CS/CAM/BME 395T - #54303
FALL
2005 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
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DATE |
LECTURES |
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August 31 |
Model and Visualize “How Things Work” spanning Organ,
Tissue, Cell, Molecular Scales Producing Effective Bio-Animations |
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September 7 |
Molecular modeling I – atomic resolution models from PDB,
VIPER Multi-grid based molecular surfaces and Docking |
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September 14 |
Molecular modeling II --- 3D EM maps from EBI, structure elucidation Structure-refinement techniques and tools |
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September 21 |
Molecular modeling III --- area/vol
derivatives, energetics, force fields Generalized Born Solvation Energies and Forces |
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September 28 |
Cell modeling I --- segmentation
from 3d EM, free-form deformable models Poisson Boltzmann Solvation Energies and Force Calculations |
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October 5 |
Cell modeling II --- Hydrodynamics, Deformable Organelles Free-form modeling of Molecular and Cell Domains |
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October 12 |
Cell modeling III --- NMJ (putting cells +molecules together) Deformable free-form modeling of Intracellular Domains |
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October 19 |
Tissue modeling I --- Brains, neurons, schwann
cells Filtering, Segmentation and Re-sampling of Multi-modal Imaging |
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October 26 |
Tissue modeling II --- Heart , myocardium, biomechanics Patient Specific Blood Vessel Extraction for Pulmonary Embolus Detection |
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November 2 |
Tissue modeling III – Putting tissue + cells +molecules Effective navigation for Interactive Animation Production |
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November 9 |
Organ modeling I --- Brain anatomy and function models Quality Meshing with Bounded Number of Elements |
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November 16 |
Organ modeling II --- Heart anatomy and function models Match and Fit Techiques for Anatomical Geometry with 3D Imaging |
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November 30 |
Organ modeling III --- Putting together organs +tissues+ cells
+molecules Presentation on multiresolution
modeling + visualization |
Exercises:
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1 |
Constructing and visualizing
computer models from the PDB, VIPER and assignments |
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2 |
Project:
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Presentations
on December 7 |
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1 |
Linking
organelles + molecular models |
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2 |
Linking cells +
organelle models |
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3 |
Linking tissue +
cell models |
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4 |
Linking organs +
tissue models |
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5 |
Modeling Organisms |
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