Course Overview: This one-day workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser (, but also provides them with the necessary background information. The workshop consists of a series of modules which include a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl.

Intended audience: Wet-lab scientists and bioinformaticians new to Ensembl

Keywords: Ensembl, Genomes, Genome Browser, Sequencing, Genomics

Skill level of training: Beginner

Language: English

Credential awarded: Certificate of Attendance

Type of training: Online learning

Venue of workshop: Online via Zoom (link to be sent in due course)

Date for the workshop: 06 September 2023

Workshop organisers: H3ABioNet and European Bioinformatics Institute

Workshop sponsors: H3ABioNet and European Bioinformatics Institute

Registration for participants opens: 14th August 2023

Registration for participants closes: 18th August 2023

Notification date for successful participants: between the 28th of August and the 1st of September 2023

Maximum number of participants that will be accepted will be capped at 40


At the end of the workshop participants should be able to:

  • Navigate Ensembl using the web browser platform
  • Access main data types in Ensembl: genomes, genes, genetic variation, regulatory features and comparative genomics
  • View genomic regions and manipulate the view to add features.
  • Explore information about genes and their sequences.
  • Analyse genomic variants and associated phenotypes and your own variation data using the Variant Effect Predictor (VEP).
  • View homologous genes and genomic regions.
  • View functional elements involved in gene regulation and their activity in different cell types.
  • Export gene data in bulk using BioMart.

 Workshop Schedule:

Time (CAT, GMT+2)


09:00 - 10:00

Introduction to Ensembl

10:00 - 10:45

Exploring genomic regions

10:45 - 11:00

Coffee break

11:00 - 12:00

Genes and transcripts

12:00 - 13:00

Lunch break

13:00 - 14:30

Variation and the Variant Effect Predictor (VEP)

14:30 - 15:30

Comparative genomics and/or Regulatory data*

15:30 - 15:45

Coffee break

15:45 - 16:45


16:45 - 17:00


* optional modules depending on the interests of the participants


Participants should have degree-level understanding of molecular biology/genetics and be proficient at using web browsers.

Workshop Requirements:

  • Computer/Laptop
  • Computer/Laptop should have a (reasonably fast) internet connection
  • Computer/Laptop should have an up-to-date internet browser installed (preferably Chrome or FireFox)

Tailored Courses: We can also run tailored courses that focus on particular aspects of the Ensembl browser or on particular topics. In the past we have held courses that focus on:

  • Comprehensive Ensembl Browser
  • Ensembl and the 1000 Genomes Project
  • Ensembl and gene regulation, including data from ENCODE, Blueprint, RoadMap epigenomics and more
  • Particular Ensembl Genomes taxa (eg Plants, Fungi, Protists, Metazoa or Bacteria)
  • Particular Ensembl species

We are open to your ideas – just let us know and we can discuss your requirements. Because of the specialisation of these courses, it is sometimes necessary to have a second instructor to teach some parts of the course. We may also suggest further pre-requisites and software requirements depending on the topics of interest.