CCMI - Presentation

UCSD – Ensembl Tutorial 2019

Hosted by Dr Erin Haskell, Ensembl Outreach Officer from the EMBL-EBI.

This full-day workshop will provide an introduction to Ensembl (, a freely available comprehensive and integrated genomic resource. Ensembl currently has over 100 vertebrate species available, including human genomes, whether in its latest assembly (GRCh38) or the previous ones (GRCh37 and NCBI36). Our sister project, Ensembl Genomes, contains an additional 40,000 bacterial, plant, fungal, protist and metazoan genomes.

Ensembl annotates genes and transcripts based on biological evidence, generates gene trees (both protein coding and non-coding) and whole genome alignments. To annotate other genomic features such as SNPs, CNVs and regulatory elements, Ensembl draws on major biological projects including 1000 Genomes, ENCODE, Roadmap Epigenomics and Blueprint epigenome. We also integrate data from many reference databases such as dbSNP, the NHGRI-EBI GWAS catalogue and OMIM. These data can be accessed through our web browser, APIs (Perl and REST), MySQL and FTP dumps, and our toolkit (e.g., our popular VEP, BioMart, BLAST/BLAT).

The only prerequisite for this workshop is general knowledge of molecular biology and genomics, and a laptop with a web browser. 


  • 9:30 am – Introduction to Ensembl
  • 10:00 am – Exploring the Genome Browser
  • 11:00 am – Coffee Break
  • 11:15 am – Genes and Transcripts
  • 12:00 pm – BioMart
  • 12:30 pm – Lunch
  • 1:15 pm – Variation and the VE
  • 3:15 pm – Coffee Break
  • 3:30 pm –Compara or Regulation
  • 4:45 pm – Wrap Up, Feedback and Questions

No Show Policy

While we do not charge a fee to attend this event, these programs would not be sustainable and available to all wanting to attend, unless all registrants abide by the 48 hour cancellation notice policy. A no-show will also limit your ability to book our events in the future. Thank you in advance for your cooperation.


Parking at UC San Diego’s School of Medicine is available to all faculty, staff, and visitors. The nearest visitor parking spaces are located in the Osler Parking Structure (within short walking distance to the MET building), Gilman Parking Structure, Lot P603 and Lot P602. A UC San Diego Parking Permit is required and may be purchased from Pay Stations in hourly or daily increments. Pay stations accept credit cards or exact cash. As of Oct 2018, rates are $3/hour or $30/day. Additional information is available here. If using the UC San Diego Shuttle, exit at Gilman and Meyers and walk south towards School of Medicine.

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