Training materials
Ensembl Training and Outreach
Ensembl, EMBL-EBI
Wednesday, 12th August 2026
2026 BIOTA Phils Annual Convention
Louisse Paola Mirabueno and Aleena Mushtaq-Stolworthy
European Molecular Biology Laboratory (EMBL)
EMBL-EBI
Bioinformatics
Grenoble
Structural biology
Barcelona
Tissue biology and disease modelling
Hamburg
Structural biology
Heidelberg
Life sciences
Rome
Epigenetics �and neurobiology
What is bioinformatics?
Bioinformatics allows you to manage, analyse and interpret enormous amounts of biological data with the use of computer science, mathematics and statistics.
Examples of the use of bioinformatics
Agriculture
Map and sequence plant genomes to identify genes for yield, drought resistance, pest resistance, and nutrient content to breed improved crops and livestock.
Food Science
Detect pathogens, allergens, and improve nutrition using DNA analyses of food ingredients and contaminants.
Environmental Science
Analyse microbial communities in soil, water, and air, to help assess ecosystem health and monitor pollution.
Medicine
Analyse genetic profiles to tailor treatments, such as choosing drugs based on a cancer patient’s unique genetic variants.
Biotechnology
Accelerate discovery of useful enzymes or bioactive molecules by analysing sequence databases for industrial, pharmaceutical, or agricultural use.
Evolutionary biology
Use of DNA, RNA, and protein sequences to construct phylogenetic trees showing evolutionary relationships between organisms and genes.
Agriculture
Map and sequence plant genomes to identify genes for yield, drought resistance, pest resistance, and nutrient content to breed improved crops and livestock.
Food Science
Detect pathogens, allergens, and improve nutrition using DNA analyses of food ingredients and contaminants.
Environmental Science
Analyse microbial communities in soil, water, and air, to help assess ecosystem health and monitor pollution.
European Bioinformatics Institute (EBI)
EMBL-EBI resources and tools
Role of genomic resources and databases
Genomic resources and databases allow us to:
What do genome browsers tell us?
CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCATTAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAATCGCTTGAACCCTGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAACATTCTTAGGAAAAATAACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTAACTAAGAATTTAAAGTTAA
What do genome browsers tell us?
CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGGGACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGTGCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCGAGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGTATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTGGCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCATTAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGGTTTCAGTACTCCTTATACTCTTAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCTTACCATATTAGAAATTTAAAACTAAGAATTTAAGGCTGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACTTGAGGCCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAATGTGCTGCGTGTGGTGGTGCGTGCCTGTAATCCCAGCTACACGGGAGGTGGAGGCAGGAGAATCGCTTGAACCCTGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAAAAACTAAGAATTTAAAGTTAATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAACATTCTTAGGAAAAATAACTTTTTGAAAACAAGTGAGTGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTGTTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGATTATTTGGAAGATAGTGGTGTTCTGAATTAACTAAGAATTTAAAGTTAA
Regulatory element
Gene
Variant
The mission of Ensembl is to provide a comprehensive and accurate annotation of genomes, integrating this information with other biological data and making it publicly accessible via the web.
In the past years, Ensembl has generated approx. 30TB of data every release for the main site alone.
HQ smartphone photo ~5MB (=0.000005 TB)
What you can find in Ensembl
The new Ensembl Data Platform
Mirrors are retired with the Ensembl 116 archive
Ensembl enables genome analyses
Public data
Genome analysis
Ensembl workflows
APIs
Genome browser
Tools
Genes & repeats
Regulatory regions
Comparative genomics
Genomic variation
Phenotype associations
The Ensembl team
The Ensembl Outreach team
Dr Jorge Batista da Rocha
Outreach Project Leader
Louisse Paola Mirabueno
Outreach Officer
Dr Aleena Mushtaq-Stolworthy
Senior Outreach Officer
Ensembl Outreach responsibilities
Ensembl Training and Outreach
ICESI, Calí, Colombia
Faculty of Medicine of Sousse, Tunisia
Pokhara University, Nepal
Ensembl as part of the academic curriculum
Using Ensembl as a teaching tool in life sciences
Using Ensembl to teach genomics concepts
Genome-scale concepts can be visually explored:
Ensembl as a first step into bioinformatics
Which Ensembl version should I teach?
If you know our current version well or if you have existing materials:
Which Ensembl version should I teach?
Do you use Ensembl BioMart or the Ensembl Variant Effect Predictor (VEP) in your training?
Which Ensembl version should I teach?
Does your audience need genome data from new genome assemblies?
Ensembl transition: taxa coming together in one site
Ensembl
Capacity building
Ensembl Train the Trainer course:
Ensembl for Educators: a resource for trainers
Ensembl is a dynamic resource that is regularly updated to reflect new data and improvements to the interface. For educators, this creates a familiar challenge: how do I teach a platform that continues to evolve while ensuring that learning materials remain accurate, accessible, and relevant?
Available materials
Materials focus on Ensembl 116 / Ensembl Genomes 63:
Ensembl for Educators
Ensembl for Educators
Please complete the feedback form when teaching Ensembl with the provided materials
Hosting an Ensembl training course
Browser course�One-day course on the Ensembl browser, aimed at wet-lab scientists.
Train-the-trainer course�One-day course on delivering bioinformatics training and teaching your own Ensembl browser course.
Visit the Ensembl Training website or email us for more information.
We can teach an Ensembl course at any institute for free (plus trainers’ expenses in high-income countries).
Ensembl Training and Outreach
ICESI, Calí, Colombia
Faculty of Medicine of Sousse, Tunisia
Pokhara University, Nepal
Ensembl training in the age of AI
Licensing
Citing Ensembl
Yates AD, Austine-Orimoloye O, Azov AG, et al. Ensembl 2026. Nucleic Acids Research. 2025 Nov;gkaf1239. DOI: 10.1093/nar/gkaf1239. PMID: 41296548.
Where to get help
Explore all help and documentation pages, including a guide to the new Ensembl platform.
Data- and tool-specific help pages.
Find out how the data was generated or how to use the tool.
Get in touch with the Ensembl Helpdesk.
Help & documentation
More info
Contact form
Reach out to us and keep up-to-date
Acknowledgements and funding
Funded by the European Union
Horizon 2020
Horizon Europe Programme
We would like to acknowledge the National Genome Research Institute (NHGRI) for funding the following grants supporting the creation of the human pangenome reference: U41HG010972, U01HG010971, U01HG013760, U01HG013755, U01HG013748, U01HG013744, R01HG011274, and the Human Pangenome Reference Consortium (BioProject ID: PRJNA730823) as well as 2U24HG007497-09 which supports the creation of HGSVC resources
Funded by Wellcome
Training materials