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Ensembl Train the Trainer Workshop

Ensembl Outreach

Thursday, 5 Nov 2026

University of Energy and Natural Resources (UENR)

Jorge Batista da Rocha

https://training.ensembl.org/events/2026/

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Materials

training.ensembl.org

https://training.ensembl.org/events/2026/

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Learning objectives

Describe what makes good / bad training and the skills needed by an effective trainer.
Appreciate your own learning approach, how it may differ from others and how you can deliver training appropriate to different learning approaches.
Use existing Ensembl training materials to create your own training materials.
Design a training session with appropriate aims and learning objectives tailored to your audience.
Deliver a training session on using an aspect of Ensembl.

https://training.ensembl.org/events/2026/

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Agenda

Thursday, 5th Nov 2026
09:00 – 11:00	Principles of bioinformatics training
11:00 – 11:20	Break
11:20 – 12:30	Components of Ensembl training
12:30 – 13:30	Lunch break
13:30 – 14:45	Practical
14:45 – 15:00	Break
15:00 – 16:00	Presentations
16:00 – 16:15	Feedback and wrap-up

https://training.ensembl.org/events/2026/

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Principles of bioinformatics training

Ensembl Train the Trainer Workshop�

https://training.ensembl.org/events/2026/

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Session overview

What makes training effective?
What makes a good trainer?
Learning approaches
Know your audience
Aims and SMART learning objectives
Encouraging and supporting training
Advertising your course
Delivery and reflection

https://training.ensembl.org/events/2026/

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Introductions

What do you hope to gain from attending this course?

Who are you, where are you from and what is your role?

Have you delivered any training? If so, what subjects?

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Effective vs less effective training

Think of all the training sessions you have attended in the past:

What makes training effective?
What makes training less effective?

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What makes a good trainer?

Subject expertise and knowledge

Subject area knowledge
Audience awareness
Knowledge of training methodology

Communication and presentation

Verbal, writing and presentation skills
Flexible in delivery
Confidence

Engagement

Listens to trainees and empathy
Promotes participation
Reacts to interventions

Organisation and structure

Prepares session with clear aims
Prepares materials timely and practise
Guides participants through the session

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But it’s not just the how – it’s also the why!

Think of a time when you learned a new skill (e.g. hobby, subject, skill):

What was the reason behind the learning?
What was your approach/method to learning
How did you feel as you were learning?
What were the major challenges you faced?
Did you ultimately achieve your learning goal?

How do you approach learning a new skill?

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But it’s not just the how – it’s also the why!

Everyone learns for different reasons and in different ways:

Motivation
Methods and strategies
Emotions
Obstacles and sticking points
What helped or hindered your success?

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How do you approach learning new things?

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Learning approaches

Take a varied approach:

Encourage involvement and independence
Draw on experience
Don’t be afraid to try out new things
Your audience can be very diverse
Active learning

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Active learning

Learner-centered, emphasizing questioning, collaboration, and high engagement through interactive discussions that follow student input.

Image from Elixir

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Know your audience

What do they need know?

What do they already to know?

Why do they need to know?

Who are they?

Where are they?

How much time do they have?

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Tips to improve a learner’s experience

Introductions from trainers and participants
Introduce training materials
Introduce short, relaxing breaks
Introduce challenges and interactive elements
Avoid homework in all-day formats

https://training.ensembl.org/events/2026/

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Your aims

What is the overall goal of your training? This is the mission statement for your course. For example:

The aim of this course is to provide trainees with an overview of publicly available data resources to support proteomics research.
This session will introduce trainees to the key concepts in the analysis of metabolomics data.

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SMART learning outcomes

Make the learning outcomes SMART:

Specific What?�Measurable By trainer, trainee or both?�Achievable Is it possible in this context?�Relevant Is the topic relevant to the trainees?�Time-limited In what timescale?

Write them using: active verb + object + context�(usually, one verb per learning outcome)

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SMART learning outcomes: examples

At the end of the session, the learner will be able to…

List all planets of the solar system in order from closest to furthest away from the sun
Write a one-page screenplay script
Compose one SMART learning outcome for an Ensembl training course

Write them using: active verb + object + context�(usually, one verb per learning outcome)

Specific

Measurable

Achievable

Realistic

Time-limited

https://training.ensembl.org/events/2026/

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SMART learning outcomes: examples

At the end of the session, the learner will be able to…

List all planets of the solar system in order from closest to furthest away from the sun
Write a one-page screenplay script
Compose one SMART learning outcome for an Ensembl training course

