�SciLifeLab/NBIS�and�Services for Sensitive Data��� Bengt Persson�Director of NBIS��20 March 2025�AIDA Data Science Platform Launch Event

Contents

• SciLifeLab – Science for Life Laboratory
• NBIS – the SciLifeLab Bioinformatics platform
• 1+MG – The European 1+ Million Genomes Initiative
• FEGA – Federated European Genome-phenome Archive
• GDI – European Genomic Data Initiative
• GDI versus EHDS (European Health Data Space)
• GoE – Genome of Europe

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What is SciLifeLab?

Founded in 2010 by Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University

National hub enabling life science research that would otherwise not be possible

Government appointed mission as a national research infrastructure

Research community gathering scientists across universities and disciplines

Today, activities at all major Swedish universities with sites launched in Linköping, Lund, Gothenburg and Umeå

… and collaborations with healthcare, industry, other governmental agencies and international organizations

Areas of activities

Provide excellent and impactful life science infrastructure

10 service areas and 40 units

1,600 users and 3,500 projects yearly

600 technology experts

Strengthen research communities, capabilities, and global partnerships

300 group leaders across all sites

Capabilities: Precision Medicine, Pandemic Laboratory Preparedness, Planetary Biology>

Drug Discovery & Development

International collaborations e.g. EMBL

Innovation and bridge-building for the benefit of society

Collaborations across sectors and boarders, with industry and healthcare

Attract scientific excellence and provide advanced training

SciLifeLab and DDLS Fellows �program

Training hub

PhD and postdoc training

Facilitate the transformation of life science data into knowledge

SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS)

Computational and data science base for open, real-time FAIR data sharing

AI and data science expertise in life science

SciLifeLab Strategy

As Sweden's National Infrastructure for Molecular Life Sciences, SciLifeLab aims to:

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Infrastructure user statistics

Infrastructure user statistics

Capabilities

Strategic capabilities around which SciLifeLab gathers infrastructure technology, research & expertise

SciLifeLab and Wallenberg �National Programme �for Data-Driven �Life Science (DDLS)��12 years, 3.7 GSEK (~340 MEUR), �11 partners, coordinated by SciLifeLab

Overall 12-year plan for the DDLS programme

39 DDLS Fellows�78 PhDs and 78 postdocs

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140 PhDs in academia and 45 industry PhDs

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90 postdocs and 45 industry postdocs

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210 MSEK WASP�35 MSEK WASP- HS

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235 MSEK

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670 MSEK

4 research areas

National Bioinformatics Infrastructure Sweden

• NBIS is a national distributed research infrastructure

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• We are a people infrastructure with currently ~120 staff

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NBIS staff at our recent retreat at Ystad Saltsjöbad 12 March 2025

Umeå

Göteborg

Lund

Linköping

Stockholm

Uppsala

Three pillars

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NBIS Units/Teams

• Support
• Five teams:
• Health and Clinical
• Cell and Molecular Biology
• Evolution and Biodiversity
• Microbiology, Immunology and �Structural biology
• Bioimage bioinformatics (BIIF)
• Infrastructure
• Data management
• Human data (1+MG, FEGA-SE, GDI, GoE)
• Systems development
• AIDA Data Hub
• SCoRe (Support for Computational Resources)
• Training & Outreach
• ELIXIR-SE

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Support currently ~55 national staff

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https://www.nbis.se/services

Cryo-EM and structural biology

AI in medical imaging

Bioimaging

Erik Ylipää

Tim Schulte, Piotr Draczkowski, Claudio Mirabello

Frontend/backend

Visualizations

Code review

Software/workflows

Anna Klemm and team

Data Management & Human Data

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Data management & Data publication support

• Be a catalyst for the Swedish Government’s national goal that the transition to open access to research data is fully implemented by 2026�
• Data Management services and support to researchers for FAIR data

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• Data Management best-practice training and guidelines

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• Collaboration with key national and international stakeholders, �e.g. SciLifeLab Data Centre, SND (Swedish National Data service), ELIXIR, EOSC, RDA

Human Data

• FEGA (Federated European Genome-phenome Archive)
• Bigpicture (digital pathology)
• EUCAIM (cancer image data)
• Orientation in the future landscape of EHDS (European Health Data Space)
• Engagement with EHM, SoS, GMS, VR and other stakeholders
• GDI – Genomic Data Infrastructure

The Swedish ELIXIR node

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• Many European projects together with other ELIXIR nodes

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• Precision Medicine (Genomics) 1+MG, FEGA, GDI, B1MGplus, GoE,� EOSC-ENTRUST, TEHDAS2, � ERDERA, CANDLE

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• Digital pathology and Digital imaging Bigpicture, EUCAIM

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• Biodiversity BGE

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• Advanced Training PHENET

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• FAIR software and Capacity building ELIXIR-STEERS

• Provision of Human Protein Atlas since 2013

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• Engagement in several areas in ELIXIR, �e.g. data management, human data, biodiversity, advanced training

1+MG Declaration of cooperation starting 2018

24 countries and 4 observers

• 1+ million whole genomes accessible in the EU�to support research, health care and prevention
• Enabling users to search and access the data through a federated secure and privacy-respecting environment
• For the benefit of Health care, Research & Industry

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1+MG Roadmap 2018 - 2027

Credit: Karen Arnott/EMBL

Institutes from Finland, Germany, Norway, Spain and Sweden are first the nodes of the Federated European Genome-phenome Archive, one of the largest international networks for discovery of sensitive human data

“Before the EGA, data from a research study were generated once, analysed once, and often ‘locked away’ on the institute’s servers.

