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: No credential awarded
Type of training: Blended/hybrid learning
Venue of the course: Online via Zoom (link to be sent in due course)
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: H3ABioNet and European Bioinformatics Institute
Participation: Maximum number of participants that will be accepted will be capped at 40
Course Sponsors: H3ABioNet Local Classrooms
Course 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.
 

Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at

Participant applications

Registration for participants opens: Mon, 14/08/2023
Registration for participants closes: Fri, 18/08/2023
Participant registration link:
Syllabus and Tools

 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
Prerequisites

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

Course limitations
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.
For more information, please visit
Training material availability