Write them using: active verb + object + context�(usually, one verb per learning outcome)

Specific

Measurable

Achievable

Realistic

Time-limited

https://training.ensembl.org/events/2026/

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SMART learning outcomes: examples

At the end of the session, the learner will be able to…

List all planets of the solar system in order from closest to furthest away from the sun
Write a one-page screenplay script about a dog on a ferry
Compose one SMART learning outcome for an Ensembl training course

Write them using: active verb + object + context�(usually, one verb per learning outcome)

Specific

Measurable

Achievable

Realistic

Time-limited

https://training.ensembl.org/events/2026/

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Use Bloom’s taxonomy to write SMART learning outcomes

Blooms level	Verbs
Create	Compose, plan, propose, design, formulate, arrange, assemble, collect, construct, create, set up, organise, manage, prepare
Evaluate	Judge, appraise, evaluate, rate, revise, assess, estimate
Analyse	Distinguish, analyse, differentiate, experiment, test, compare, contrast, criticise, diagram, inspect, debate, question, relate, solve, examine, appraise
Apply	Interpret, apply, employ, use, demonstrate, sketch, dramatise, practice, illustrate, operate, schedule
Understand	Translate, restate, discuss, describe, recognise, explain, express, identify, locate, report, review, tell
Remember	Define, repeat, record, list, recall, name, relate, underline

Shabatura, Jessica. Bloom’s Taxonomy. 2022. University of Arkansas. https://tips.uark.edu/using-blooms-taxonomy/.

https://training.ensembl.org/events/2026/

To help you write effective SMART learning outcomes, you can refer to Bloom’s taxonomy, which is a concept used in pedagogy. Bloom’s taxonomy is a hierarchical framework that categorises learning objectives into 6 levels: remember, understand, apply, analyse, evaluate and create. And how it works is that, first, the students needs to be able to remember before they can understand something. And before they can apply any facts or rules, they will first need to understand it, and so on.

Let’s use fundamental principles in biology as an example to apply Bloom’s taxonomy. So for example:

First, you will need to remember the names of the organelles in a cell or the steps of mitosis.
Only then will you understand the material. For example, now you can explain why cells divide or describe the function of different organelles.
Now, you can apply your understanding to new situations. For example, you might predict what would happen to a cell if you placed it under UV light (the DNA will degrade).
Now that you remember, understand and apply your understanding, you can analyse: This involves breaking down complex information into smaller parts. You might analyse the different stages of cell division or compare different types of genes.
Then comes evaluate: At this level, you will be able to make judgments based on criteria and standards. For example, you might evaluate the specificity of primers for your PCR.
The highest level of Bloom’s taxonomy is create, where you will now be able to put together information to form a new theory. For example, now you are able to design an experiment to test a hypothesis.

So according to Bloom’s taxonomy, in order for a learner to be able to even start thinking about designing experiments, they must first understand the fundamentals. And you can use Bloom’s taxonomy to write SMART learning objectives. For **each** level in the taxonomy, you can use certain verbs to compose your SMART learning outcome.

For example, if you are trying to teach the steps of cell division, your learning outcome could be “List down the different phases of mitosis”

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CLEAR AIM�+�CLEAR LEARNING OBJECTIVES�=�CLEAR CONTENT

https://training.ensembl.org/events/2026/

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Encouraging and supporting learning

How to deliver the learning experience:

Project-based learning with real-life data analysis
Inquiry-based activities and problem-solving challenges
Hands-on use of bioinformatics tools and practical exercises
Live coding demonstrations and walk-throughs
Guided exploration with Jupyter notebooks or virtual labs
Student-driven projects, such as researching their own gene or protein

https://training.ensembl.org/events/2026/

To encourage learning in bioinformatics, you can use active, hands-on approaches like project-based learning, inquiry-based activities, and real-life data analysis tasks that foster problem-solving and collaboration. Techniques such as live coding demonstrations, use of bioinformatics tools in practical exercises, peer instruction, group projects—often crossing life sciences and computing disciplines—and guided exploration with resources like Jupyter notebooks or virtual labs help make concepts accessible and engaging. Incorporating feedback, supporting multiple learning styles (visual, auditory, kinesthetic), building on existing curricula, and promoting student ownership (e.g., having students research their own gene or protein) further enhance motivation and understanding in bioinformatics education.

