We’re holding an Ensembl Perl API course at the Genome Campus in the UK in April. The course give you chance to learn how to access the database directly from the people who produce the databases and write the APIs themselves. It is aimed at bioinformaticians and wet-lab scientists who are familiar with Object Oriented Perl.

This four-day course costs only £140, which includes daily transport to the campus from Cambridge city centre and refreshments (the fee is to cover only these expenses).

Please visit the course page for more details on the content and how to apply.

We’re always looking to improve Ensembl to make your research easier. To do this, we’re looking to find out more about you, how you use Ensembl and what you find useful or would like to see improved. The survey should take no more than 10 min. If you’d like to help make Ensembl better, please click on the link below:

I am writing in my capacity as leader of the Ensembl project based at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) based near Cambridge, England. Ensembl is one of the world’s leading sources of genome information and a central aggregation point for genomic data.

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We’re really excited to be a part of the ASHG conference again, this time in Orlando from the 17th-21st October. We can’t wait to see all the great science that’s going to be presented, but here’s a guide to the talks, workshops and posters from Ensembl and some of our close friends:

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Ensembl 91 is scheduled for December 2017 and we’re continuing our push to include the genome annotation for lots of new species. This time, we’re adding a whole new set of primate species to Ensembl.

Here’s what you can look forward to:

New assemblies, gene sets and annotations

  • Annotation of 12 new primate genomes, as well as updates to 6 existing genomes:
    • Nancy Ma’s night monkey
    • White-headed capuchin
    • Sooty mangabey
    • Angola colobus
    • Crab eating macaque
    • Southern pig-tailed macaque
    • Drill
    • Bonobo
    • Coquerel’s sifaka
    • Black snub-nosed monkey
    • Golden snub-nosed monkey
    • Black-capped squirrel monkey
    • Chimpanzee (update)
    • Gibbon (update)
    • Gorilla (update)
    • Mouse lemur (update)
    • Olive baboon (update)
    • Tarsier (update)
  • Annotation on the latest Cat genome assembly, Felis_catus_8.0
  • C. elegans gene set and annotation updated to Wormbase release WS260
  • Fruitfly gene set and annotation updated to Flybase release FB2017_04 (dmel_r6.17)
  • Updated Human cDNA alignments
  • Updated Mouse cDNA alignments
  • Updated microarray probe mappings and comparative genomics analyses for all new and updated species

Other updates and highlights

  • Updating our human variation database with:
    • COSMIC 82 somatic variants
    • HGMD 2017.2
    • DGVa structural variants
    • Phenotypes from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Cosmic Gene Census, DDG2P, MIM Morbid and Orphanet
  • In other species we also have variation updates as follows:
    • dbSNP 150 in macaque, mouse, zebrafish, sheep, pig, horse, cow and chicken
    • DGVa in cow, dog and mouse, horse, macaque, pig, sheep and zebrafish
    • Phenotype updates from relevant databases in rat, zebrafish and mouse
  • Links to PharmGKB added from human variants
  • New web tool for Linkage Disequilibrium (LD) calculation
  • Updated GRCh37 regulatory features

For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.