The CINECA project, funded by the European Union's Horizon 2020 program, aims to improve disease research and health through transcontinental human data exchange and the promotion of FAIR (Findable, Accessible, Interoperable, Reusable) principles in genomics and healthcare. The project includes a webinar series led by Andrew Stubbs, focusing on the practical implementation of FAIR data management and sharing, with applications in personalized medicine and global genomic data collaboration. The proposed solutions address barriers to data use across healthcare institutions, advocating for reproducible and valid clinical research through innovative tools and collaborative platforms.

1. This project has received funding from the European Union’s Horizon 2020 research and
Innovation programme under grant agreement No. 825775
Practically FAIR
Presenter: Andrew Stubbs (Erasmus Medical Center)
Host: Marta Lloret Llinares (EMBL-EBI)

2. This webinar is being recorded

3. Audience Q&A Session
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4. The challenges:
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informed
@CinecaProject
www.cineca-project.eu
Common Infrastructure for National Cohorts
in Europe, Canada and Africa
This project has received funding from the European Union’s Horizon 2020 research and
Innovation programme under grant agreement No. 825775
Accelerating disease research and
improving health by facilitating
transcontinental human data exchange
The vision:
This project has received funding from the Canadian Institute of Health
Research under grant agreement #404896

5. Context for the webinar
• CINECA “How FAIR are you?” webinar series and hackathon:
• https://www.cineca-project.eu/news-events-all/how-fair-are-you-webinar-series-and-
hackathon
• Webinar series Jan-April
• Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?
• Making cohort data FAIR
• FAIR software tools
• Practically FAIR
• How to make training FAIR
• Ethics/ELSI considerations
• Hackathon 28-29th April 4 hours per day
• 3 streams: cohort data, software, training materials

6. Today’s presenter
Dr Stubbs is an Associate Professor in the Department of Pathology and Clinical Bioinformatics.
The Stubbs group is focused on Artificial Intelligence (AI) in Healthcare, Translational
Bioinformatics and FAIR data management in translational and clinical research. His group
have applied Machine learning to discriminate bacteria from viral infections to reduce the use
of antibiotic treatment (Tailored treatment H2020: cordis.europa.eu/project/id/602860) and
Deep Learning to deliver predictive models form multi-omics experiments to improve patient
stratification in pancreatic cancer patients (Eurostars iKnowIT grant: www.erasmusmc-
rdo.nl/project/iknowit-integrated-knowledge-discovery-it/; Hanarth Fonds: www.erasmusmc-
rdo.nl/project/5702/).
His team are the Dutch lead for the European Galaxy project and have implemented Galaxy servers and services
supporting Cancer research (including and neo-antigen prediction), metagenomics (NanoGalaxy) and for immune
repertoire analysis (ARGalaxy). FAIR data management is a prerequisite for reproducible science and required by all
H2020 projects. To address this requirement we have developed a cloud based FAIR data management and analysis
platform (myFAIR) for use in the Canada-European Big Data Federated analysis (CINECA: www.cineca-project.eu/)
H2020 project.

7. This project has received funding from the European Union’s Horizon 2020 research and
Innovation programme under grant agreement No. 825775
Practically FAIR?
CINECA “How FAIR are you” webinar series #1:
Introduction to FAIR Principles
Andrew Stubbs
a.stubbs@erasmusmc.nl

8. Outline
1. Genomics in Healthcare
2. FAIR Genomics in Healthcare
3. FAIR(-R)
4. Practically FAIR-R.

9. Personalized Medicine
Precision Medicine Informatics: Principles, Prospects, and Challenges. Afzul et al 2019 . arXiv:1911.01014
Percentage of patients for which a
certain drug is ineffective, by therapy
class

10. Genomics in Healthcare

11. Requirements
• Clinical data: anonymous patient data
• Genomics NGS platforms both internal and
external to Hospital
• Genomics Analytical Workflows both
internal and external to Hospital
Genomics Healthcare Data Lifecycle

12. (Gen)-omics Translational Research
Experimental Design Multi-omics Data

13. FAIR Genomics in Healthcare

14. What is FAIR Genomics?

15. What is FAIR Genomics?

16. Genomic Data Management
https://github.com/fairgenomes
What is FAIR Genomes
• Aim to develop a national guideline to
promote optimal (re)use of NGS data in
research and healthcare.
• 61 people from 14 institutes (NL).
• Interacting with EJP-RD CDE, Solve-RD RD3,
1+MG, GA4GH, Phenopackets, X-omics, and
others.

