Module 1: Ensembl

Ensembl is a comprehensive genome browser and database that provides a central resource for geneticists, molecular biologists, and plant scientists to explore and analyse integrated genomic data, including genes, variants, comparative genomics, and gene regulation. Originally developed in response to the Human Genome Project, it has become a trusted one-stop resource for high-quality genome annotation and interpretation.

For more than 20 years, Ensembl has supported research across the global genomics community. Today, the project provides genome annotation for more than 5,000 eukaryotic and more than 30,000 prokaryotic genomes, making it a valuable platform for researchers at all career stages, from early-career scientists to experienced group leaders.

As genomic data continue to expand rapidly, the new Ensembl Data Platform has been developed to provide a more robust, efficient, and user-friendly experience. This module introduces the new platform, which presents genomic features for approximately 5,300 species through a redesigned interface, including visualisation of genes and variants.

Participants will explore the range of data available through the new platform, gain practical experience navigating the website to retrieve and interpret information, and consider how these data can support their own research. The module also highlights key improvements in the new platform and how these features can strengthen genomic research and data exploration. In addition, participants will learn how to find support through the Ensembl community, including documentation and help resources.

Due to the transition from the legacy version of Ensembl to the new data platform, we may need to use alternative methods to retrieve some data, and these methods may not be the final approach in the fully developed version of the new site.

Key Topics

  • Foundations in genomics and context
  • The importance of genomic resources and databases
  • An introduction to the new Ensembl Data Platform and genomic annotation
  • Available data in the new Ensembl Data Platform and how to export these

Learning Objectives

By the end of the session, participants will be able to:

  • Differentiate the types of genomic data available in Ensembl
  • Navigate the Ensembl Beta website and familiarise yourself with the new interface
  • Discover the list of species currently available in Ensembl Beta
  • Export genomic sequences via the browser, FTP and REST API

Training Materials

All training materials, including presentation slides and practicals, are available on the Ensembl Training website. Participants will have access to these training materials indefinitely.