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<!DOCTYPE html>
<html>
<head>
<title>bootcamp</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<link rel="stylesheet" href="fonts/quadon/quadon.css">
<link rel="stylesheet" href="fonts/gentona/gentona.css">
<link rel="stylesheet" href="slides_style2.css">
<script type="text/javascript" src="assets/plotly/plotly-latest.min.js"></script>
<script src="assets/fontawesome.js"></script>
</head>
<body>
<textarea id="source">
<!-- class: middle -->
#### Open Access to the Brain: a Computer "Connectome" Links Brain Images in Fine Detail
<!-- Connectal coding: discovering the structures linking cognitive phenotypes to individual histories -->
Joshua T. Vogelstein
<img src="images/neurodata_purple.png" style="height:450px; float:right;"/>
<br><br><br><br><br><br><br><br><br>
<!-- <img src="images/funding/jhu_bme_blue.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KNDI.png" STYLE="HEIGHT:95px;"/> -->
.footnote[[jovo@jhu.edu](mailto:[email protected]) | <http://neurodata.io/> | [@neuro_data](https://twitter.com/neuro_data)]
<br>
---
class: middle, inverse
# .center[Motivation]
---
# .center[Brains are Beautiful]
<iframe src="https://www.youtube.com/embed/1aVNRZtxeIU?rel=0&autoplay=1" frameborder="0" style="overflow:hidden;overflow-x:hidden;overflow-y:hidden;height:80%;width:100%;position:absolute;left:0px;right:0px;bottom:0px"></iframe>
---
# .center[Brains are Ubiquitous]
<img src="images/multicolor-faces2.jpg" style="position:absolute; top:160px; left:0px; width:100%;"/>
.footnote[source: [Ethnic Origins of Beauty](http://www.lesoriginesdelabeaute.com/en/accueil.html)]
---
# .center[Brains are Ubiquitous]
<img src="images/species.jpg" style="position:absolute; top:160px; right:0px; height:100%;"/>
.footnote[source: [Earth BioGenome Project](https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life)]
---
# .center[Brains are Awesome]
<img src="images/westworld.jpeg" style="position:absolute; top:160px; left:0px; width:100%;"/>
.footnote[source: [hbo](https://www.hbo.com/westworld/season-2/1-journey-into-night/premiere-reactions-roundup)]
---
# .center[Brains are Expensive]
<img src="images/nami-facts.png" style="position:absolute; top:160px; left:0px; width:100%;"/>
.footnote[source: [nami](https://nami.org/Learn-More/Mental-Health-By-the-Numbers)]
---
# .center[Changing the World]
- Democratize intelligences
- Understand intelligences
- Enhance intelligences
<!-- (3 columns), image of the world, westworld guy, einstein with lightbulb, -->
---
class: middle, inverse
# .center[Approach]
---
# .center[Gather the Data]
.pull-left[
- 20+ labs
- 30+ datasets
- 100+ terabytes
]
.pull-left[
- from nano to macro
- worm, fly, mouse, primate, human
- largest and most diverse open repository in brain science
]
<img src="images/neurodata_home.png" style="position:absolute; top:260px; left:150px; height:100%;"/>
<!-- - image of OCP webpage, description of each dataset being > 100 GB, ie, 1 4K movie, an image of a pile of 1000 DVDs -->
---
# .center[Manage the Data]
.pull-left[
- too big for your hard drive
- too big to open in Preview or Photos
- too big to visualize online
]
.pull-right[
- too many files to keep track of
- too expensive to download data
- big data systems
]
<img src="images/High_Performance_Computing_Center_Stuttgart_HLRS_2015_07_Cray_XC40_Hazel_Hen_IO.jpg" style="position:absolute; top:260px; left:0px; width:100%;"/>
.footnote[source: [wikimedia](https://commons.wikimedia.org/wiki/File:High_Performance_Computing_Center_Stuttgart_HLRS_2015_07_Cray_XC40_Hazel_Hen_IO.jpg)]
---
# .center[Process the Data]
.pull-left[
- convert bits to networks
- distributed pipelines
- integrated quality assurance
]
<img src="images/Culture_Matrix_Code_corridor.jpg" style="position:absolute; top:260px; left:0px; height:100%;"/>
.footnote[source: [wired](https://www.wired.com/story/the-matrix-code-sushi-recipe/)]
---
# .center[Model the Data]
.pull-left[
- statistical models of networks
- incorporate uncertainty
- address populations
]
.pull-right[
- develop estimators
- prove theorems
]
<img src="images/brain-cicruit.svg" style="position:absolute; top:260px; left:240px; height:60%;"/>
---
# .center[Analyze the Data]
.pull-left[
- 4 different populations
- dots represent brain regions
- lines represent connections
]
.pull-right[
- each brain is an average over many people
- averages look similar to one another
]
<img src="images/megamean3.png" style="position:absolute; top:300px; left:60px; width:90%;"/>
---
### Differences Between Studies
.pull-left[
- 20 studies of ~100 individuals each
- each line is the difference between a pair of studies
- right to left: small to large differences
]
<img src="images/inverse_batch.png" style="height: 400px;"/>
<!-- - 20 datasets, >3000 individuals -->
<!-- .footnote[https://neurodata.io/ndmg] -->
---
### Differences Between Sexes
.pull-left[