17. Genomic Data Management
https://github.com/fairgenomes

18. Genomic Data Management
https://figshare.com/articles/poster/FAIR_Genomes_Standardizing_a_meta-data_schema_for_FAIRifying_personal_genome_data_workflows/11694693

19. Genomic Data sharing

20. • Beacon Protocol for Genomic Data Sharing
• Beacons provide discovery services for
genomic data using the Beacon API developed
as a key driver project of the Global Alliance
for Genomics and Health (GA4GH).
• The Beacon protocol itself defines an open
standard for genomics data discovery. It
provides a framework for public web services
responding to queries against genomic data
collections, for instance from population
based or disease specific genome
repositories.
Genomic Data sharing
Nature Biotechnology | VOL 37 | MARCH 2019 | 215–226 |

21. Genomic Data sharing

22. Beacon Data Access Control (DAC)
Data Access Phases for Controlled Access

23. Beaconize Hospitals
Benefit : identify if the pathogenic or non-
pathogenic variant was sequenced at
another hospital!
Benefit : The aim is a secure standardized data
sharing without compromising patient confidentiality.

24. FAIR-R

25. Why create FAIR-R analysis?

26. Beyond FAIR is FAIR-R
We would like to be Practically …

27. Beyond FAIR is FAIR-R
We would like to be Practically …
and Reproducible, Replicable, ….

28. Reproducible, Replicable, …

29. • Data Analysis platform
• Web-based
• Easy to use
• Free and Open Source
• Many tools (~8000)
• Popular (>10.000 publications)
• Extensive Training Materials
(training.galaxyproject.org)
Homepage: galaxyproject.org
Galaxy as a solution

30. Multitude of Galaxies

31. • All tools and workflows are publicly accessible via
GitHub
• 6 different types of analysis
• 5 different Galaxy servers - including Galaxy
Australia
• Workflows and tools available on all servers
• Workload shared amongst global clouds and
compute resources
• Reproducible across multiple servers
https://covid19.galaxyproject.org
Galaxy for COVID-research
Adapted from “Viral Beacon and Galaxy variant workflows” , Singh, Grüning & Maier ELIXIR

32. Galaxy integrated with COVID Beacon
Adapted from “Viral Beacon and Galaxy variant workflows” , Singh, Grüning & Maier ELIXIR

33. Galaxy integrated with COVID Beacon
Adapted from “Viral Beacon and Galaxy variant workflows” , Singh, Grüning & Maier ELIXIR

34. FAIR-R Containerized Tools

35. Practically FAIR – Solution 101

36. How to stream data from BEACONS
https://htsget.readthedocs.io/en/latest/

37. Request DAC
AAI DAC access and htsget in Galaxy
1
Login and stream data with htsget Galaxy
2

38. Reproducible Cancer Workflows

39. myFAIR: prototype FAIR-R application

40. In Summary
• The barriers (e.g privacy, security, ..) to the use of FAIR genomes across hospitals
can be addressed using the tools presented today.
• The FAIR-R concept and associated applications are essential for valid clinical and
translational research
• The combination of BEACON, FAIR genomes and Galaxy together provide a simple
framework to deliver FAIR-R services to medical and translational researchers.
• Better practical FAIR-R applications need to developed to improved the uptake by
medical researchers.

41. Erasmus MC
• Saskia Hiltemann
• Helena Rasche
• Willem de Koning
• Jie Ju
• Teodora Trandafir
• David van Zessen
• Yunlei Li
Our fabulous colleagues from CINECA
• Also Marta and Daniel for todays meeting.
Acknowledgements

42. Questions?
Title: Practically FAIR
Presenter: Andrew Stubbs
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questions window of the GoToWebinar
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43. Next CINECA webinars
Title: How to make training FAIR
Presenter: Anna Swan and Sarah Morgan
Date: Thurs 18th March 2021
Time: 3:00 PM GMT / 4:00 PM CET
Registration and details:
https://www.cineca-project.eu/news-
events-all/how-to-make-training-fair
Title: Ethics/ELSI considerations - From
FAIR to fair data sharing
Presenter: Melanie Goisauf
Date: Thurs 15th April 2021
Time: 4:00 PM BST / 5:00 PM CEST
Registration and details:
https://www.cineca-project.eu/news-
events-all/ethics/elsi-considerations