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.
Wet-lab scientists and bioinformaticians new to Ensembl
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
Participant applications
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
Participants should have degree-level understanding of molecular biology/genetics and be proficient at using web browsers.
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.
