CCMI - Tutorial

UC San Diego – 2020 Ensembl Tutorial

Hosted by Dr. Astrid Gall, Ensembl Outreach Officer from the EMBL-EBI.

This full-day workshop will provide an introduction to the Ensembl genome browser (, a freely available comprehensive and integrated genomic resource. Ensembl currently has over 220 vertebrate species available, including human genomes, whether in its latest assembly (GRCh38) or the previous versions (GRCh37 and NCBI36). The database additionally includes 14 popular laboratory mouse strains. Our sister project, Ensembl Genomes (, contains an additional 53,000 bacterial, fungal, metazoan, plant, and protist genomes.

Ensembl annotates genes and transcript models 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. VEP, BioMart, BLAST/BLAT).

The only prerequisites for this workshop are a general knowledge of molecular biology and genomics and a laptop with a web browser.


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


Parking at UC San Diego requires a valid permit. Hourly rates are posted at pay stations; credit cards are accepted. A map of the MET Building and nearby parking lots can be viewed here. The nearest parking lots are the Osler Parking Structure, the Gilman Parking Structure, and lots P602 and P603. If using the UC San Diego Shuttle, exit at Gilman Dr and Meyers Ln, then walk south towards School of Medicine.

No Show Policy

If you are unable to attend for any reason, please cancel your registration at least two business days prior to the event. Your cooperation ensures our programs can be made available to interested attendees and remain fiscally sustainable. A no-show may limit your ability to book our events in the future. Thank you for your understanding.

Stay In Touch 

Join the CCMI mailing list to receive notice of future events.

Pictures of Scientists Having Fun 

Share event by Email

ERROR : Field not found : eveny-share-by-email-text