31 August, 2010

Ensembl Genomes Release 6

The Ensembl Genomes Project is pleased to announce release 6 of Ensembl Genomes.

The highlights of this release are:

  • Software migration to Ensembl 59.
  • Two new rodent malarial genomes: Plasmodium berghei and Plasmodium chabaudi and an update to the Plasmodium falciparum gene-set in Ensembl Protists.
  • Variation BioMarts added for Plasmodium falciparum, Saccharomyces cerevisiae (Ensembl Fungi), Arabidopsis thaliana, Oryza sativa indica, Oryza sativa japonica, Vitis vinifera (Ensembl Plants), Anopheles gambiae and Drosophila melanogaster (Ensembl Metazoa).
See the individual homepages for Bacteria, Protists, Fungi, Plants and Metazoa for more information.

25 August, 2010

Ensembl Events in September 2010

The Summer seems to have gone (at least here in Britain), so Ensembl outreach activities are picking up again:

7 & 8 Sep: Browser workshops at the University of Toronto, Canada
13-15 Sep: Developers workshop at the Genome Informatics Meeting 2010, Hinxton, UK
16-17 Sep: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
17 Sep: Demo at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
27-28 Sep: Browser workshop at the University of Cambridge, UK

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

23 August, 2010

Ensembl browser workshops Western US January 2011

The Ensembl Outreach team is currently looking into the possibility of giving some 1-day Ensembl browser workshops in the Western US in the period directly before or after the Plant and Animal Genome Conference in San Diego, which takes place from 15-19 January 2011. Hosting institutions would only have to pay the instructor's expenses (accommodation and subsistence) and would share the domestic travel costs, but we would not otherwise charge for the workshops.

For more information about our browser workshops, please have a look here.

Interested? Please contact me for more details at bert@ebi.ac.uk.

19 August, 2010

Networks problems at the Sanger site

The Systems team at the Sanger Institute have resolved the network problems and http://www.ensembl.org is now back up and running as normal.

The Sanger Institute is currently experiencing networks problems which have taken the main Ensembl site offline. Please use one of our two mirror sites http://uswest.ensembl.org and http://useast.ensembl.org We will update the blog when the main site is working again, we apologise for any inconvenience caused.

18 August, 2010

Maintenance Finished

Hi Ensembl Users,

The work is finished, and search is working on archives again.

Just a warning. Maintenance work this afternoon (18 Aug, 2:45 to 5 PM in the UK) could affect the live site. If this is the case, please try our mirror site at uswest.ensembl.org

Search will be temporarily disabled on the archive sites for versions 55-57. If BioMart queries are slow, please use the interface at www.biomart.org.

The Ensembl Team

16 August, 2010

Ensembl in Toronto

Ensembl will be training at the Terrence Donnelly Centre for Cellular and Bio-molecular Research, University of Toronto this coming month of September, where we will be running two workshops (7 & 8 September).

In these workshops we will provide an overview of recent and future developments in the Project, as well as focus on some particular topics such as variation or gene annotation. As always, we encourage participants to come with their own research questions. Note that participants have to come with their own laptop, other than that you only need some general knowledge of molecular biology/genomics and familiarity with web browsers. If you have any additional questions you can get information from the organisers. In addition to the University of Toronto, this course is sponsored by the OICR, CIHR-IRSC, and EMBL-EBI.

Regulatory Build now Cell Type specific

Since release 58, the Ensembl Regulatory Build has been cell type specific. Regulatory Features are defined as sites of open chromatin which are potentially involved in gene regulation. These are built using data from different cell types, resulting in differing structures, attributes and classifications across the various cell types.

Release 59 also boasts greater coverage due to the incorporation of more data sets (see previous blog post), and a new 'projection' methodology. Projection allows Regulatory Features to be built on cell lines with sparse data, and also consolidates existing higher quality builds. The result of these changes is an increase in the number of Regulatory Features per cell type, as well as an improvement in the number of features which are assigned a classification e.g. Gene Associated or Promoter Associated etc.

The 'Regulation' panel has also been updated to reflect the new cell type specific nature of the build e.g. ENSR00000515919. The 'Details by cell line' view is now split into several sections, each showing data for a specific cell line. The uppermost section details a species 'MultiCell' cell line, showing data used to define the core regions of the given Regulatory Feature. More information on this view can be found here. We are always looking at ways to improve our Regulatory Build process, some areas we are currently considering are listed in our development road map.

13 August, 2010

New ChIP-Seq data and visualisation

Over the last 3 releases we have significantly increased the content of the functional genomics databases, by including data from large public projects such as ENCODE and The Epigenomics Roadmap. In release 59 we have over 200 human data sets representing 10 cell types, 41 histone modifications and 14 transcription factors. These numbers will steadily increase in the forthcoming releases as more data is incorporated.

These data sets are now available in 'Region In Detail'. Cell type tracks can be turned on via the 'Functional genomics' menu of the configuration panel - click on 'configure this page' on the left to access it. These are split into 'Core' and 'Other' evidence types, reflecting how we deal with these data within the Regulatory Build. Display options include a peak track, with the underlying raw data is available as a 'multi-wiggle' track. Further configuration is available via the 'Cell/Tissue' tab, where individual feature types can be turned on or off.

Work is ongoing to improve the flexibility of these displays.

05 August, 2010

Human GRCh37 assembly patches

Ensembl release 59 includes the first human assembly patches released by the Genome Reference Consortium (GRC).

The goal of the GRC is to ensure that the human reference assembly is biologically relevant by closing gaps, fixing errors and representing complex variation. Their ongoing efforts are made available to the community via minor releases called patches. The patches do not change the chromosome coordinate system but do provide either a new alternate haplotype (novel patch) or provide a preview of the chromosome tiling path for that region in the next major release (fix patch).

The patched update GRCh37.p1 affects only 2 regions of the reference assembly.The patch update GRCh37.p1 includes:

Fix Patch: HG79_PATCH (GL339450.1) on chromosome 9, correction for the ABO gene. Click here for an example region.

Novel Patch: HSCHR5_1_CTG1 (GL339449.1) on chromosome 5. This patch provides an alternative region (haplotype). Click here for an example region.

The two patched regions have undergone preliminary gene annotation. Human cDNAs with their annotated ORFs were aligned to the genome using the Exonerate cdna2genome model to generate coding transcripts.

We expect future patch releases on a quarterly basis.