoy! We look forward to supporting all your cutting-edge scientific endeavors in 2011.

The Ensembl Team

15 December, 2010

Ensembl Events in January 2011

Merry Xmas and a Happy New Year!

All Ensembl events for 2010 are done .... but we already have lined up quite a few for 2011!

Here are the ones for January:

16 Jan: Demo at the Plant and Animal Genome XIX Conference, San Diego, CA, US
18 Jan: Ensembl module in Primers for Predocs, Hinxton, UK
18-19 Jan: Ensembl module in the Workshop on Comparative Genomics, Europe 2011, Cesky Krumlov, Czech Republic
20-21 Jan: Ensembl module in the EBI workshop at City of Hope, Duarte, CA, US
21 Jan: Developers workshop at the Hubrecht Institute, Utrecht, The Netherlands
24 Jan: Browser workshop at the UCSC Genome Browser Group, Santa Cruz, CA, US
26 Jan: Developers workshop at Stanford University, Palo Alto, CA, US
27 Jan: Browser workshop at Stanford University, Palo Alto, CA, US
27 Jan: Browser workshop at The University of Nottingham, UK

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

14 December, 2010

Beds, Wigs, BAMs and Variants for Flies, Rust, Aphids and 301 other species

Now that Ensembl Genomes has moved onto the 60 code base, all the goodies in Ensembl's user data site are available across all 304 species in Ensembl genomes - from tiny bacteria to crazy big plants.

One of these is uploads of BAMs, Wigs, Beds in the location based view. For example, if you have the following file to specify a SNP in Drosophila

2L 356013 356013 C/T

By using the Variant Effect Predictor, accessible from Tools on the top of each page, or the 'Manage your data' link at the left of pages, one can get the effect (synonymous, non synonymous, in a UTR etc) for the variant.

(You click on "Variant Effect Predictor", upload a text file of chr, position, allele and hit go) This can also be run as script using the API (the database is internet accessible so you just need to have an internet connection, Perl, MySQL client libraries and the Ensembl code base installed).

In addition, the full set of visualisation tools for your own data is also now accessible for all Ensembl Genomes species. For example, this bedGraph file:

track type=bedGraph name="BedGraph Format" description="BedGraph format" priority=20
2L 21302000 21302300 -1.0
2L 21302300 21302600 -0.75
2L 21302600 21302900 -0.50
2L 21302900 21303200 -0.25
2L 21303200 21303500 0.0
2L 21303500 21303800 0.25
2L 21303800 21304100 0.50
2L 21304100 21304400 0.75

Will render a nice little variable height picture in the main contigview display. Other options are available (like Bed and Wig format) - many of which people will know from UCSC. Come, try it out, and give us feedback at helpdesk@ensembl.org

01 December, 2010

Ensembl Genomes Release 7

The Ensembl Genomes Project is pleased to announce release 7 of Ensembl
Genomes (http://www.ensemblgenomes.org/).

The main highlights of this release are:

* Software migration to Ensembl 60

* 66 new genomes added for Ensembl Bacteria and updated functional
genomics databases for Escherichia/Shigella and Staphylococcus

* Puccinia graminis f sp tritic genome added to Ensembl Fungi

* Zea mays and Physcomitrella patens genomes added to Ensembl Plants,
new variation datasets for Oryza sativa and updates to the
functional genomics databases for Oryza sativa indica, Oryza sativa
japonica and Arabidopsis thaliana

* Acyrthosiphon pisum genome added to Ensembl Metazoa

Please see the individual homepages for more detailed information: