by ·Comments Off on 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!

by ·2 Comments

The next release (50) will happen in just under a week’s time. This will retain the old (classic) look, with the Ensembl interface you are all used to! The new interface will be released in August as a publicly accessible beta testing site alongside our usual Ensembl, in order to make sure everything is running smoothly before we switch over completely. This will give us time to collect feedback from you about the new interface, before we completely switch over to the new interface in release 51 (due in September).

What can you expect in release 50?

A new gene set for human, where UTRs (UnTranslated Regions) are based on ditags. An improved merge between the new human Ensembl gene set and the latest manually annotated gene set from Havana will be available. Also, new gene sets for tetraodon (genes from the Ensembl pipeline along with other genes from the genoscope set), C. elegans (WS190), and projection of the new human set against pika and cat.

Cow has a new assembly and geneset! The Ensembl automated pipeline was run on Btau 4.0 for this release.

New variation sets will be available for orangutan, tetraodon, cow and human.

We will keep you posted about the new interface, beta testing surveys, and upcoming organisms and annotation in release 51.

Thanks to all our users.

by ·Comments Off on Technical Difficulties

For the past two days, Ensembl has been slow or has not returned the page (instead offering an ‘Ensembl is down’ yellow screen).

Be assured we are working on the problem. It is a hardware issue, but should be resolved soon.

From all of us in the Ensembl team, thanks for your patience!

by ·Comments Off on Upcoming Workshops – Summer

Hello all,

There are a few Ensembl training events taking place this summer:

(2-day) Browser workshop in the Dept. of Genetics, University of Cambridge, UK (5-6 June)

Module in a Wellcome Trust Mini-Open Door Workshop (ODW) for MalariaGEN in Hinxton, UK (20 June)

Module in a Mini-ODW at the ICG in Berlin (12 July)

Programmers’ group at the ISMB meeting in Toronto, Canada (19-23 July)

As ever, email us with any questions (or comments).

Best Wishes,
Helpdesk

by ·Comments Off on Upcoming Workshops and Instructional Videos

Hello to our readers, I hope everyone is having a nice April. In the UK we are experiencing a long winter with some rain, but spring seems to be around the corner… as are these upcoming workshops…

Did you know? The EBI has released tutorial videos.

Have a look at the Ensembl browser videos for information and direction to some of its pages! Or, learn more about BioMart, a fast data mining tool.

Upcoming workshops- May

Browser workshop at the WHO in Cairo (12-13 May)
Module in the Open Door Workshop at the Sanger (12-14 May)
Ensembl in China: The Shanghai Center for Bioinformation Technology (14-16 May)
Ensembl in China: Center for Bioinformatics, Beijing (19-21 May)
Browser and API workshops at the GTPB in Oeiras, Portugal (27-30 May)
Presentation at the European Human Genetics Conference in Barcelona (30 May)

by ·Comments Off on Ensembl Release 49!

Yesterday, Ensembl released a new version of the browser and database (version 49). Along with new species, homologue predictions, and new code in our API, there have been changes in how the multiple alignments are done on the whole-genome scale. Have a look at the news for more details.

We are looking forward to release 50! as we are working on some new features. Keep your eye out in August for this next release. A reminder, we will not release another version between now and August, and updates may appear in the Pre! site but not in the main site, for that time.

Please explore features on release 49 such as BLAST which is now configured to align queries against top-level sequences (i.e. chromosomes and scaffolds), and BLAT, a fast alignment program which is now the default selection.

Paralogues are shown in blue in GeneTreeView to help aid your eye.

Upcoming workshops -April

(March workshops are listed in a previous post)

Browser workshops at the VIB Ghent and Leuven (31 Mar – 2 Apr)
Browser workshop (focus: rat) at the ULB Brussels (EURATools) (16 Apr)
Browser workshop at the BCB UCL/Birkbeck (21 Apr)
Module in the EBI roadshow in Poitiers (23, 24 Apr)
API workshop at the Dept. of Genetics, Cambridge (28, 29, 30 Apr)

by ·Comments Off on New Release notes and BAC clones in mouse

Keep your eye out for Release 49, which is due on Tuesday 18 March. The delay is due to the scheduled downtime and maintance at the Sanger and EBI this weekend, which has caused some trouble. However, Release 49 will soon be visible to the community!

New features in release 49 will includeBLAST against top-level sequences on all species, updates on theGeneTreeView page that should make things easier to see, and new Ensembl gene sets for Orangutan, Horse and and Takifugu. FlyBase 5.4 will be imported for Fruitfly. For API users, the regulatory features will be moved from the core API to the functional genomics API.

Also, a word of warning to those using our mouse clones under ‘DAS sources’. MICER clones and the bMQ set (129S7/AB2.2 in the ‘DAS Sources’ menu of ContigView). The clones, originally mapped to NCBI M36, are lifted over to the new assembly (NCBIM 37) coordinates. The drawing indicates where the clone lifts over to in the new assembly. However, the pop-up box shows the coordinates of the original mappings. This is indicated in Ensembl by the ‘NCBIM36’ label above the coordinates.

Write our helpdesk if you are confused!

by ·Comments Off on March workshops, release and down time


We are looking forward to Ensembl release 49, which has been delayed to 13 March, 2008. This is a result of some downtime planned at the Wellcome Trust Sanger Institute. Users, beware! Ensembl will not be available from: Friday 7 March – Sunday 9 March

On the 13th March Ensembl version 49 will be available. Keep an eye out for:
Drosophila melanogaster (assembly BDGP 5.4)
Horse (first gene build)

Viral genes have been removed in multiple species. ncRNA updates will be ready for Pika and Mouse Lemur, and new variations from dbSNP 128 (mouse, chicken, cow, and zebrafish) and dbSNP 126 (rat) will be available. Have a look at the new pairwise alignments between human and horse genomes.

Upcoming Workshops – March

A series of talks and workshops are happening in March.

Browser Workshop (2-day course at the EBI) 5-7 March
Browser Workshop (part of a 2 day course, MRC London: EBI Roadshow) 11-12 March
Presentation at the Genomes to Systems 2008 conference in Manchester, 17-19 March

Interested in organising a course in Ensembl and BioMart? Contact our helpdesk.

-The Ensembl Outreach team

by ·Comments Off on Upcoming Workshops – February

Ensembl Workshops in January took us to the West Coast (USA) and the Netherlands. Workshops in February:

Browser workshop (Institute for Animal Health) Compton, UK 12 Feb

Browser workshop (EURATools, University of Edinburgh) Edinburgh, UK 12 Feb

Browser workshop (Cambridge University, Dept of Genetics) Cambridge, UK 28-29 Feb


Picture: Nijmegen, the Netherlands. The NBIC was the site of an Ensembl Browser workshop on 16 Jan, 2008

Interested in hosting a workshop? Contact us!