Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here

Ensembl Tutorial

Monday, May 8, 2017, from 8:30 am – 4:30 pm

Medical Education & Telemedicine Building, Room 141

Hosted by Helen Sparrow – Ensembl Outreach Officer

European Bioinformatics Institute (EMBL-EBI)


Register for the event here



This full-day workshop will provide an introduction to Ensembl (, a freely available comprehensive and integrated genomic resource. Ensembl currently has over 80 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).


Depending on a pre-event survey of registered attendee’s interests, the workshop will cover the following topics on the Browser:


  • Introduction to Ensembl: origin, goals and organisation of the Ensembl project
  • Genebuild: how are Ensembl gene and transcripts predictions made?
  • Data export with BioMart: building queries to access data in our databases, using a web interface (no programming required)
  • Variation: SNPs and other polymorphisms, structural variants, the variant effect predictor
  • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
  • Regulation (Human and Mouse): Sequences that may be involved in gene regulation


For each module, there will be a presentation, a hands-on demonstration, followed by the opportunity to do exercises.



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



8:30 – 9:00 am:  Introduction to Ensembl
9:00 – 10:00 am: Exploring the Genome Browser
10:00 – 10:15 am: Coffee break
10:15 – 11:15 am: Genes and transcripts
11:15 – 12:00 pm: BioMart
12:00 – 1:00 pm: Lunch
1:00 – 2:45 pm :  Variation and the VEP
2:45 – 3:00 pm: Coffee break
3:00 – 4:15 pm: Compara or Regulation
4:15 – 4:30 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 closest parking lots are P602, P603, and the Gilman Parking structure. A map of MET and the nearby parking lots can be viewed here. Hourly rates are posted at meters; cards are accepted. If using the UC San Diego Shuttle, exit at Gilman and Meyers and walk south towards School of Medicine.