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And now the good news

Cath Brooksbank PhD

Head of Training

www.ebi.ac.uk/training | cath@ebi.ac.uk

Bioinformatics training with EMBL-EBI and friends

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What is EMBL-EBI?

World leading source of public biomolecular data
Our vision is to benefit humankind by advancing scientific discovery and impact through bioinformatics.
Part of the European Molecular Biology Laboratory (EMBL), Europe’s flagship laboratory for the life sciences.

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Our mission

Deliver data resources

Perform excellent research

Train the next generation of scientists

Engage with�industry

Coordinate bioinformatics�in Europe

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Data services

www.ebi.ac.uk/services

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Data resources at EMBL-EBI

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Artificial intelligence and machine learning

Researchers and data scientists who develop AI algorithms use high quality data managed by EMBL-EBI to train AI systems.
We add value to data submitted to our resources through expert curation and annotation.
When appropriate, we integrate AI predictions into the bioinformatics ecosystem.

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AlphaFold – using AI to advance biology

Google DeepMind used public databases UniProt, PDB and MGnify to train the AlphaFold algorithm, which predicted the structure of all known proteins.
EMBL-EBI made +200 million protein structure predictions openly available in the AlphaFold Database.
Potential applications of AlphaFold:
Drug discovery and vaccine development
Neglected diseases
Plastic pollution

AlphaFold – using AI and open data to advance biology

EMBL-EBI works with industry to advance scientific knowledge. We teamed up with the AI experts at DeepMind to make protein structure predictions for almost all catalogued proteins freely available to the world.

AlphaFold Database in numbers

+200 million protein structure predictions
1 million organisms
98.5% of human proteins

AlphaFold predictions have already been used by researchers working on the following challenges:

Drug discovery
Neglected diseases
Antibiotic resistance
Plastic pollution
Increase health of honey bees
Understand how ice forms

AlphaFold is a useful tool for the life sciences, and marks a revolution in biology and medicine. It was built on open data such as those managed by EMBL-EBI, and thanks to DeepMind and EMBL-EBI, its predictions are freely and openly available to all.

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Genomic medicine

Healthcare experts, including NHS England and the German Genome Phenome Archive, use EMBL-EBI data resources to deliver thousands of genetic diagnostics to patients every month.
We develop analysis tools to understand genome sequencing data from rare disease and cancer patients, to improve diagnosis and treatment.
We help train the next generation of genomic medicine experts.

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Biosecurity

Healthcare and public health specialists use EMBL-EBI’s Pathogens Portal to access data about 200,000 pathogen species and strains
We support countries to build national Pathogen Portals, to get insights from patient data in their healthcare systems (e.g Swedish Pathogen Portal)
This helps to monitor outbreaks and antimicrobial resistance, identify new pathogen strains, and develop new treatments and vaccines.

Take the COVID-19 pandemic as an example. Data science was essential in the pandemic response.

EMBL-EBI was one of the first organisations to recognise the value of sharing scientific data about the virus internationally. We supported the pandemic response:

Set up the COVID-19 Data Portal to access SARS-CoV-2 molecular and genomic data from all over the world
Supported countries to set up data sharing platforms
Revealed insights on new ‘variants’ / lineages
Analysed molecular causes of different immune responses

Building on the lessons learned from the COVID-19 pandemic, in 2023, EMBL-EBI launched the Pathogens Portal, which hosts molecular and genomic data for over 200,000 pathogen species and strains affecting humans and animals. Essential for disease reserach, monitoring and pandemic preparedness.

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Biodiversity conservation

Ecologists and conservation biologists use bioinformatics and genomics to:

understand and protect biodiversity
develop clean technologies to reduce environmental pollution

TREC

EMBL’s scientific expedition to�study European coastlines from�molecules to ecosystems.
The data gathered will be�made publicly-available through�EMBL-EBI resources.

Biodiversity project examples:

Biodiversity projects Darwin Tree of Life

Our Ensembl teams play a leading role in the genome annotation work and scientific training for large biodiversity initiatives, including the European Reference Genome Atlas, Darwin Tree of Life Project, and the African Biogenome Project.

TREC (TRaversing European Coastlines)

EMBL flagship project - 2 year expedition collecting data from European coastlines (soil and water samples, multiomics data) to explore the biodiversity and

molecular adaptability of microbial communities as well as key selected organisms.

