29 September, 2009

Release 56

The Ensembl project is pleased to announce release 56 of Ensembl (http://www.ensembl.org/). Highlights of this release are:

Reintroduction of our multi-species views. Alignments (image), formerly alignsliceview, shows pairwise or multiple alignments from the Ensembl Compara database, highlighting any gaps in the alignment.

Multi-species view, formerly known as multicontigview, displays pairwise alignments without gaps; multiple pairwise alignments can be configured to create a multiple alignment display. As well as genes, other types of features such as regulatory features can be displayed in this view, making this a very useful display for comparative genomic analysis.

A new tab has been added in release 56 based on a Regulatory Feature object. This will enable better display some of the data underlying the Ensembl regulatory build. The new pages are accessed from the gene displays by clicking on the 'Regulation' link in the left-hand menu and then clicking on a regulatory stable ID in either the image popup menus or the table.

From release 56, users can upload wiggle plot data in WIG and bedGraph formats and view this data on various location-based views. At the moment, only a single style, "wiggle", is available on Region in Detail, whereas a selection of density plots are available on whole chromosome and karyotype images. In addition, Region in Detail now supports greyscale rendering of BED scores via the useScore parameter in the file, and rendering of features in different colours via the itemRgb parameter and per-feature values.

New data in this release includes gene sets on two new species (Pig and Marmoset) and a new gene set on the existing Rat Rnor3.4 assembly. Also in this release is an updated human gene set which includes all the Havana manual annotation in the merge with the Ensembl automatic annotation set. This set represents the Encode project GENCODE 3b gene set. Also included is a new human variation database based on dbSNP 130 and mapped to assembly GRCh37.

For more information on these and other new features in this release visit:


28 September, 2009

Ensembl website downtime

We are currently in the process of releasing Ensembl 56, and should be back online within an hour or so.

Please note that all Ensembl-based sites will be offline at this time whilst we upgrade our user account database. Affected sites include Vega, Pre, the Ensembl archives and the US mirror. Please accept our apologies for any inconvenience caused.


18 September, 2009

Ensembl events in October 2009

In October Ensembl will feature on 4(!) different continents:

7 Oct: Browser workshop at the Centro de Biologia Molecular Severa Ochoa, Madrid, Spain
9 Oct: Browser workshop at the Instituto de Biologia Molecular e Celular, Porto, Portugal
12-15 Oct: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence, Bangkok, Thailand
20 Oct: Demo for the National Genetics Reference Lab, Manchester, UK
20 Oct: Ensembl module in the Hands-on training at EBI - A dip into EBI resources: understanding your data - New resources and Future Directions, Hinxton, UK
22-23 Oct: Browser workshop at the University of the Witwatersrand, Johannesburg, South Africa
23 Oct: Demo at the ASHG 2009 meeting, Honolulu, Hawaii, US
23 Oct: Developers workshop at the Bejing Genomics Institute at Shenzhen, China
27 Oct: Browser workshop at the Centro Nacional de Investigaciones Oncológicas, Madrid, Spain *postponed to 24 Nov*
27-28 Oct: Browser workshop at Cape Biotech, Cape Town, South Africa
30 Oct - 2 Nov: Developers workshop at the CSHL Genome Informatics 2009 meeting, Cold Spring Harbor, NY, US

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

15 September, 2009

NCBI36 Ensembl Site

Ensembl announces the release of http://ncbi36.ensembl.org. This Ensembl site is for users who still need access to the NCBI36 human assembly. It is actually a complete copy of the Ensembl 54 release which was the last Ensembl release containing NCBI36.

Although access was already possible through the Ensembl archive sites, the new ncbi36.ensembl.org site will provide better performance because it is running on separate hardware. Also ncbi36.ensembl.org provides Blast/Blat search support which the archives do not.

The main reason we have provided a dedicated site for NCBI36 is for two large projects (Encode and 1000 Genomes) which have some of their data aligned on this assembly. ncbi36.ensembl.org will only be up for as long as there is significant need for it. We will be reviewing usage in Spring 2010 and currently plan to remove the site by Summer 2010. After that time users will still be access the NCBI36 assembly via the archive sites, there just won't be a dedicated site for it anymore.