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Ensembl for Educators


Who is this page for?

Ensembl is a genomic resource that serves as a great introduction to bioinformatics concepts - it allows users to visually explore genomic features and understand how large-scale data are processed. It is also free to use, making it accessible for researchers around the world.

Here we provide up‑to‑date training materials and guidance for teaching your own Ensembl course. These materials are focused on the Ensembl versions up to 116, which provide genome annotation data from June 2026. We encourage you to continue teaching with these and over 2026 and 2027, and we will continously share materials for the new Ensembl site over time.

You will have long term access to this Ensembl 116 from this URL - jun2026.archive.ensembl.org

This page is designed for those who are already teaching or planning to teach Ensembl as part of a curriculum or recurring workshop, such as:

  • University lecturers and course organisers integrating Ensembl into undergraduate or postgraduate modules
  • Bioinformatics trainers running local workshops
  • Teaching assistants and demonstrators supporting practical sessions

Use this page to find the latest teaching materials, ready‑made modules, and guidance to help keep your course current with Ensembl. If you have any questions about teaching Ensembl, please do not hesitate to contact us.

If you teach Ensembl using materials from our Training website, please complete a short survey.
Your responses help us improve our material so it’s even more useful for educators.



Teaching Ensembl

Ensembl is a great resource for beginners in bioinformatics with a background in molecular biology and/or genetics. The recommended modules listed below are aimed at wet-lab scientists and bioinformaticians who are new to using Ensembl or have not yet discovered the power and depth of this resource. These modules are aligned with existing Ensembl browser workshops and are suitable for university teaching.

Introduction to the Ensembl Genome Browser

Level: Beginner (BSc./MSc.)
Duration: 60–90 minutes

Learning outcomes:

  • Explain what Ensembl is and where the data come from
  • Navigate the homepage and use the main search
  • Open a genomic region, gene and transcript in Region in detail and Gene views

Genes and Transcripts

Level: Intermediate
Duration: 60 minutes

Learning outcomes:

  • Explore gene pages, transcript structure, and sequence views

Variation and the Ensembl Variant Effect Predictor (VEP)

Level: Intermediate / Applied
Duration: 60–90 minutes

Learning outcomes:

  • Find germline and somatic variants, associated phenotypes, and linkage information
  • Use the web interface of Ensembl VEP with example datasets

Regulation and Comparative Genomics

Level: Intermediate / Advanced
Duration: 60–90 minutes

Learning outcomes:

  • View regulatory features, activity across cell types, and integrated functional genomics data
  • Explore whole‑genome alignments, synteny, and orthologues
  • Identify gene trees and orthologues for comparative analyses



Teaching Materials Library

Use this section as an up‑to‑date repository of Ensembl teaching materials.

Ensembl is updated regularly, and the interface and data may change. We ensure the standard slide deck stays up‑to‑date. The date of the last slide deck update can be found in the speaker notes of the title slide.

To be notified about major Ensembl training material updates, join our Announce low‑volume mailing list.



Example Course Outlines

These are ready‑made outlines you can copy into your own syllabus, based on established Ensembl workshop programmes.

One‑Day Ensembl Browser Practical (On‑Site)

Audience: Wet‑lab scientists / mixed cohort

Structure:

  • 09:30–10:30 – Introduction to Ensembl & Region in detail
  • 10:30–10:50 – Break
  • 10:50–12:00 – Genes and transcript annotation
  • 12:00–13:00 – Lunch
  • 13:00–14:30 – Variation and Ensembl VEP
  • 14:30–14:50 – Break
  • 14:50–15:30 – Regulation (optional)
  • 15:30–16:10 – Comparative genomics (optional)
  • 16:10–17:15 – BioMart and wrap‑up


Two‑ or Three‑Session University Module

Example: 3 × 2‑hour sessions for an MSc bioinformatics course, combining browser, variation, and BioMart components.


One‑ or Two‑Hour Lecture/Seminar

Ideal for:

  • Introduction to genome browsers
  • Overview of Ensembl
  • Introduction to Ensembl practical demo



Virtual and Hybrid Teaching

All standard Ensembl workshops can be delivered online. The same principles work when you teach Ensembl virtually.

Tips for running virtual courses:

  • Test audio, screen sharing, polls, and breakout rooms beforehand
  • Send joining instructions, expectations, schedule, and materials in advance
  • Start with an agenda slide introducing session flow (e.g. presentation → demo → exercise)
  • Provide exercise links and data files early; recommend practice via Ensembl and available online courses
  • Split sessions into shorter blocks (e.g. 2 × 90‑minute sessions)
  • Include regular breaks to prevent fatigue
  • Explain how participants can ask questions (raise hand, chat, or unmute)
  • Keep camera use flexible for bandwidth or privacy reasons
  • Use interactive quizzes (e.g. Slido,Mentimeter) and breakout rooms to encourage engagement



Training on other Ensembl sites and species

Ensembl Genomes provides access to genome annotation for other major taxa - plants, metazoa, bacteria, fungi and protists. You may adapt these resources for these sites accordingly. Note that there are diverse annotation providers across the Ensembl Genomes resources.

The new Ensembl: The Ensembl project is moving to a new platform to better support genome annotation for more species than ever before. This site is available now at beta.ensembl.org, and it will become the default Ensembl at ensembl.org in summer 2026. This site supports all species together in one site, and provides a fast genome browsing experience to explore the latest genomes from major projects such as the Human Pangenome Reference Consortium, Darwin Tree of Life Project, and Earth Biogenome Project.

This page will share training materials for the new Ensembl over time and key advice points on major features that will help you and your participants transition.

Support and Community

Contact Us About Teaching Ensembl

If you have questions about using or adapting these materials or need help planning an Ensembl‑based course you can contact us via the Ensembl website contact form
or email helpdesk [at] ensembl [dot] org.

To be notified of major Ensembl updates, join our Announce low‑volume mailing list.


Host a Workshop

If you’d prefer a trainer from the Ensembl Outreach team to deliver a live Ensembl course (on‑site or online), see how to host a workshop.


Community Resources

  • Coming soon.


Share Your Experience

We’d love to see how you teach Ensembl! Tag us when running a course or showcasing materials:



Survey

If you use Ensembl training materials in your teaching, please fill out a short survey.

Your participation is voluntary and helps improve our training materials.
Responses are collected for internal evaluation only. No identifying information is required unless you request follow‑up contact.



Licensing

All Ensembl training materials are provided under a CC BY 4.0 license.
If you reuse or adapt these resources, please credit “Ensembl, EMBL‑EBI” as the original source.



FAQs for Educators

How often are teaching materials updated?
After each major Ensembl release, materials are reviewed and key items updated where interface or data changes affect exercises.

Can I adapt and translate Ensembl slides?
Yes, within the stated licence. Please retain Ensembl/EMBL‑EBI attribution and do not imply official endorsement of modified materials.

What is the difference between using these materials and hosting an Ensembl‑led workshop?
Ensembl‑led workshops are delivered live by the Ensembl Outreach team, at no charge to academic hosts (except trainer travel in high‑income countries).
This page supports independent Ensembl teaching.