neurostorm

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name:opening

## NeuroStorm

.center[
questions: [jovo@jhu.edu](mailto:jovo at jhu dot edu)
 
slides: <http://brainx.io/neurostorm>
 
working white paper: [link](https://www.overleaf.com/read/zskcqybmpvfh)
]

---

#### A Short History: Global Brain Workshop

- brainx-1: proposed 3 projects & 1 common resource ([arxiv](https://arxiv.org/abs/1608.06548))
    - what makes our brains unique?
    - how does the brain solve complex problems?
    - how can we augment clinical decision making with data
    - neurostorm ([neuron](http://dx.doi.org/10.1016/j.neuron.2016.10.033), top 5% altmetric)

- Lots of press (much to my surprise)
    - [MIT Technology Review](https://www.technologyreview.com/s/602274/three-grand-challenges-for-brain-science-that-can-be-solved-in-10-years/)
    - [Science](http://science.sciencemag.org/content/352/6283/277) & [Nature](http://www.nature.com/news/worldwide-brain-mapping-project-sparks-excitement-and-concern-1.20658)
    - [State Department announces "The International Brain Station"](https://2009-2017.state.gov/r/pa/prs/ps/2016/09/262200.htm)

---

### Where are we now?

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## Science in the Cloud

1. Globally democratizes science
2. Accelerates discovery

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### Where are we now?

- International Brain Lab
- NeuroNex Innovation Awards
- New companies
- I lost greg :(
- here. now.

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### Goals for Next 24 Hours

- **Accelerate Brain Science Discovery in the Cloud**
- Appreciate the progress our community has made so far
- Learn about on-going (funded) related work
- Make plans for immediate next steps to *coordinate* efforts

---

## Tonight

- this overview
- 1 min schpiel's from everybody in room
- discuss group foci for tomorrow over desserts
- potential sessions are: data, infrastructure, explore, model

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## Tomorrow Morning

- 08:00 breakfast
- 08:45 welcome and break into groups
- 09:00 break-out sesssion #1
- 10:20 demo's and 30 min break
- 10:50 break-out session #2
- 12:15 lunch
- 13:15 summary of morning results (5 min per group)

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## Tomorrow Afternoon

- 13:45 break-out sesssion #3
- 15:10 demo's and 30 min break
- 15:40 break-out session #4
- 17:00 wine and refreshments
- 18:00 summary of afternoon results (5 min per group)
- 18:30 wrap up
- 18:45 celebratory working dinner

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### Logistics

- *Moderators*: ~uniform distribution of time per person
- *Rapporteurs*: taking notes
- *M+R*: presenting at lunch and dinner
- Regular participants:
    - encouraged to attend 2 different morning sessions
    - and 1 new afternoon session
- *Funders*: do whatever you want :)
- *Next Gen Leaders*: injenct postive energy & youthful spirit!

