CS/CAM/BME 395T - #56630,#66537
FALL
2006 Wed 2:00 – 5:00pm BUR 116
Multi-scale
Bio-Modeling and Visualization
Picture is from [5] under suggested reading
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Name |
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Office |
ACES 2.324 |
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Phone |
512-471-8870 |
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Office hours |
By appt. via robert@ices.utexas.edu |
CS 395T Course Outline
Biomedical modeling and visualization has roots in
medical illustration and communication for the health sciences, with branches
of application to mathematical modeling and computer simulation of artificial
life. In this course we shall emphasize computational image processing, and
modeling algorithms with emphasis on spatial realism, and the programmatic use
of simulation and visualization to quantitatively depict "how things
work" at the molecular, cellular, tissue, and organ level scales.
Computational methods shall include multi-scale geometry representations, image
filtering, contrast enhancement, segmentation, fusion, boundary and finite
element meshing, spline interpolants
and approximants and, their use in integral and differential equation solving, quadrature and cubature formulas, volumetric contouring,
volumetric rendering, volumetric texture-based image and geometry composition,
combinatorial, topological and integral/differential metric quantitation.
Practical exercises on computational domain and physiological modeling and visualization at multiple
scales, shall be drawn from cardiology (heart, cardiac tissue, myocytes,ion-channels), and
neurology (brain, spinal cord, neurons, Schwann
cells, neurotransmitters), and their interactions (synaptic transmission at the neuro-muscular
junction).
Grading
You will be graded on the successful completion and presentation of the assigned project.
There shall also be two reports due:
- a mid-semester report on the project
- and a final report (and additionally a demo), summarizing results obtained and lessons learned
Lectures
Exercises:
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1 |
Constructing and visualizing computer models from the PDB, VIPER and
assignments |
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2 |
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1 |
Molecular Modeling, Drug Binding, with TexMol
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2 |
Multiscale Molecular & Cell Electrostatics Models with LBIE-Mol
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3 |
Multiscale Isotropic & Anisotropic Diffusion
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4 |
Multiscale Drift & Diffusion Phenomena
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5 |
Stokesian Flows & Deformable Bio-Modeling with Tile Tools
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6 |
Acoustic Scattering, Sound Localization with Prism
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Subsequent
meetings shall also include discussions of assigned projects respectively. We
shall discuss algorithms, data structures and system level issues pertaining to
the projects.
Pictures and Animations
Suggested
1. Data Visualization Techniques, ed. C. Bajaj, John Wiley, 1999
2. Finite Element Methods with B-splines, K. Hollig, SIAM Frontier
in App. Math., 2003
3. BioNanoTechnology, Lessons from Nature, D. Goodsell, Wiley-Liss, Inc, 2004
4. On Growth and Form, D’Arcy Thompson,
5. Brain, Mind, and Behavior, F. Bloom, A. Lazerson, W. H. Freeman and Company,1999
6. Biomechanics, Y. Fung,
Springer Verlag, 1993
7. Immunology, R. Coico,
G. Sunshine, E. Benjamini, John Wiley, 2003
8. Viruses and Human Disease, J. Strauss, E.
Strauss, Academic Press, 2002
9. Structural Aspects of Protein Synthesis,
A. Liljas, World Scientific, 2004
10.
Introduction
to Protein Structure, C. Branden & J. Tooze,
11.
Geometric Modeling and
Quantitative Visualization of Virus Ultrastructure
, C. Bajaj, 2005
12.
Geometric Processing of Reconstructed 3D Maps of Molecular
Complexes, C. Bajaj & Z. Yu, 2005
Links