Aims: Measure the amounts and study the effects of organic and inorganic pollutants. Survey biodiversity loss and monitor the impact of invasive species. Identify

carbon fixation pathways and develop new harnessing strategies. Measure the impact of global warming and acidification on ecosystems; study molecular

Adaptations. Explore symbioses to understand molecular mechanisms of organismal interactions. Identify new antibiotics, track antimicrobial resistance spread,

and design control strategies.

Mapping plankton

The Tara schooner collects samples of marine plankton from the world’s oceans to enable holistic investigations of the marine ecosystems, their potential applications and fragility. EMBL-EBI makes the data accessible through the European Nucleotide Archive and MGnify data resources.

Enzymes with useful functions

EMBL-EBI’s microbiome data resource MGnify helps researchers find enzymes with useful functions such as the ability to degrade plastic or replace industrial processes.

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Sustainable food production

Farmers, animal breeders and agricultural scientists use our data resources to:

Identify which species and cultivars are tolerant to climate change while still providing optimum nutrition
Inform strategies for dealing with pests while protecting pollinators
Link genes to traits to make food production more robust, effective and sustainable

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Training throughout EMBL

www.embl.org/training/

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EMBL’s 9-year rule: Spreading excellence

The principle of regular staff turnover – generally a 9-year limit to employee tenure – enables EMBL to be agile and evolve rapidly by recruiting talented scientists and professionals

After leaving EMBL, alumni transition to leadership �positions in academia, industry, �government, and NGOs

of EMBL group and team leaders turnover during a 5-year period

EMBL’s dynamic turnover model is the cornerstone of creativity, interdisciplinarity and a distinctive culture of excellence and openness

44%

2022 metrics

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Scientific Training at EMBL

EICAT Internal training

EICAT External training

Sci. Ed & Pub. Eng.

EMBL-EBI training

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Partners: Bio-IT: computational skills for life sciences | ARISE: career accelerator for research infrastructure scientists

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EIPOD LinC: Life in Context

EIPOD-LinC is a postdoctoral fellowship programme for researchers from around the world who are passionate about interdisciplinary research

Fellows work on a �self-designed interdisciplinary research project aligned with the Molecules to Ecosystems Programme

Projects form collaborations between EMBL labs or EMBL and member state labs from academic, industry, or clinical institutes

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ARISE: Shaping the next generation of infrastructure leaders

ARISE is a fellowship programme for research infrastructure scientists who are trained to both advance technology and methods in life sciences and to manage service-providing facilities, infrastructures, and enterprises

Fellows are hosted �by EMBL group �and team leaders across all sites and perform one or more secondments with more than 50 partner organisations around the globe

ARISE

Shaping the next generation of infrastructure leaders

As part of ARISE, EMBL hires researchers and engineers for three years to advance technology and methods in life sciences and learn how to lead service providing research infrastructures

ARISE fellows work on a technology or method development project of their choice as part of one of the EMBL groups and teams.

In parallel EMBL organises a unique training that teaches fellows how to run service and manage teams, how to support users, manage their and your projects, and promote innovation.

After the fellowship, it is expected that you will be qualified to take a senior position in core facilities, service teams, big research infrastructures, technology development groups in academia, industry, healthcare, or other sectors, or that fellows start their own service providing enterprise.

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CPP funded visit scheme for PhD and postdoc fellows

CPP Visitor Fellowship

Award of up to EUR 4000

For PhD or postdoc level visitors based anywhere in the world (non-EMBL home institute)

Priority given to candidates visiting EMBL for the first time, and international mobility

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Home

countries

3

EMBL

sites

15

awards

(Since March 2022)

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Impact – EMBL Visitors in 2022

45%

of visits result in a publication

98%

recommendation

rate

68%

of visitors establish research collaboration

64%

of visits motivated

by specific equipment

670

visiting scientists & students from all over the world per year

73%

from EMBL Member States, Associate & Prospect MS

43

home institute

countries

62

visitor

nationalities

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Science education and public engagement

TREC public

engagement

World of

Molecular Biology

EMBL’s educational and outreach experiences share scientific discoveries with young people, teachers, and diverse publics in Europe and beyond

Science

education

Science education and public engagement

EMBL’s educational and outreach experiences share scientific discoveries with young people, teachers and diverse publics in Europe and beyond

TREC public engagement

EMBL aims to engage European citizens along the TREC route and beyond with human & planetary health, fostering active science participation, and empowering educators and young learners.

