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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
Venue of workshop: Online via Zoom (link to be sent in due course)
Date for the workshop: 06 September 2023 from 9 am to 5 pm CAT
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.
Training material availability: Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://training.ensembl.org/events/2023/2023-09-06-UCT_browser. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.