- 20 studies of ~100 individuals each
- each line is the difference between a pair of studies
- right to left: small to large differences
]
.pull-right[
- sex differences are small
- could be due to demographics
- could be due to study artifacts
]
<img src="images/inverse_batch_sex.png" style="height: 400px;"/>
<!-- - 20 datasets, >3000 individuals -->
<!-- - sex effect is smaller than site effect -->
<!-- .footnote[https://neurodata.io/ndmg] -->
---
# .center[Share the Data]
.pull-left[
- 1000+ unique visitors / week
- ~100,000 unique visitors
]
.pull-left[
- 200+ cities
- 130+ countries
- all inhabited continents
]
<img src="images/google-analytics.png" style="position:absolute; bottom:0px; left:130px; width:70%;"/>
---
# .center[Next Steps]
<br>
- Working with Amazon to provide free storage for everyone
- Make software "self-serve" to eliminate the bottleneck of us
- Require more data to pool together
- New AI to harmonize data
- Discover more connections across datasets
---
# .center[Summary]
<br>
- Brains are beautiful
- Brains are ubiquitous
- Brains are awesome
- Brains are circuits
- We build big data systems and machine learning algorithms to make sense of them
- Everyone can access and benefit from this work
---
# .center[References]
<br>
- Open Connectome Project [[1]](https://doi.org/10.1145/2484838.2484870)
- A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data [[2]](https://www.nature.com/articles/s41592-018-0181-1)
- A High-Throughput Pipeline Identifies Robust Connectomes But Troublesome Variability [[3]](https://doi.org/10.1101/188706)
- Discovering and Deciphering Relationships Across Disparate Data Modalities [[4]](https://elifesciences.org/articles/41690)
---
## .center[Acknowledgements]
<!-- ✉ [[email protected]](mailto:[email protected]) | [neurodata.io](https://neurodata.io) | <img src="images/Twitter_Logo_Blue.svg" width="22" height="22" align="top"/> [neuro_data](https://twitter.com/neuro_data)
-->
<div class="small-container">
<img src="faces/cep.png"/>
<div class="centered">Carey Priebe</div>
</div>
<div class="small-container">
<img src="faces/randal.jpg"/>
<div class="centered">Randal Burns</div>
</div>
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<img src="faces/mim.jpg"/>
<div class="centered">Michael Miller</div>
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<div class="centered">Brian Caffo</div>
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<div class="centered">Cencheng Shen</div>
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<div class="centered">Jeremias Sulam</div>
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<div class="centered">Benjamin Falk</div>
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<div class="centered">Youngser Park</div>
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<div class="centered">Eric Perlman</div>
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<img src="faces/kwame.jpg"/>
<div class="centered">Kwame Kutten</div>
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<div class="centered">Shangsi Wang</div>
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<div class="centered">Tyler Tomita</div>
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<div class="centered">Disa Mhembere</div>
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<div class="centered">Eric Bridgeford</div>
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<div class="centered">Vikram Chandrashekhar</div>
</div>
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<img src="faces/pedigo.jpg"/>
<div class="centered">Ben Pedigo</div>
</div>
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<img src="faces/jaewon.jpg"/>
<div class="centered">Jaewon Chung</div>
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<img src="faces/gkiar.jpg"/>
<div class="centered">Greg Kiar</div>
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<div class="centered">Ronak Mehta</div>
</div>
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<div class="centered">Satish Palaniappan</div>
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</div> <span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span>
</div>
<img src="images/funding/nsf_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/nih_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/darpa_fpo.png" STYLE=" HEIGHT:95px;"/>
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<img src="images/funding/KAVLI.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/schmidt.jpg" STYLE="HEIGHT:95px;"/>
<!-- .footnote[<a href="https://neurodata.io/"><img src="images/internet-icon-26.jpg" style="height:32px"/></a>,
<a href="mailto:[email protected]"><i class="fas fa-envelope"></i></a>, <a href="https://bitsandbrains.io/"><i class="fas fa-rss"></i></a>, <a href="https://twitter.com/neuro_data"><i class="fab fa-twitter"></i></a> ] -->
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