Think about a course you attended and list what helped you with your learning

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Encouraging and supporting learning

More ways to encourage learning in bioinformatics:

Be clear about expectations, your aim and content (helps learners focus)
Tailor your course to the attendees' interests by including examples
Give opportunities to apply the knowledge they just learned (e.g. exercises, projects)
Encourage collaboration and interaction
Allow time for and welcome questions
Be approachable and enthusiastic about the work you do

https://training.ensembl.org/events/2026/

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Resources to support bioinformatics training

https://training.ensembl.org/events/2026/

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Encouraging and supporting learning

How to deliver the learning experience:

What methods and activities can we employ to encourage learning?

Can you think of ways to make the learning experience more exciting?

https://training.ensembl.org/events/2026/

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Advertising your course

Ensure you start advertising your course early
Make use of free marketing methods:

Social media and online communities
Mailing lists and email threads
Advertise at your institute
Reach out to colleagues outside your institute to share the course

https://training.ensembl.org/events/2026/

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Delivering your course

Don’t forget to consider:

Resources required to deliver the session (in-person / virtual, trainer checklist)
Setting expectations from the outset; what you will cover, how you are going to run the session
Breaks
Be flexible
Time for questions, reflection and exercises

!!!

https://training.ensembl.org/events/2026/

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Reflective practice

After you complete your training session:

Think about what worked well and what you were less happy with
Try not to be too negative – remember groups vary (consider the environment, participants’ backgrounds and things that were out of your control)
Use all sources of feedback available to you (self, audience interaction, colleagues and end-of-course survey)

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Additional resources in the Knowledge Doc

Knowledge sharing doc

https://training.ensembl.org/events/2026/

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Principles of bioinformatics training: summary

Think about what makes a good trainer and good training
Set out key aims and SMART learning objectives for your course
Get to know your audience and be aware of their motivation to learn
Create a supportive learning environment, use resources available to you and advertise your course early
Practise your delivery if you can
Reflect on your session and consider feedback
Preparation and organisation is key!

https://training.ensembl.org/events/2026/

A good trainer has: Knowledge, organisation, communication and engagement
We also explored the different approaches to learning and that this can be very diverse depending on the trainee
It’s really good to get to know your audience before your course as it will help you set out key aims and come up with SMART learning outcomes for your course
We also touched on creating an environment that supports and encourages learning by setting out different activities if this is feasible
The delivery is also important to get across your point
And my personal tip is to reflect on your course after delivery and look at feedback as this will help you improve for future courses.

SMART:

Specific (What)

Measurable (By trainee / trainer or both)

Achievable (Is it possible in this context)

Realistic (Can we really train them to do this)

Time-limited (In what timescale)

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Components of Ensembl training

Ensembl Train the Trainer Workshop

https://training.ensembl.org/events/2026/

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Session overview

Modules
Workshop structure
Tailoring your course
Effects of release cycles
Ensembl isn’t working - help!

https://training.ensembl.org/events/2026/

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Ensembl modules

Introduction to Ensembl (history and background, finding genomes)
Exploring genomic regions (visualising and exploring regions)
Genes and transcripts (annotation and types)
Variation and the Ensembl Variant Effect Predictor (VEP)
Practical modules

Optional modules

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Ensembl workshop structure

Presentation

What is the data / tool?
How do we produce / process the data?

Demonstration

Getting the data and using the tool

Exercises

Try things out for yourself and go beyond the demo
Remember: this is not a test

https://training.ensembl.org/events/2026/

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Tailoring your Ensembl course

Use your knowledge of the institute or if you’re going somewhere else, ask the host
Pre-course surveys can help you find out:

What species participants are working with
What topics participants are interested in
The level at which you are teaching

Use answers to:

Select the modules to include in your course
Point out features and data types specific to participants’ species of interest
Use species of interest in exercises and demos

https://training.ensembl.org/events/2026/

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Ensembl site

Ensembl (new)
Ensembl 116 (vertebrates)
Ensembl Genomes (non-vertebrates)
Portals:

EnsemblPlants

EnsemblMetazoa

EnsemblBacteria

EnsemblProtists

EnsemblFungi

EnsemblCOVID-19

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Ensembl training materials

Previous materials
Additional exercises available on the Ensembl Training site
Write your own or copy the style:

Use species of interest to the participants
Pick a gene/variant which allows you to showcase all the features of interest
VEP can be very helpful for exploring/variants

https://training.ensembl.org/events/2026/

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Ensembl Release cycle

Integrated Release

1

Partial

Release

Linkage Release

Linked data frozen at a point in time

Data Release

Assemblies
Genesets
Sequences

Regulation data
Comparative genomics
Linked data

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Effects of release cycles

If you’re planning a training course, email us at helpdesk@ensembl.org for upcoming releases and assistance with training materials
Be aware of workarounds, e.g.

