Keynote as Supercomputing 15, New Orleans, November 20, 2015. Goal: to engage the HPC community in the work of the NIH.

1. Meeting the Computational
Challenges Associated with Human
Health
Philip E. Bourne, PhD
Associate Director for Data Science
National Institutes Health
SC14 New Orleans
November 20, 2014

2. We have come a long way in just one
researcher’s career

4. We Have Both Been Very Successful
World Climate Report 2011
http://www.cnet.com/news/china-unseats-u-s-in-supercomputer-ranking/

5. We Have Both Been Very Successful
World Climate Report 2011
http://www.cnet.com/news/china-unseats-u-s-in-supercomputer-ranking/

6. SDSC Abbreviated Timeline
1985 1990 1995 2000 2005 2010
Cray-XMP48
220 Mflops
Cray C90
5 Gflops
Cray T3E
1 Tflops
http://www.sdsc.edu/News%20Items/PR101510_25years.html

7. .. But There is Much to Do
 Number of drugs is:
– Too few
– Too Long to get to market
– Not personalized
 Rare diseases are ignored
 Clinical trials are too limited in the number of patients
too expensive and not retroactive
 Education & training does not match well to current
market needs
 Research is not cost effective
– Not easily replicated
– Too slow to disseminate
 …..

8. .. And there is much ferment in
research ..
http://fora.tv/2012/04/20/Congress_Unplugged_
Phil_Bourne

9. .. and healthcare systems
http://www.genomicsengland.co.uk/the-100000-genomes-project/

10. But we can see the promise and much
of that promise is driven by the data
revolution

11. The NIH Fire Hose Slide

12. An Example of That Promise:
Comorbidity Network for 6.2M Danes
Over 14.9 Years
Jensen et al 2014 Nat Comm 5:4022

13. What is the NIH Doing to Fulfill
That Promise?

14. ADDS Mission
Statement
To foster an open ecosystem that
enables biomedical* research to be
conducted as a digital enterprise that
enhances health, lengthens life and
reduces illness and disability
* Includes biological, biomedical, behavioral, social,
environmental, and clinical studies that relate to understanding
health and disease.

15. Elements of The Ecosystem
Community Policy
Infrastructure
• Sustainability
• Collaboration
• Training

16. Elements of The Ecosystem
Community Policy
Infrastructure
• Sustainability
Collaboration
• Training
Virtuous
Research
Cycle

17. Policies – Now & Forthcoming
 Data Sharing
– Genomic data sharing announced
– Data sharing plans on all research awards
– Data sharing plan enforcement
• Machine readable plan
• Repository requirements to include grant numbers
http://www.nih.gov/news/health/aug2014/od-27.htm

18. Policies - Forthcoming
 Data Citation
– Goal: legitimize data as a form of scholarship
– Process:
• Machine readable standard for data citation (done)
• Endorsement of data citation for inclusion in NIH bib
sketch, grants, reports, etc.
• Example formats for human readable data citations
• Slowly work into NLM/NCBI workflow

19. Infrastructure - The
BD2K
Center
Commons
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
DDICC
Software
Standard
s
Labs
Labs
Labs
Labs

20. What is the Commons?
 A Conceptual Framework for sharing and
being FAIR:
– Finding
– Accessing
– Integrating,
– Reusing
 digital research objects with attribution
 The Commons is agnostic of computing platform

21. The Commons
Digital Objects
(with UIDs)
Search
(indexed metadata)
Computing
Platform
The Commons

22. The Commons
Digital Objects
(with UIDs)
Search
(indexed metadata)
Computing
Platform
The Commons

23. The Commons: Compute Platforms
The Commons
Conceptual Framework
Public Cloud
Platforms
Super Computing
(HPC) Platforms
Other
Platforms ?
 Google, AWS (Amazon)
 Microsoft (Azure), IBM,
other?
 In house compute
solutions
 Private clouds, HPC
– Pharma
– The Broad
– Bionimbus
 Low access by NIH PIs
 Super Computing 2014
 ADDS coordinating
meeting with SC centers
 NERSC “Commons Pilot”

24. The Commons
Digital Objects
(with UIDs)
Search
(indexed metadata)
Computing
Platform
The Commons

25. The Commons:
Research Objects APIs and Search
The Commons
Conceptual Framework
Public Cloud
Platforms
 Research Object IDs under discussion by the community
– BD2K centers, NCI Cloud pilots (Google & AWS supported)
– Large Public Data Sets, MODs
 Search
– BD2K Data and Software Discovery Indices
– Google Search functions
 Appropriate APIs being developed by the community eg
GA4GH
 Use cases

26. The Commons:
Next Steps
The Commons
Conceptual Framework
 Next Steps
– Currently identifying pilot projects
Public Cloud
Platforms
 Interested speak with Vivien Bonazzi

27. Commons – Simple Implementation
Stack
App
Store
AAPPIIss App
Store
Biomedical Data
Biomedical Data
Software
Software
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28. The Commons:
Business Model
[George Komatsoulis]

29. Community: Training
Data Science Training Goals
1) Build an OPEN digital framework for data
science training:
NIH Data Science Workforce Development Center
1) Develop short-term training opportunities:
Courses, educational resources, etc.
1) Develop the discipline of biomedical data
science and support cross-training – OPEN
courseware
All goals have a diversity component and manate

30. What Is Needed? – Some Examples
from Across the ICs
 Homogenization of disparate large unstructured
datasets
 Deriving structure from unstructured data
 Feature mapping and comparison from image data
 Visualization and analysis of multi-dimensional
phenotypic datasets
 Causal modeling of large scale dynamic networks
and subsequent discovery
 Utilize data that are sparsely and irregularly sampled
and noisy
BD2K can offer reference datasets and points of
domain expertise to explore these questions

31. Potential Outcomes
 Mobility: improve the outcomes of surgeries in
children with cerebral palsy and gait pathology
 Wellness: markers derived from constantly monitored
eHealth/mobile health devices – apply to smoking
cessation, weight loss
 Cancer: further personalization of treatment
 Mental Health: better identify factors that resist and
promote brain disease e.g., schizophrenia, bipolar
disorder, major depression, attention deficit
hyperactivity disorder (ADHD), obsessive compulsive
disorder (OCD), autism
 Addiction: utilizing social media to track and treat
drug use and addiction

32. In Summary
CIA World Fact Book

33. Associate Director for Data Science
Scientific Data Council External Advisory Board
Programmatic Theme
Sustainability Education Innovation Process
Deliverable
Commons Training
BD2K Efficiency
Example Features • IC’s
• Cloud – Data &
Compute
• Search
• Security
• Reproducibility
Standards
• App Store
• Coordinate
• Hands-on
• Syllabus
• MOOCs
• Community
• Centers
• Training Grants
• Catalogs
• Standards
• Analysis
• Data
Resource
Support
• Metrics
• Best
Practices
• Evaluation
• Portfolio
Analysis
Collaboration
Partnerships
• Researchers
• Federal
Agencies
• International
Partners
• Computer
Scientists
The Biomedical Research Digital Enterprise

34. NNIIHH……
philip.bourne@nih.gov
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