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<textarea id="source">
class: center, middle
name:opening
## Opportunities and Challenges in Big Data Neuroscience
<br>
.center[
Joshua T. Vogelstein
<br>
<!-- JHU Kavli Neuroscience Discovery Institute -->
{[bme](http://www.bme.jhu.edu/),[icm](http://icm.jhu.edu/),[cis](http://cis.jhu.edu/),[idies](http://idies.jhu.edu/),[kavli](http://kavlijhu.org/),[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/dc-sfn>
<br>
Co-Founder: [NeuroData](http://neurodata.io) & [gigantum](http://gigantum.io)
]
---
## Introductory Comments
<br><br>
- Please interrupt with questions!
- Please come work with us (postdocs & software engineers)!
---
## Outline
- NeuroData Challenges
- Science 2.0
---
class: center, middle
# NeuroData
---
### Challenges
<center>
<img src="images/ndspiral3.png" STYLE="position:absolute; LEFT:150px; WIDTH:600px;"/>
</center>
---
class: center, middle
# Collect
---
<div id="contentframe" style="position:relative; top: 50px; left: -100px;">
<iframe width="900" height="440" src="https://www.youtube.com/embed/1aVNRZtxeIU" frameborder="0" allowfullscreen></iframe>
</div>
---
<div id="contentframe" style="position:relative; top: 0px; left: -100px;">
<iframe width="900" height="700" src="https://www.youtube.com/embed/jziqfFp9Rq0" frameborder="0" allowfullscreen></iframe>
</div>
---
<div id="contentframe" style="position:relative; top: 10px; left: -100px;">
<iframe width="900" height="600" src="https://www.youtube.com/embed/gJdKSxKRtVI" frameborder="0" allowfullscreen></iframe>
</div>
---
<div id="contentframe" style="position:relative; top: 0px; left: -100px;">
<iframe width="900" height="600" src="https://www.youtube.com/embed/CySDbTH46P4" frameborder="0" allowfullscreen></iframe>
</div>
---
<div id="contentframe" style="position:relative; top: 0px; left: -100px;">
<iframe width="900" height="600" src="https://www.youtube.com/embed/c-NMfp13Uug?start=118" frameborder="0" allowfullscreen></iframe>
</div>
---
class: center, middle
# Store
---
### Multiresolution Space Filling Curve
<img src="images/zorderpart.png" STYLE="position:absolute; LEFT:25px; TOP:175px; WIDTH:400px;"/>
<img src="images/reshier.png" STYLE="position:absolute; LEFT:475px; TOP:150px; WIDTH:400px;"/>
---
## Benchmark
<center>
<img src="images/store2.png" STYLE="position:absolute; LEFT:0px; TOP:140px; WIDTH:900px;"/>
</center>
---
<center>
<img src="images/table1.png" STYLE="position:absolute; LEFT:20px; TOP:100px; HEIGHT:500px;"/>
</center>
---
<center>
<img src="images/table2.png" STYLE="position:absolute; LEFT:60px; TOP:100px; HEIGHT:500px;"/>
</center>
---
class: center, middle
# Wrangle
---
<center>
<img src="images/analyze-draft-fig.png" STYLE="position:absolute; LEFT:100px; TOP:0px; HEIGHT:680px;"/>
</center>
---
class: center, middle
# Explore
---
<br><br>
<center>
<img src="images/CLARITY.png" STYLE="position:absolute; TOP:-20px; LEFT:-100px; WIDTH:1200px;"/>
</center>
---
<center>
<img src="images/CLARITY.png" STYLE="position:absolute; TOP:-20px; LEFT:-100px; WIDTH:1200px;"/>
</center>
---
<center>
<img src="images/CLARITYoverlay.png" STYLE="position:absolute; TOP:-20px; LEFT:-100px; WIDTH:1200px;"/>
</center>
---
<center>
<img src="images/CLARITYnative.png" STYLE="position:absolute; TOP:-20px; LEFT:-100px; WIDTH:1200px;"/>
</center>
---
class: center, middle
# Model
---
<center>
<img src="images/table3.png" STYLE="position:absolute; LEFT:0px; TOP:100px; HEIGHT:370px;"/>
</center>
---
<br>
<center><img src="images/rob2.png" style="position:absolute; LEFT:50px; width: 750px; TOP:50px;"/></center>
---
### Challenges
<center>
<img src="images/ndspiral3.png" STYLE="position:absolute; LEFT:150px; WIDTH:600px;"/>
