We will make changes to the directory layouts of both the Ensembl Genomes FTP server (ftp://ftp.ensemblgenomes.org/pub/) and the Ensembl GRCh37 FTP server (ftp://ftp.ensemblorg.ebi.ac.uk/pub/grch37/) that may affect your pipelines. These changes will come into effect in Ensembl Genomes release 43/Ensembl release 96, which are scheduled for April 2019. Here are the details, so that you can plan any required updates to existing scripts and pipelines ahead of the releases.
As of Ensembl release 96/Ensembl Genomes release 43, we will retire rest.ensemblgenomes.org and invite you to use rest.ensembl.org instead.
In the next release of Ensembl (Ensembl 96) we will remove our ontology database patching scripts from the main Ensembl repository.
There is now a dedicated module using the EBI OLS service to load Ensembl required ontologies. Considering this module is now in charge of loading the required data, the previous databases patches have been moved to the ols-ensembl-loader repository.
If you need to update your system with future patches, please now refer to the ols-ensembl-loader repository sql directory where files are already available.
Please contact the Ensembl Helpdesk if you have any questions or want to find out more about how this might affect your work.
Today we are meeting Guy, who works in the Plants team of Ensembl Genomes. He talks about how he came to Ensembl, his interests and experiences so far.
Due to a major loss of cooling incident at one of the EMBL-EBI data centres, there was reduced Ensembl functionality between Saturday 2nd February and Wednesday 6th February.
However, as of Wednesday 6th February, all Ensembl and Ensembl Genomes services have now been restored and are working as normal.
If you encounter any further issues, please report them to the Ensembl Helpdesk.
Thank you for your understanding and patience while we worked to fully restore our services.
A brand new regulatory build for the human GRCh38 and GRCh37 assemblies was released in Ensembl 95 earlier this week. The new regulatory build incorporates data for 55 new and 38 updated epigenomes from the ENCODE project. So what are the differences from the previous regulatory build?
The latest version of Ensembl, release 95, is out. This release brings a brand new human regulatory build for GRCh37 and GRCh38, incorporating new data from the ENCODE and Roadmap epigenomics project, plus an update to the mouse GENCODE gene set. We’ve also got a whole host of new vertebrate species, updated genome assemblies for some important agricultural species and the brand new protein structure viewer.
We’re planning to release the next versions of Ensembl and Ensembl Genomes in December.
We’ve got some exciting new genomes, including polar bear, as well as updated genome assemblies for three important agricultural species. We’ve also got a new regulatory build for the human GRCh38 and GRCh37 assemblies and a brand new protein structure variation view.
Today we are meeting Irina, who joined the Variation team earlier this year. She talks about how she came to Ensembl, her interests, experience so far and more.
This guest blog is a joint contribution by Laura Harris (GWAS Catalog) and Astrid Gall (Ensembl Outreach). You can contact our colleagues of the GWAS Catalog at gwas-info[at]ebi.ac.uk.
This year marks a special anniversary for the GWAS Catalog, as we have reached ten years since our launch in 2008. The GWAS Catalog is a widely used publicly available resource of all published human genome wide association studies (GWAS) and association results. Each GWAS study contains a wealth of information which is effectively inaccessible to researchers and clinicians without them spending a lot of time undertaking regular systematic reviews of the literature. This is where we can help you!