---

## Demo's

- Storage & Viz in da Cloud
  - [A dentrite meshed using marching cubes](https://viz-dev.boss.neurodata.io/#!{'layers':{'em':{'type':'image'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/em'}_'meshes':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical'_'segments':['113']}_'smooth':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical_smooth'_'segments':['113']_'visible':false}}_'navigation':{'pose':{'position':{'voxelSize':[2_2_50]_'voxelCoordinates':[4107.341796875_4073.96826171875_97.36589813232422]}}_'zoomFactor':8}_'perspectiveOrientation':[-0.32683029770851135_0.8050894737243652_-0.3860739767551422_0.3097737729549408]_'perspectiveZoom':203.750147310818_'layout':'xy-3d'})
  - [Same thing but smoothed](https://viz-dev.boss.neurodata.io/#!{'layers':{'em':{'type':'image'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/em'}_'meshes':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical'_'segments':['151'_'113'_'129']_'visible':false}_'smooth':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical_smooth'_'segments':['113']}}_'navigation':{'pose':{'position':{'voxelSize':[2_2_50]_'voxelCoordinates':[4107.341796875_4073.96826171875_97.36589813232422]}}_'zoomFactor':8}_'perspectiveOrientation':[-0.755286455154419_0.5536582469940186_0.11311593651771545_0.33196958899497986]_'perspectiveZoom':203.750147310818_'layout':'xy-3d'})
  - [Orthogonal views of some neurons](https://viz-dev.boss.neurodata.io/#!{'layers':{'em':{'type':'image'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/em'}_'meshes':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical'_'segments':['169'_'129'_'214'_'250']}_'smooth':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical_smooth'_'segments':['113']_'visible':false}}_'navigation':{'pose':{'position':{'voxelSize':[2_2_50]_'voxelCoordinates':[4204.427734375_4105.89794921875_134.603759765625]}}_'zoomFactor':8}_'perspectiveOrientation':[-0.2354082614183426_0.4365214705467224_-0.6046097278594971_-0.6232808232307434]_'perspectiveZoom':89.07372238668175_'layout':'4panel'})
  - [Reconstruction near a synapse](https://viz-dev.boss.neurodata.io/#!{'layers':{'em':{'type':'image'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/em'}_'meshes':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical'_'segments':['193'_'105']}_'smooth':{'type':'segmentation'_'source':'boss://https://api.boss.neurodata.io/kharris15/apical/anno?meshurl=https://s3.amazonaws.com&meshpath=meshes.boss.neurodata/harris15/apical_smooth'_'visible':false}}_'navigation':{'pose':{'position':{'voxelSize':[2_2_50]_'voxelCoordinates':[4124.359375_3857.3212890625_118.16165161132812]}}_'zoomFactor':7.470331534224511}_'perspectiveOrientation':[-0.13435348868370056_-0.017281968146562576_0.9906467199325562_-0.016351474449038506]_'perspectiveZoom':65.16015519693725_'layout':'xy-3d'})
  - usr/pword: neurodemo/neurostorm
  - all data from [Harris et al. 2015](https://neurodata.io/data/kharris15)
- Scalabel Machine Learning in da Cloud
  - password 123456
  - [k-means NUMA optimized routines](http://awesomer.cs.jhu.edu:8888/notebooks/Jupyter%20Notebook/knor/knorR.ipynb)
  - [Demo for GMM, LOL and spectral embedding accelerated by FlashX](http://awesomer.cs.jhu.edu:8888/notebooks/Jupyter%20Notebook/brainx2-FlashX-demo.ipynb)
  - [GMM and spectral embedding in R](http://awesomer.cs.jhu.edu:8888/notebooks/Jupyter%20Notebook/brainx2-R-demo.ipynb)
- [sic/ndmg](http://cortex.jhu.edu/notebooks/sic_ndmg.ipynb)
- [fngs](http://cortex.jhu.edu:8062/notebooks/sic_fngs.ipynb)

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## And Beyond

- Hackathon & Data Science Room at OHBM
- Hackathon at MBL in October
- NeuroData booth & hackathon at SfN

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### Deliverables from this workshop

- white paper (possibly with NCBM & [NeuroComp17](https://conferences.discovery.wisc.edu/neurocomp17/))
- it will list, for each participant, achievement & link to resource
- for example, at ODEN, i committed greg to write a draft of the SIC paper (published [here](https://doi.org/10.1093/gigascience/gix013) within 100 days)
- hackathon at MBL will demo functionality and  build on success
- white paper on arxiv by SfN

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### Examples

- NwB + MINC + BIDS?
- CATMAID + Boss?
- Reconstruct in Cloud?
- Docker + Jupyter + Models?
- How to share X kind of data?
- How to publish Y kind of analysis?

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## Acknowledgments

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# Questions?

### Hiring Postdocs & Software Engineers Now!

e: [jovo@jhu.edu](mailto:jovo@jhu.edu)

w: [neurodata.io](http://neurodata.io)