NeoCortical Repository NeoCortical Repository and Reports: and Reports:

Database and Reports for NCSDatabase and Reports for NCSEdson O. Almachar, Alexander M. Falconi, Katie A. GilgenEdson O. Almachar, Alexander M. Falconi, Katie A. Gilgen, ,

Devyani Tanna, Nathan M. Jordan, Roger V. Hoang, Devyani Tanna, Nathan M. Jordan, Roger V. Hoang, Sergiu M. Dascalu, Laurence C. Jayet Bray, Frederick C Harris, Jr.Sergiu M. Dascalu, Laurence C. Jayet Bray, Frederick C Harris, Jr.

Brain Computation LabBrain Computation LabDepartment of Computer Science and EngineeringDepartment of Computer Science and Engineering

University of Nevada, RenoUniversity of Nevada, Reno

OutlineOutline

IntroductionIntroduction BackgroundBackground Design OverviewDesign Overview Conclusion and Future WorkConclusion and Future Work

Human BrainHuman Brain

Neurons : ~ 8.6 x 10^10 (86 Billion)Neurons : ~ 8.6 x 10^10 (86 Billion) Synapses: ~ 1x 10^14 (100 Trillion)Synapses: ~ 1x 10^14 (100 Trillion)

Brain BackgroundBrain Background

NeuronNeuron ( C ) - cell that ( C ) - cell that uses electrical signals to uses electrical signals to send information, as send information, as well as process it well as process it

AxonAxon ( A) - the nerve ( A) - the nerve fiber that a neuron’s fiber that a neuron’s electric pulse flows electric pulse flows throughthrough

Brain BackgroundBrain Background

SynapseSynapse - the transmission of - the transmission of information from one neuron information from one neuron to another to another

Network Network - a computational - a computational model of a cluster of neurons model of a cluster of neurons sending information sending information

Neural SimulatorsNeural Simulators

Allow users to create systems of neurons with Allow users to create systems of neurons with parameterized cell data and connection parameterized cell data and connection informationinformation

Simulate brain activity using biological and Simulate brain activity using biological and mathematical modelsmathematical models

Build a foundation for more research on the Build a foundation for more research on the processes of the brainprocesses of the brain

Levels of Organization of Levels of Organization of ModelingModeling

What is NCS?What is NCS? Developed and maintained by the UNR Brain Developed and maintained by the UNR Brain

Computation Laboratory Computation Laboratory The NeoCortical Simulator is designed for The NeoCortical Simulator is designed for

modeling large-scale neural networks and systemsmodeling large-scale neural networks and systems Can model millions of neurons in real timeCan model millions of neurons in real time

Open sourceOpen source Runs on a heterogeneous cluster of CPUs and Runs on a heterogeneous cluster of CPUs and

NVIDIA GPUsNVIDIA GPUs First simulator to support real-time neurorobotics First simulator to support real-time neurorobotics

applicationapplication

Building Better SolutionsBuilding Better Solutions

Users are usually researchers in the Users are usually researchers in the nneuroscienceeuroscience field. field.

User Inconveniences for Neural SimulatorsUser Inconveniences for Neural Simulators Learning to code brain modelsLearning to code brain models Time spent organizing output dataTime spent organizing output data Generally Low UsabilityGenerally Low Usability

Building Better SolutionsBuilding Better Solutions

Building Better SolutionsBuilding Better Solutions

The Primary UsersThe Primary Users NeuroscientistsNeuroscientists

The Primary UsageThe Primary Usage ResearchResearch

Design GoalsDesign Goals SimplicitySimplicity UsabilityUsability LearnabilityLearnability Easy CollaborationEasy Collaboration FastFast

Brain Model Database DesignBrain Model Database Design

Three Neuron Model TypesThree Neuron Model Types Izhikevich, Leaky-Integrate-And-Fire, Hodgkin Izhikevich, Leaky-Integrate-And-Fire, Hodgkin

HuxleyHuxley Necessary CapabilitiesNecessary Capabilities

Storage, Searching, UpdatingStorage, Searching, Updating Storage StructureStorage Structure

JSON format, Using MongoKitJSON format, Using MongoKit

Brain Model Database DesignBrain Model Database Design

Reports DesignReports Design

Graph Types Graph Types Raster Plot, Line Graph Raster Plot, Line Graph

Understandable Real Time Reporting Understandable Real Time Reporting CustomizationCustomization

Color, Size, Type, Neuron Selection Color, Size, Type, Neuron Selection Ability to Easily Save ReportsAbility to Easily Save Reports

FrameworkFramework

FLASK : python microframework FLASK : python microframework MongoDB : nonrelational database MongoDB : nonrelational database D3.Js : Graphing Library D3.Js : Graphing Library jQueryUI.JS : javascript UI libraryjQueryUI.JS : javascript UI library

