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AnimatLab: A Toolkit for Analysis and Simulation of the Neural Control of Behavior

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SURA Cyberinfrastructure Workshop: Life Sciences and the Grid AnimatLab: A Toolkit for Analysis and Simulation of the Neural Control of Behavior – PowerPoint PPT presentation

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Title: AnimatLab: A Toolkit for Analysis and Simulation of the Neural Control of Behavior


1
AnimatLab A Toolkit for Analysis and Simulation
of the Neural Control of Behavior
SURA Cyberinfrastructure Workshop Life Sciences
and the Grid
  • Ying Zhu
  • Department of Computer Science
  • Georgia State University

2
My Research Background
  • Extensive experience on real-time 3D graphics,
    visual simulation, and medical visualization
  • Recent projects
  • 3D visualization and simulation for neuroscience
  • Collaborative virtual environment for molecular
    modeling

3
Outline
  • What is AnimatLab?
  • Why build AnimatLab?
  • Modeling and simulation of crayfish escape
    behavior
  • The next generation AnimatLab and the Grid
  • Summary

4
What is AnimatLab?
  • A 3D computer graphics environment for
    neurobiologists to visualize and test
    computational models of neurons, neural circuits,
    sensors, and muscles, and their control of a
    model animals behavior in a physically realistic
    virtual world
  • Animat artificial animals, including physical
    robots and virtual simulations

5
AnimtLab Interface
6
System Architecture
7
Neural (Behavior) Editor
8
3D Body Editor
9
Sensory Receptor
10
Simulation
11
Data Display
12
How does AnimatLab work?
13
Why build AnimatLab?
  • A central goal of neuroscience is to understand
    how the nervous system is organized to control
    behavior
  • This control must be dynamic and depend on a
    constant dialog between sensory input, including
    feedback, and motor commands

14
Why build AnimatLab?
  • This important dynamic relationship between
    nervous function and behavior is poorly
    understood because of technical limitations to
    record neural activity in freely behaving animals
  • Currently it is only possible to record from
    central neurons in restrained or anesthetized
    animals

15
Why build AnimatLab?
  • AnimatLab can help formalize and evaluate
    hypotheses about the neural and physical
    mechanisms for dynamic control of behavior by
    simulating freely behaving animals

16
Related Works
  • AnimatLab and other computational neuroscience
    tools (e.g. NEURON and GENESIS)
  • AnimatLab and computational neuroethology
  • AnimatLab and biorobots

17
Related Works
  • Other computational simulationsof animal
    behavior exist
  • But they were built for a specificanimal
  • AnimatLab is a general purposetoolkit

18
Crayfish Escape Behavior
  • The neural circuits of crayfish escape are among
    the best understood neural circuits in any
    animal, and for 60 years have provided a model
    for sensorimotor integration

19
Crayfish Escape Behavior
20
Create a 3D Crayfish Model
21
Simulation of Crayfish Escape
22
The Result
  • We were able to use AnimatLab to simulate the
    fast abdominal flexion that evokes an upward
    directed movement of the model crayfish
  • But the subsequent abdominal re-extension and
    swimming are ineffective
  • The challenges
  • Need more detailed neural model
  • Need more sophisticated muscle simulation
  • Need more realistic crayfish body parts
  • Some important circuit elements may not have been
    identified

23
Next Generation AnimatLab
  • A more powerful and extensible neural simulator
  • A more extensible and transparent physics
    simulator architecture
  • A more sophisticated muscle simulator

24
Next Generation AnimatLab
  • An improved hydrodynamic simulator
  • A better 3D body editor
  • Optimization for new computer hardware

25
AnimtLab and the Grid
  • Grid computing can
  • provide the ability to search through vast
    parameter spaces such as various muscle
    parameters
  • allow the user to evolve the neural network, the
    body of the organism, or both at the same time in
    order to meet some desired goal

26
AnimatLab and the Grid
  • The grid would allow us to perform the search in
    a parrallel fashion on thousands of computers
    simultaniously.
  • This vastly decreases the time it takes to
    perform such an evaluation.

27
AnimatLab and the Grid
  • Grid services will be implemented as a plug-in
    for AnimatLab with four components
  • search algorithm
  • population generator
  • grid manager
  • visualization tools

28
Grid Computing at GSU
  • GSU is deploying 1000 United Devices license
    across the campus
  • We are working closely with Art Vandenbergs
    group to take full advantage of this resource as
    well as SURAgrid

29
Summary
  • We have been developing AnimatLab for 2 years
  • Version 1.0 is expected to be released in the
    next six months for evaluation and user feedback
  • Version 2.0 will be our focus for the next 3 5
    years
  • Interest among neuroscientists is high
  • AnimatLab will be a useful toolkit for
    computational neuroscience

30
The Team
  • PI Donald H. Edwards
  • Professor of Biology
  • Director of GSU Brains Behavior Program
  • Co-PI Ying Zhu (Computer Science) and Gennady
    Cymbalyuk (Physics)
  • Collaborators William Heitler (University of St.
    Andrews, UK) and Andrei Olifer (Emory University)
  • PhD students David Cofer, James Reid

31
Sponsors
  • Preliminary work has been funded by
  • NIH P20-GM065762
  • GSU Brains Behavior Program
  • A grant proposal was submitted to NSF
    Collaborative Research in Computational
    Neuroscience (CRCNS) in January 2006

32
Thank you!
  • Questions?
  • yzhu_at_cs.gsu.edu (Ying Zhu)
  • or
  • biodhe_at_langate.gsu.edu (Don Edwards)
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