class: center, middle name:opening # NeuroData: ## Enabling Terascale Neuroscience <br><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,[cs](http://engineering.jhu.edu/computer-science/), [ams](http://engineering.jhu.edu/ams/), [neuro](http://neuroscience.jhu.edu/)} | [jhu](https://www.jhu.edu/) --> <br> slides: <http://neurox.io/brain2016> ] --- ## Upward Spiral of Science <img src="images/Fig1d.png" STYLE="position:absolute; TOP:120px; LEFT:100px; WIDTH:700px;"/> --- ## Goals 1. Globally democratize science 2. Accelerate discovery <img src="images/world.gif" STYLE="position:absolute; TOP:300px; LEFT:0px; WIDTH:910px;"/> --- background-image: url(images/to_the_cloud.jpg) <!-- <img src="images/to_the_cloud.jpg" STYLE="position:absolute; TOP:0px; LEFT:0px; WIDTH:1200px; "/> --> ## To the Cloud! <br><br><br> 1. Data 2. Pipelines 3. Science --- ## Data in the Cloud <img src="images/table1.png" STYLE="position:absolute; LEFT:15px; TOP:150px; HEIGHT:500px;"/> --- ## Data in the Cloud <br><br><br> Anybody in the world can: - [Visualize](http://viz.neurodata.io/) - [Download](http://docs.neurodata.io/ndstore/) arbitrary subvolumes --- <a href="http://viz.neurodata.io/project/Fear199/4/250/250/0/"> <img src="images/CLARITY2.png" STYLE="position:absolute; TOP:0px; LEFT:0px; HEIGHT:700px; "/> <p style="color:white; position:absolute; TOP:580px; LEFT:170px; text-shadow:1px 1px 8px #000;"> http://viz.neurodata.io/project/Fear199/4/250/250/0/ </p> </a> --- <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/) - [Download](http://docs.neurodata.io/ndstore/) arbitrary subvolumes But not yet easily - Reproduce & extend analysis --- ## Pipelines in the Cloud <a href="http://scienceinthe.cloud/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 <br><br> | Requirement | Implementation | | :--- :--- | | Data in Cloud | Amazon S3 bucket | | Data Spec | BIDS | | Notebook | Jupyter | | Virtualization | Docker | | Deployment | Always up | | Cloud Computing | Amazon EC2 | | **Continuous Integration** | BrainCI | --- ## 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> - [Open Connectome Project....](https://arxiv.org/abs/1306.3543) SDDBM, 2013 - [Science in the Cloud...](https://arxiv.org/abs/1610.08484) arXiv, 2016 - [To the Cloud!...](http://dx.doi.org/10.1016/j.neuron.2016.10.033) Neuron, 2016 --- ## 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? <br> <br> [jovo@jhu.edu](mailto:jovo@jhu.edu) | [neurodata.io](http://neurodata.io)