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

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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

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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

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Outline

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

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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

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AnimtLab Interface
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System Architecture
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Neural (Behavior) Editor
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3D Body Editor
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Sensory Receptor
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Simulation
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Data Display
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How does AnimatLab work?
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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

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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

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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

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Related Works

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

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Related Works

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

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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

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Crayfish Escape Behavior
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Create a 3D Crayfish Model
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Simulation of Crayfish Escape
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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

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Next Generation AnimatLab

• A more powerful and extensible neural simulator
• A more extensible and transparent physics
  simulator architecture
• A more sophisticated muscle simulator

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Next Generation AnimatLab

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

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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

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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.

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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

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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

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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

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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

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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

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Thank you!

• Questions?
• yzhu_at_cs.gsu.edu (Ying Zhu)
• or
• biodhe_at_langate.gsu.edu (Don Edwards)