</center>
---
class: center, middle
# Science 2.0
---
## Where are we now?
<br><br>
- Data in the Cloud
- Pipelines in the Cloud
- Science in the Cloud
---
<div>
<a href="http://cloud.neurodata.io/nd/ca/kasthuri11cc/xy/2/2056,2856/3196,3996/2/">
<img src="http://cloud.neurodata.io/nd/ca/kasthuri11cc/xy/2/2056,2856/3196,3996/2/" STYLE="position:absolute; TOP:0px; LEFT:0px; WIDTH:1200px; "/>
<p style="color:white; position:absolute; TOP:50px; LEFT:50px; text-shadow:0px 0px 8px black;">
http://cloud.neurodata.io/nd/ca/kasthuri11cc/xy/2/2056,2856/3296,3896/2/
</p>
</a>
</div>
---
## Data in the Cloud
<br><br><br>
Anybody in the world can:
- [Visualize](http://viz.neurodata.io/project/Fear199/4/250/250/0/)
- [Download](http://cloud.neurodata.io/nd/ca/kasthuri11cc/xy/2/2056,2856/3196,3996/2/) arbitrary subvolumes
But not yet easily
- Reproduce & extend analysis
---
## Pipelines in the Cloud
<a href="http://cortex.jhu.edu/notebooks/sic_ndmg.ipynb">
<img src="images/sic.png" STYLE="position:absolute; TOP:150px; LEFT:0px; WIDTH:910px;"/>
</a>
---
## Pipelines in the Cloud
<br><br>
| Requirement | Implementation |
| :--- :--- |
| Data in Cloud | Amazon S3 bucket |
| Data Spec | BIDS |
| Notebook | Jupyter |
| Virtualization | Docker |
| Deployment | Always up |
| Cloud Computing | Amazon EC2 |
---
## Pipeline in the Cloud
<br><br><br>
Anybody in the world can:
- [Visualize](http://viz.neurodata.io/)
- [Download](http://docs.neurodata.io/ndstore/) arbitrary subvolumes
- [Reproduce and extend](scienceinthe.cloud) analysis
But not yet quite:
- "Continuously integrated"
---
## Science in the Cloud
<br><br>
- Maintain a single "science in the cloud" digital experiment
--
- Make "tests" to perform quality control for new data & analyses
--
- Every new contribution should be tested before integrated
--
- Everything should be able to run locally as well as in the cloud
--
- Easy for anybody else to benefit/contribute
---
## Science in the Cloud
1. Globally democratizes science
2. Accelerates discovery
<img src="images/world.gif" STYLE="position:absolute; TOP:300px; LEFT:0px; WIDTH:910px;"/>
---
# References
<br><br>
- [Science in the Cloud](https://academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/gix013)...arXiv, 2016
- [To the Cloud!](https://doi.org/10.1016/j.neuron.2016.10.033)... Neuron, 2016
- [Cosmos to Connectomes](http://www.sciencedirect.com/science/article/pii/S0896627314007466)...Neuron, 2014
- [Open Connectome Project](https://arxiv.org/abs/1306.3543)...SSDBM, 2013
---
## Acknowledgments
| Role | Person |
| :--- | :--- |
| Data | Bock, Lee, Reid, Kasthuri, Lichtman, Collman, Weiler, Micheva, Smith, Crow, Deisseroth, Bloss, Spruston, Hildebrand, Engert, Harris, Zlatic, Cardona, Wanner |
| Theory | Priebe, Lyzinski, Sussman, Tang, Ketcha, Wang, Fishkind, Durante, Dunson, Chen, Shen, Lindquist, Caffo |
| Computer Vision | Kazhdan, Dyer, Gray Roncal, Kutten, Miller, Hager, Chevillet, Simhal, Patsolic, Saalfeld, Sapiro |
| Computer Science | Zheng, Lillaney, Baden, Manavalan, Mhembere, Perlman, Koutra, Faloutsos, Szalay, Burns |
| Analysis | Kiar, Kleissas, Litt, Wandell, Poldrack, Wiener, Vogelstein |
<img src="images/funding/nsf_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:10px; HEIGHT:100px;"/>
<img src="images/funding/nih_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:120px; HEIGHT:100px;"/>
<img src="images/funding/darpa_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:230px; HEIGHT:100px;"/>
<img src="images/funding/iarpa_fpo.jpg" STYLE="position:absolute; TOP:550px; LEFT:430px; HEIGHT:100px;"/>
<img src="images/funding/kavli_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:550px; HEIGHT:100px;"/>
<img src="images/funding/kndi_fpo.png" STYLE="position:absolute; TOP:550px; LEFT:650px; HEIGHT:100px;"/>
---
class: middle, center
# Questions?
<!-- ### Funding -->
<!-- <br /> -->
<!-- <br>
<br> -->
## Hiring Postdocs & Software Engineers Now!
e: [[email protected]](mailto:[email protected])
w: [neurodata.io](http://neurodata.io), [gigantum.io](http://gigantum.io)
<!-- ____ -->
<!-- [more slides](http://docs.neurodata.io/ndintro/more.html) -->
</textarea>
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