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 (https://ensembl.org/), 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

Objectives:

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)

Module

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

BioMart

16:45 - 17:00

Wrap-up

* optional modules depending on the interests of the participants

Prerequisites:

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.