EMBL shows the power of molecular biology in tackling societal challenges, highlighting the connectivity and interaction between humans and the planet as well as the connection between the environments of land and sea.

World of molecular biology

EMBL’s vibrant, interactive permanent exhibition in Heidelberg celebrates molecular biology with a focus on the work, people, and technologies of EMBL.

A combination of images, animations, film, and interactive games will take you on an exciting journey through the inner workings of life at all scales.

Science education

Our inspiring educational experiences share the scientific discoveries of EMBL with young learners aged 10-19 years and teachers in Europe and beyond.

Hands-on experiences such as the Microscope in Action (pictured) help educators inspire and fascinate students through active STEM learning.

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EMBL-EBI Training

www.ebi.ac.uk/training

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EMBL-EBI Training in a nutshell

Live training

On-demand training

Join us – virtually or in person –�to learn with other scientists�from around the world

Support for trainers

We support you and your�courses with open resources�and skills development

Dive straight into learning�through our online tutorials,�course materials and�recorded webinars

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Live bioinformatics courses open for applications

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Date	Title	Closes	Venue
8–9 Jul	Hands on arthropod bioinformatics workshop	N/A	Calí, CO
23–27 Sep	Metagenomics bioinformatics at Mgnify	09 Jun	Virtual
23–27 Sep	Single-cell RNA-seq analysis with Python	09 Jun	Virtual
29–31 Oct	Managing a bioinformatics core facility	28 Jul	EMBL-EBI
18–22 Nov	Genome bioinformatics: from short to long-read sequencing	22 Jul	EMBL-EBI
17–21 Feb	Single-cell RNA-seq analysis with Python	05 Aug	Virtual
24–28 Feb	Introduction to RNA-seq and functional interpretation	TBC	Virtual
3–7 Mar	Introduction to multi-omics data integration and visualisation	TBC	EMBL-EBI
17-21 Mar	Gene–Environment interactions in health and disease	TBC	EMBL-EBI

www.ebi.ac.uk/training/live-events

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Recent webinars

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Dates	Title
6 Mar	Strain-resolved approaches for human microbiome studies*
20 Mar	Microbial biodiversity in schools and its link with children’s health*
27 Mar	The Pathogens Portal: A gateway to vast biomolecular data for pathogen research
28 Mar	Explore Human Pangenome Reference Consortium data in Ensembl
17 Apr	Statistical thinking for microbial ecology*
1 May	Harmony in diversity: exploring the rich microbiomes of South American wildlife*
8 May	Wine yeasts as a model system in community ecology*
9 May	Exploring human disease and protein variant data in UniProtKB

www.ebi.ac.uk/training/live-events. click ‘past events’ to access recordings

*Series on microbial ecosystems

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Catch up if you missed it…

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Materials from live courses are openly accessible to all (35 sets, 2022 onwards)

Webinars are recorded and made openly accessible (201 videos)

www.ebi.ac.uk/training/on-demand

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Online tutorials and curated collections

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81 openly accessible tutorials on bioinformatics tools and methods; 11 (and growing) themed collections
Quizzes, interactive activities and videos built in
Create an account to choose favourites, track progress and create shareable playlists of courses

www.ebi.ac.uk/training/on-demand

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Impact of attending a course on an individual

Increased knowledge / awareness of resources

Ability to teach others

Improved interactions with Bioinformaticians

Better understanding of techniques / methods

Gained confidence

More control over my analysis

What impact has the course had on your research?

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Quality, reach and impact

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	Quality	Reach	Impact
Live training	86% Rate courses as excellent or very good	~500 participants reached per year (EMBL courses)	56% Pass their learning �on to others
On-demand training	80% Rate webinars as excellent or very good	~500,000 Unique users per year (online tutorials)	Widespread use of tutorials in undergraduate and graduate courses

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An open science vision for biodata science training

Enable scientists at all levels, regardless of location, sector, personal characteristics or career stage, to make full use of public biodata and to share their expertise openly with others

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Thank you!

www.ebi.ac.uk

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