Ensembl Online Training

A range of online resources is available to help you explore Ensembl and learn about its underlying data. Training resources are available for:

• the new Ensembl Genome Data Platform
• Legacy Ensembl (Ensembl release 116/Ensembl Genomes release 63 and earlier)

Find out more about Ensembl’s transition to the new platform in our Ensembl 116 and Ensembl Genomes 63 release blog.

The new Ensembl Genome Data Platform

Step-by-step walkthroughs

Our short demonstrations guide you through common tasks on the new Ensembl Genome Data Platform, from finding and selecting a genome to exploring genes, transcripts and their annotation. Choose the format that suits you best: click through annotated screenshots at your own pace, or watch a narrated video.

Screenshot demonstrations

These interactive slide shows walk you through each task one step at a time, using annotated screenshots of the Ensembl apps. Move forwards and backwards through the steps as needed.

• An overview of the Ensembl Genome Data Platform
• Exploring genome assemblies with the Genome selector app
• Viewing genes and transcripts in the Genome browser app
• How to search for a variant in Ensembl
• Investigating genes with the Feature explorer app
• Visualising transcripts of a gene and comparing their sequences
• Exporting sequence files from the Feature explorer app
• Visualising and exporting data from Ensembl
• Exporting whole-genome files from the FTP server

Video demonstrations

These short, narrated screen recordings show the Ensembl apps in action and are available on YouTube.

Demo: How to select a genome in the new Ensembl Genome Data Platform

• Search for and select genomes
• Explore genome and assembly information
• Organise your selected genomes, ready to search for genes and other genomic features in Ensembl

Demo: Navigating the Feature Explorer app

• Search for genes and navigate the Ensembl Feature Explorer app
• Explore transcripts, exon structures, sequences and external references
• Investigate homology relationships and navigate from a gene to its orthologues in other species

EMBL-EBI Training portal

The EMBL-EBI Training portal gives you free, flexible access to Ensembl training whenever it suits you. New online tutorials for the Ensembl Genome Data Platform are added regularly. For an overview of the new platform, start with the Ensembl Genome Data Platform Quick Tour.

The portal also offers many other free, high-quality on-demand bioinformatics courses. Each course is designed to support both new and experienced users, guiding you through practical tasks with plenty of opportunities for hands-on learning.

Recorded webinars

The following webinar recordings are available through the EMBL-EBI Training portal:

• Transitioning to the new Ensembl platform for genome data and annotation: learn about the transition to the new Ensembl platform and what to expect from Ensembl resources during the move.
• Programmatic access to new Ensembl services and data: discover the new ways to access Ensembl data programmatically as we move towards a more scalable and accessible architecture.

Documentation

Extensive documentation is available on the Ensembl Genome Data Platform help pages. Below are quick links to some of the most useful pages:

• Ensembl archives and previous sites: information about Ensembl releases and legacy archive sites.
• Partial and integrated data releases: an explanation of the differences between partial and integrated data releases.
• Ensembl apps: learn how to select a genome using the Genome Selector, navigate the Genome Browser, and find information about genes, transcripts and variants using the Feature Explorer.
• BLAST: learn how to run BLAST for sequence similarity searches.
• Alignments Viewer: learn how to configure and use the comparative genomics Alignments Viewer.
• Ensembl Variant Effect Predictor (VEP): learn how to use Ensembl VEP to annotate your own variants.
• Ensembl GraphQL service: explore example GraphQL queries for genes, transcripts, assemblies and their associated metadata.
• Ensembl refget service: learn how to access Ensembl’s refget service to retrieve genomic, cDNA, CDS and protein sequences.

Legacy Ensembl

Ensembl 116 and Ensembl Genomes 63 are the final releases of the legacy Ensembl sites. These releases, and earlier ones, remain available through the Ensembl Archives. The resources below cover the legacy Ensembl browser, tools and APIs, and will remain useful if you are working with data from these archived releases.

Step-by-step walkthroughs

The Ensembl Genome Browser Walkthroughs provide a clear series of screenshots and explanations showing how the legacy Ensembl browser is structured and how to browse and download different types of genomic data. They are ideal if you want to get to grips quickly with Ensembl’s main features and data views. You are welcome to download and print the walkthroughs for reference.

Note: the walkthroughs focus on browser principles and frequently used pages; they do not cover every available feature or view.

EMBL-EBI Training portal

Online tutorials for Legacy Ensembl are available on the EMBL-EBI Training portal, including:

• a filmed version of the Ensembl browser workshop
• the Ensembl REST API course, which uses Jupyter notebooks

YouTube

Visit the Ensembl Training YouTube channel for a selection of short videos, tutorials and webinar recordings. These show you how to access and retrieve different types of data, and demonstrate how to use Ensembl’s most popular tools.

Webinars

We regularly deliver live webinars as part of EMBL-EBI’s live training programme. Check back regularly for upcoming webinars from Ensembl and other EMBL-EBI resources. Recordings of past webinars are also available.

Licensing

All Ensembl training materials are provided under a CC BY 4.0 licence. If you reuse or adapt these resources, please credit Ensembl as the original source.