Talk presented at workhop for Establishing a node for FAIRifying metabolomics and phenomics data in the European Open Science Cloud in Leiden

1. Christoph Steinbeck
and the
PhenoMeNal consortium
European Bioinformatics Institute, Hinxton
Friedrich-Schiller-University, Jena
Large scale computing with medical
metabolic phenotyping data

2. Understanding Phenotypes

3. Reaction times following
external change
• Genetics (decades, centuries…)
• Epigenetics (days, month, years,…)
• Gene Expression (hours)
• Metabolism (seconds)

4. The Metabolome
is the most accessible and
dynamically changing
Molecular Phenotype

5. Untargeted Metabolomics
of Cerebrospinal Fluid
AD – red; MCI- blue
Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN)
AD – red; CN- blue

6. Untargeted Metabolomics
of Cerebrospinal Fluid
AD – red; MCI- blue
Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN)
AD – red; CN- blue
Basis for a
diagnostic tool

7. Metabolomics On The Rise
Source: Google Scholar

8. Phenome Centres popping
up all over the world
• London
• Birmingham
• Shanghai
• NIH RCMRCs
• …

10. > 100,000 patient samples / year
> Several PetaBytes/year
=> ExaBytes of human data at
moderate scale-up

11. Metabolomics On The Rise

12. How do you make sense
of all that data?

13. Make data FAIR
-
Share them
-
Free and Open

14. •500 Million people in European Union
•Full Genomes (soon for less than $1000 p. P.)
•Urine/Blood Metabolome < 20 Euros per Patient

15. Large Scale Computing
with Medical
Metabolomics Data
• EBI lead
• H2020
• 3Years
• 13 Partners
• 8 Mio €
• 830 PM
• Kick-off 9/15
• H2020 e-infra

16. An e-infrastructure for
Large Scale Computing
with Medical
Metabolomics Data

17. Why
Research
Infrastructures?

18. PhenoMeNal Objectives
1. Integrate existing open source tools, resources
into a secure and sustainable e-Infrastructure

19. PhenoMeNal Objectives
2. Operate and consolidate the PhenoMeNal e-
infrastructure based on existing internal and external
HPC (High-performance computing) resources

20. PhenoMeNal Objectives
3. To improve and scale-up tools used within the
infrastructure to cope with very large datasets
4.To establish technology for a water-tight audit trail

21. PhenoMeNal Objectives
5. To establish privacy-protection methods
6.To foster the worldwide adoption of PhenoMeNal
7. To develop a model to ensure sustainability of the
PhenoMeNal network

22. Generic Cloudification

23. Large Scale Computing
with Medical
Metabolomics Data

25. Large Scale Computing
with Medical
Metabolomics Data

26. Networking Activities -EOSC
As part of EOSC and
GO FAIR,
PhenoMeNal helps
building a hub for
verifying
FAIR metabolomics
data

27. Funding and Collaborators
UK Research Councils (BBSRC, MRC)
European Commission

29. Slides on
http://www.slideshare.net/csteinbeck

30. Metabolights-help@ebi.ac.uk
Thank you!