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
Syllabus and Tools
|
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
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.
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.