NCR Database GoalsNCR Database Goals

Increased CollaborationIncreased Collaboration Simple LayoutSimple Layout Easy SearchingEasy Searching

Database Tab ComponentsDatabase Tab Components

Database Model Preview Headers Database Model Preview Headers Sorting Feature for Quick Searching Sorting Feature for Quick Searching Listed in Ascending or Descending Order Listed in Ascending or Descending Order Simple Preview InformationSimple Preview Information

Database Tab ComponentsDatabase Tab Components

Left Search Panel Left Search Panel Collapsable Grouping Structure Collapsable Grouping Structure Can Select Entire Types Can Select Entire Types Specify Parameter Values Specify Parameter Values

As Value or Range of ValuesAs Value or Range of Values

Database TabDatabase Tab

Database Tab ComponentsDatabase Tab Components

Detailed View Detailed View Opens when model preview is selectedOpens when model preview is selected

Report Tab GoalsReport Tab Goals

Management Control PanelManagement Control Panel Dynamic Creation & DeletionDynamic Creation & Deletion Ability to Save ReportsAbility to Save Reports

Reports Tab ComponentsReports Tab Components

Raster PlotsRaster Plots

Reports Tab ComponentsReports Tab Components

Line GraphsLine Graphs

Reports Tab ComponentsReports Tab Components

CustomizationsCustomizations Color PickerColor Picker Drag and DropDrag and Drop Scale AxisScale Axis

Reports Tab ComponentsReports Tab Components

CustomizationsCustomizations Cell SelectionCell Selection Pause and Pause and

PlaybackPlayback

Reports Tab ComponentsReports Tab Components

Saving Reports Saving Reports Image: GIF or SVG Image: GIF or SVG Animation: Animated GIFAnimation: Animated GIF

ConclusionConclusion

Web Application aims to make using NCS Web Application aims to make using NCS easy, Leading to more time spent on researcheasy, Leading to more time spent on research

Future WorkFuture Work Complete full front end application by Complete full front end application by

merging NCB with NCR and Virtual Robotmerging NCB with NCR and Virtual Robot NCBNCB

Brain BuilderBrain Builder Simulation BuilderSimulation Builder

NCRNCR Reports Reports Model DatabaseModel Database Virtual RobotVirtual Robot

NeoCortical Repository and NeoCortical Repository and Reports: Reports:

Database and Reports for NCSDatabase and Reports for NCSEdson O. Almachar, Alexander M. Falconi, Katie A. GilgenEdson O. Almachar, Alexander M. Falconi, Katie A. Gilgen, ,

Devyani Tanna, Nathan M. Jordan, Roger V. Hoang, Devyani Tanna, Nathan M. Jordan, Roger V. Hoang, Sergiu M. Dascalu, Laurence C. Jayet Bray, Frederick C Harris, Jr.Sergiu M. Dascalu, Laurence C. Jayet Bray, Frederick C Harris, Jr.

Brain Computation LabBrain Computation LabDepartment of Computer Science and EngineeringDepartment of Computer Science and Engineering

University of Nevada, RenoUniversity of Nevada, Reno

30

Hodgkin-Huxley Neurons Hodgkin-Huxley Neurons (Added in NCS 7.0)(Added in NCS 7.0)

Biologically accurateBiologically accurate Developed in 1952 by Alan Developed in 1952 by Alan

Hodgkin and Andrew Huxley Hodgkin and Andrew Huxley from their experiments on the from their experiments on the giant axon of a squidgiant axon of a squid

Set of four differential Set of four differential equationsequations

Three variables n, m, hThree variables n, m, h

Hodgkin-Huxley (cont)Hodgkin-Huxley (cont)

Leaky Integrate-and-FireLeaky Integrate-and-Fire Comprised ofComprised of

Sub-threshold leaky-integrator dynamicSub-threshold leaky-integrator dynamic Firing thresholdFiring threshold Reset mechanismReset mechanism

Leakage ChannelsLeakage Channels Drive the neuron to higher Drive the neuron to higher

voltagevoltage Let the voltage decay to its Let the voltage decay to its

resting potentialresting potential

IzhikevichIzhikevich

Created by Eugene M. IzhikevichCreated by Eugene M. Izhikevich Published in 2003Published in 2003 Most SimplisticMost Simplistic Computationally efficient and captures large Computationally efficient and captures large

variety of response properties of real neuronsvariety of response properties of real neurons Only 6 variables!Only 6 variables!

Image Source: http://www.izhikevich.org/publications/spikes.htm

Izhikevich (Added in NCS 6.0)Izhikevich (Added in NCS 6.0)

Izhikevich OutputIzhikevich Output