Screenshots

Note: if the current site does not match what’s in your materials, that’s just a lesson in how bioinformatics databases are constantly changing!

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Ensembl isn’t working – help!

https://training.ensembl.org/events/2026/

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Ensembl isn’t working – help!

Photo by Steven Paton

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Ensembl isn’t working – help!

Errors (e.g. AJAX):

Refresh page
Change browser

The server is down:

Fall back on your screenshots

The page is not loading:

Refresh page
Try incognito / private window (clear browser cache)

AI-generated stock image from Vecteezy

Photo by Steven Paton

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A few tips to avoid difficult situations

Connect the materials to the learners’ interest

Create assignments that provide an appropriate level of challenge

Show your own passion and enthusiasm for the discipline

Have a back-up plan (e.g. offline training materials, flexible timetable, etc.)

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Practical

Ensembl Train the Trainer Workshop

https://training.ensembl.org/events/2026/

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Responsible use of AI in training

AI can be used to quickly generate examples, exercises, and code snippets tailored to your learning objectives

Be cautious of the following issues:

Accuracy
Consistency
Plagiarism and copyright

Check your institutes guidelines on the use AI

Do you need to disclose this?

https://training.ensembl.org/events/2026/

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What have we done so far?

Principles of bioinformatics training

Effective training and trainers
Learning approaches
Know your audience
Aims and SMART learning objectives
Encouraging learning
Advertising your course
Delivery and reflection

Components of Ensembl training

Modules
Workshop structure
Tailoring your course and training materials
Effects of release cycles
Ensembl workarounds

https://training.ensembl.org/events/2026/

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Practical: deliver an Ensembl training session

You have one hour to prepare a five-minute Ensembl training session on any topic listed in the practical guide. Your session can include:

A genomic feature that you are particularly interested in
Some background information about the data
A step-by-step demonstration

Generate 1x SMART learning objective with the help of an AI client
Your target audience is Master’s and PhD students in molecular biology
Upload your slides to the shared Google Drive

https://training.ensembl.org/events/2026/

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Feedback and closing remarks

Ensembl Train the Trainer Workshop

https://training.ensembl.org/events/2026/

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Feedback survey

Feedback surveys help us improve our courses for future participants
You can opt to receive an electronic attendance certificate
This is a certificate that you have attended this course, it does not confer any qualification

https://forms.gle/hyErLNUBp8yU2inY7

https://training.ensembl.org/events/2026/

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Key messages

Get to know your audience – who, where, what, why, when?
Be very clear on their goals, your session aims and outcomes

Use those required / anticipated outcomes as the starting point to plan your course

Don’t try to cram everything in - less is more and balance is key!
Provide opportunities for challenge, assessing progress and reflection
Collect valuable feedback and use it for your personal development and further course development
Have fun (a bored trainer is not an effective one)

https://training.ensembl.org/events/2026/

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Reach out to us

@ensembl.org

/Ensembl.org

/EnsemblGenomeBrowser

ensembl.info

@Ensembl

helpdesk@ensembl.org

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Help and documentation

Online courses https://www.ebi.ac.uk/training/

Ensembl tutorials https://www.ensembl.org/info/website/tutorials/

https://www.youtube.com/user/EnsemblHelpdesk

Mailing lists dev@ensembl.org

announce@ensembl.org

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Publications

List of Ensembl publications:�https://www.ensembl.org/info/about/publications.html
Topic-specific articles mentioned throughout the workshop

Yates AD, Austine-Orimoloye O, Azov AG, Ensembl 2026, Nucleic Acids Research, Volume 54, Issue D1, 6 January 2026, Pages D1053–D1060, https://doi.org/10.1093/nar/gkaf1239

Yates AD, Allen J, Amode RM, et al. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. 2022 Jan;50(D1):D996-D1003. DOI: 10.1093/nar/gkab1007. PMID: 34791415; PMCID: PMC8728113.

https://www.ensembl.org/info/about/publications.html

https://training.ensembl.org/events/2026/

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Acknowledgements and funding

Funded by the European Union

Horizon 2020

Horizon Europe Programme

https://training.ensembl.org/events/2026/

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Training materials

Ensembl training materials are protected by a CC BY license:�https://creativecommons.org/licenses/by/4.0/
If you wish to re-use these materials, please credit Ensembl for their creation.
If you use Ensembl for your work, please cite our papers:�https://www.ensembl.org/info/about/publications.html

https://training.ensembl.org/events/2026/