DIBS@BME/JHU

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## Engineering the Future of Medicine:

### Data Intensive Biomedical Science

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Joshua T. Vogelstein
<br>
Dept. Biomedical Engineering
<br>
Kavli Neuroscience Discovery Institute
<br>
Johns Hopkins University

<br>
questions: [jovo@jhu.edu](mailto:jovo at jhu dot edu)
<br>
slides: <http://brainx.io/dibs>

]

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### DIBS vs Data Science

- Opportunities
  - low  vs. high sample size
  - images vs. tables data types
- Challenges
  - Data storage, management, visualization & access
  - Data analysis

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<img src="images/genetics_w355.jpg" style="width: 50%;"/>
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#### Data Intensive Biomedical Science (DIBS)

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### From Cosmos to Connectomes: The Evolution of Data-Intensive Science

- Cosmology (at JHU/IDIES) founded data intensive science
- We extended their framework to support brain sciences
- Brain sciences are more heterogeneous than SDSS

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#### Data Management, Storage, Visualization and Access: [Open Connectome Project](http://neurodata.io)

- 200+ TB (largest)
- 20+ publications/labs (Cell, Nature, Science)
- 9+ species (most diverse)
- many spatiotemporal scales

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### Data Analysis: the "best"....

- [LOL](https://github.com/neurodata/LOL):  linear classifier
- [QOQ](https://github.com/neurodata/LOL):  quadratic classifier
- [RerF](https://github.com/neurodata/R-RerF/):  nonlinear classifier
- [MGC](https://github.com/neurodata/mgc):  independence test
- [FlashMatrix](https://github.com/flashxio/FlashX):  matrix analysis library
- [FlashGraph](https://github.com/flashxio/FlashGraphR):  graph analytics library
- [knor](https://github.com/flashxio/knor):  k-means

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<img src="images/FigHDPower.png" style="width: 60%;"/>
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### Global Leadership

- [1st Global Brain Workshop](http://brainx.io) @ JHU, Spring 2016
  - 60+ scientists, 15+ funders, 12+ countries
  - [Report in Neuron](http://dx.doi.org/10.1016/j.neuron.2016.10.033) (top 5% most popular article)
  - [Science](http://science.sciencemag.org/content/352/6283/277), [NIH](http://www.braininitiative.org/2016/04/22/international-brain-projects-considered/), [MIT Tech Review](https://www.technologyreview.com/s/602274/three-grand-challenges-for-brain-science-that-can-be-solved-in-10-years/), [Nature](http://www.nature.com/news/worldwide-brain-mapping-project-sparks-excitement-and-concern-1.20658) cover it.
- 2nd Global Brain Workshop  @ Rockefeller, Fall 2016
  - 400+ scientists
  - [Report in Cell](http://dx.doi.org/10.1016/j.cell.2017.02.023)
  - [US State Dept Announcement](https://2009-2017.state.gov/r/pa/prs/ps/2016/09/262200.htm)
- [3rd Global Brain Workshop](http://brainx2.io) @ JHU, Summer 2017
- [1st Global Brain Hackathon](http://neuroscience.uchicago.edu/hackathon/) @ MBL, Fall 2017
  - 24 hackers
- Chair of BRAIN/NIH Data Science Core Consortium
- Member of Global Brain Initiatve

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### What's Next

- Globally democratizing science
- Lowering the barrier to entry

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Internal Collaborations:
- BME (Miller)
- AMS (Priebe)
- CS (Burns)
- ChemBE (Schulman)
- Physics (Szalay)
- BioStats (Caffo)
- Neuroscience (Huganir)
- Applied Physics Lab

Industry:
- Google
- Amazon
- [gigantum](http://gigantum.io/)
- [d8alab](https://d8alab.com/)
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External Collaborations:
- Allen Institute (Smith)
- Janelia Research Campus
- Stanford (Deisseroth)
- Harvard (Engert)
- Duke (Sapiro)
- Baylor (Tolias)
- Argonne National Labs (Kasthuri)

Questions?
- [jovo@jhu.edu](mailto:jovo@jhu.edu)
- [neurodata.io](http://neurodata.io)
]

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### Our Work @ BME/JHU

| Agency | Year | RFP |
| :--- | :--- | :--- |
| NIH | 2012 | CRCNS Data Sharing |
| DARPA | 2012|  XDATA
| NSF | 2013|  BigData
| NIH | 2014 | Transformative Research Award
| DARPA | 2015| SIMPLEX
| IARPA | 2016| MICrONS
| NSF | 2016 | EAGER
| NIH | 2017| Data Science Core
| NSF | 2017| NeuroNex
| Schmidt | 2018 | Science

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##### Where Are We Now: Mesoscale Whole Clear Brain

<!-- 200 TB, 20+ publications (Cell, Nature, Science), 20+ labs, 9+ species

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##### Where Are We Now: Nanoscale Brain Connectivity

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##### Where Are We Now: Whole Brain Activity