Biologically Inspired Model Visualization Capstone Project

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Biologically Inspired Model Visualization
Capstone Project

• Winter Semester 2005
• Mentor Dr. William L. Harrison
• Members Pericles S. Kariotis
• William L. Moore
• Arthur C. Huggard

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Theory

• Domain Specific Languages for Cellular
  Interactions
• w/ Robert W. Harrison
• Bioinformatics
• Domain-Specific Programming Languages Haskell
• Rhodobacter Sphaeroides

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Status Quorum

• Manual!
• Execute Simulation
• Convert POV?Image
• Convert image formats
• Compile Image?Movie
• Fixed Point of View

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The Old System (Ugly)
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Even uglier
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Gentlemen, we can rebuild him. We have the
technology Better than he was before. Better,
stronger, faster.

• What we want
• Automation
• Intuitive Interface
• Floating Camera
• Immediate Results
• Maintain Current Functionality

The Six Million Dollar Man
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Tools of the trade

• C
• OpenGL
• QT
• Many Compilers
• POVRay
• MPlayer
• ImageMagick
• And More

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Primary Contributions

• Pericles
• OpenGL/Qt Simulation Interface
• Billy
• POV-Ray/MEncoder and integration
• Charlie
• CellSys interaction

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Controlling the DSLCellSys

• The DSL is invoked from the GUI application.
• Specify POV file output directory
• Specify the language interpreter
• Specify the DSL program file
• Specify the command to execute

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The Input Module

• Responsible for accepting the data from the DSL
• Currently uses file I/O (inefficient!), but could
  easily be re-written to use a more direct
  communication method
• Other alternatives Haskell FFI, shared memory,
  even stdout

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The OpenGL Simulation

• Simulation save/load
• Interactive camera
• Display boxes
• Timing slider
• Configurable play speed/direction
• Cell shadows (vapor trails)
• Cell tracking (different colors)

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Interface Design
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Encoding an AVI

• New application maintains and automates the
  previous methodology
• Specify a directory of POVs to encode, no further
  interaction is necessary
• Renders images with POV-Ray, instead of OpenGL
• Intrinsically supports anything native to POV

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System Diagram
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Implementation Issues

• Requires many packages
• Integration of pvengine is not seamless
• Further OpenGL support must be built-in
• I/O Module (file I/O is inefficient)
• Platform-specific details
• CellSys DSL
• State sampled with every update
• Information output is sparse
• Bugs "header" file

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Performance

• Actual Frame rates lower than Nominal Frames
  rates
• Frame rate decreases as number of cells increases
• Viewpoint Manipulation and Bounding Box decrease
  performance
• Color Codes and Clipping Box have negligible
  performance delays
• .csm file loads significantly faster than .pov
  files

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Test Results
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Test Results
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Optimizations

• More efficient data structure for frame data
• Display lists to boost OpenGL rendering
  performance
• Less viewpoint sampling
• Cells built with fewer polygons

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Future Work

• Implement additional OpenGL primitives
• Tabbed simulation
• More cell tracking features
• User-driven coloring
• Instant velocity vectors
• Display more information
• Light concentration
• Cell behavior
• Cell reproduction