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<!DOCTYPE html>
<html>
<head>
<title>DIBS@BME/JHU</title>
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<textarea id="source">
class: center, middle
name:opening
## Engineering the Future of Medicine:
### Data Intensive Biomedical Science
.center[
<img src="images/biomedical-engineering.small.horizontal.white.png" STYLE="HEIGHT:100px;"/>
Joshua T. Vogelstein
<br>
Dept. Biomedical Engineering
<br>
Kavli Neuroscience Discovery Institute
<br>
Johns Hopkins University
<!-- {[bme](http://www.bme.jhu.edu/),[icm](http://icm.jhu.edu/),[cis](http://cis.jhu.edu/),[idies](http://idies.jhu.edu/),kavli,[cs](http://engineering.jhu.edu/computer-science/), [ams](http://engineering.jhu.edu/ams/), [neuro](http://neuroscience.jhu.edu/)} | [jhu](https://www.jhu.edu/) -->
<br>
questions: [[email protected]](mailto:jovo at jhu dot edu)
<br>
slides: <http://brainx.io/dibs>
]
---
### DIBS vs Data Science
- Opportunities
- low vs. high sample size
- images vs. tables data types
- Challenges
- Data storage, management, visualization & access
- Data analysis
.center[
<img src="images/genetics_w355.jpg" style="width: 50%;"/>
]
---
#### Data Intensive Biomedical Science (DIBS)
<iframe width="700" height="500" src="https://www.youtube.com/embed/c-NMfp13Uug?autoplay=1&loop=1&start=110&end=221" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
---
class: center, middle
<img src="images/sejnowski.jpg" style="width: 100%;"/>
---
### 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
<img src="images/sdss.png" style="width: 100%;"/>
---
#### 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
<img src="images/OCPaper.png" style="position:absolute; bottom:20px; right:300px; width: 40%;"/>
---
### 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
.center[
<img src="images/FigHDPower.png" style="width: 60%;"/>
]
---
### 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
---
### What's Next
- Globally democratizing science
- Lowering the barrier to entry
<img src="images/world.gif" STYLE="position:absolute; TOP:300px; LEFT:400px; WIDTH:500px;"/>
<img src="images/lion-one.JPG" style="position:absolute; top:250px; left:100px; width:25%;"/>
---
class: top, left
.pull-left[
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/)
]
.pull-left[
External Collaborations:
- Allen Institute (Smith)
- Janelia Research Campus
- Stanford (Deisseroth)
- Harvard (Engert)
- Duke (Sapiro)
- Baylor (Tolias)
- Argonne National Labs (Kasthuri)
Questions?
- [[email protected]](mailto:[email protected])
- [neurodata.io](http://neurodata.io)
]
<!-- ### Funding -->
<!-- <img src="images/lion3.jpg" STYLE="position:absolute; TOP:200px; LEFT:0px; WIDTH:400px;"/> -->
<!--
<br>
<br>
<br>
-->
<img src="images/funding/nsf_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:10px; HEIGHT:100px;"/>
<img src="http://brainx.io/images/funding/nih_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:120px; HEIGHT:100px;"/>
<img src="http://brainx.io/images/funding/darpa_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:230px; HEIGHT:100px;"/>
<img src="http://brainx.io/images/funding/iarpa_fpo.jpg" STYLE="position:absolute; TOP:550px; LEFT:430px; HEIGHT:100px;"/>
<img src="http://brainx.io/images/funding/kavli_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:550px; HEIGHT:100px;"/>
<img src="http://brainx.io/images/funding/kndi_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:650px; HEIGHT:100px;"/>
---
### 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
---
##### Where Are We Now: Mesoscale Whole Clear Brain
<iframe width="700" height="550" src="https://www.youtube.com/embed/c-NMfp13Uug?autoplay=1&start=110&end=221&loop=1" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
<!-- 200 TB, 20+ publications (Cell, Nature, Science), 20+ labs, 9+ species
<img src="images/table1b.png" style="width: 70%;"/> -->
---
##### Where Are We Now: Nanoscale Brain Connectivity
<iframe width="700" height="550" src="https://www.youtube.com/embed/nvXuq9jRWKE?autoplay=1&start=70&end=101&loop=1" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
---
##### Where Are We Now: Whole Brain Activity
<iframe width="700" height="550" src="https://www.youtube.com/embed/U_NvQ2g6dGc?autoplay=1&loop=1" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
<!-- background-image: url("images/OCPaper.png")
background-size: contain;
-->
<!-- <img src="images/OCPaper.png" style="width: 100%;"/> -->
</textarea>
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