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The Federated EGA expands the benefits of data reuse across national borders and increases the value and impact of the data.”

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Mallory Freeberg

EGA Coordinator

at EMBL-EBI

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FEGA – Federated European Genome-phenome Archive�Swedish node in production since Feb 2024

Federation of human genomic data

GDI – European Genomic Data Infrastructure

• 40 MEUR over 4 years (2022–2027) to implement the infrastructure for the European 1+ Million Genomes initiative�(Sweden was one of the first members in 2018)
• 26 European countries, 60+ partners, 500+ people
• NBIS (ELIXIR-SE) together with ELIXIR-FI leads the work to deliver, deploy, operate and maintain the infrastructure and services defined by the 1+MG/B1MG Proof of Concept that will provide the specifications and operational service model for federated national nodes
• Collaboration with GMS (Genomic Medicine Sweden) on the Swedish 1+MG node

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What is GDI setting out to do?

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Support the 1+Million Genomes (1+MG) initiative ambition to enable secure access to high-quality genomics and the corresponding clinical data across Europe for better research, personalised healthcare and health policy making

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Establishing a federated, sustainable and secure infrastructure based on open community standards to access genomic and related phenotypic and clinical data across Europe

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Building on the Beyond 1 Million Genomes (B1MG) project outputs

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Countries’ commitment to GDI by 2026

Fully operational and integrated into 1+MG infrastructure: Belgium, Czech Republic, Denmark, Estonia, Finland, France, Germany, Italy, Luxembourg, Portugal, Slovenia, Spain, Sweden, The Netherlands, Norway�

Fully operational national node but not yet integrated in the 1+MG infrastructure:�Bulgaria, Latvia, Lithuania�

Onboarding:�Croatia, Cyprus, Hungary, Ireland, Malta, Romania

GDI project receives funding from the European Union’s Digital Europe Programme under grant agreement number 101081813.

Current work

Governance model - EDIC

Infrastructure products

Exploring federated learning

Data mgmt policy

Make it work

Make it useful

Make it last

P1

P2

P3

NBIS co-lead

Project coordination: ELIXIR hub

GDI

GDI project receives funding from the European Union’s Digital Europe Programme under grant agreement number 101081813.

Overview of the GDI major components

Data�Discovery

Data Access �Management

Storage & �Interfaces

Data�Reception

Data�Processing

Find applicable datasets based on phenotype

Authenticate yourself

Search mutation and/or phenotype

Apply for data access, �DAC evaluates request, approves

Data made available

Access data

Perform analysis

GDI project receives funding from the European Union’s Digital Europe Programme under grant agreement number 101081813.

Difference between EHDS och 1+MG

• European Health Data Space (EHDS)
• “Health data holders” are actors in healthcare and/or pursuing research with a right to process electronic health data as controller; they have an obligation to
• characterise their data for the national data catalogue
• make electronic health data available on request by the HDAB
• “Health data access bodies” (HDABs) act as permit authorities and review and approve data access requests by users and disclose data in a secure processing environment (SPE)
• 1+MG EDIC as authorised participant of the EHDS
• A data infrastructure does not qualify as any of the above actors
• EDICs and ERICs can join the EHDS as “authorised participant”
• Authorised participants must be able to connect to the HealthData@EU communication infrastructure and fulfil other requirements to be determined in an Implementing Act

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GDI project receives funding from the European Union’s Digital Europe Programme under grant agreement number 101081813.

Comparison between EHDS and 1+MG

EHDS

• Data from all hospitals / labs / research �can be requested
• Data must be extracted each time from the (different) sources
• In case of cross-border access, this happens in parallel in the different countries
• Available data not harmonised
• Federated computing difficult without harmonisation; central SPE as solution
• Subject-level data discovery is impossible

Query

Response

Query

Response

EC SPE

HDAB

HDAB

HDAB

1+MG EDIC Infrastructure

1+MG

• Availability is limited to data brought into the EDIC
• Data are available in a harmonised fashion
• Data can be queried “in situ” and remain in the country
• Subject-level data discovery is possible

GDI project receives funding from the European Union’s Digital Europe Programme under grant agreement number 101081813.

�NBIS is leading WP4 on Data Infrastructure

Anna Hagwall

anna.hagwall@nbis.se, UU

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WP4 lead

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Anna-Lena Ellasdotter

anna-lena.ellasdotter@nbis.se, UU 

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WP4 co-lead

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Funded by the European Union’s Digital Europe Program, Grant agreement #101168231 || Part of 1+MG Initiative

GoE kickoff meeting

30^th-31^st October 2024

Task 1: Identify infrastructure gaps and implement advanced GoE use cases

Identify gaps between GoE needs and GDI infrastructure

• Disseminate information about gaps �among GoE WPs and between GDI and GoE

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Communication partner on advanced use cases

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Susanna Repo and Tuuli Järvinen

Task 2: Data management

Expert network

- Data manager job profile

- Knowledge transfer to other data stewards

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Submit data at GoE partners

- Synthetic 

- Real

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Niclas Jareborg and Karin Granström

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Thank you for your attention!

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Questions? Comments?