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:

* 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.