[Bioclusters] Bio-Viz: Porous-Solid Geometry

Nathaniel Bobbitt flautabaja at hotmail.com
Tue Apr 25 11:12:41 EDT 2006

Hi Scooter,

I agree with your point on Perl/Python. I keep trying not to skip important 
steps. Like the system of external representation.  I take this approach to 
look at visualization as a problem of measurement (drawing vs. packing) and 
relationship extraction not a display of known data relationships and levels 
of protein structure. The issue I see in terms of the external 
representation and the approach to graph within a visual language framework, 
multiphysics (Weinan), and geometric motives (Hales).

I am revisiting diagramming as the old school sentence diagram technique and 
the spatial organization of mechanical drawing. The engine in my technique 
uses physical behaviors that help to mark intensities of difference within 
the display tool itself.

We have seen in computer graphics the advent of 3-d geometric primitives. My 
focus is on contributing to the capacity of comutational models/tools for 
bio-tech researchers. I have a system of rulers. A system of rules-only 
cannot mark difference in the cases you have mentioned.

The basic issue is how to develop a rewriting system in a 4-D space. I 
understand the 4-D space and others can populate it with further 
understanding of the conformal geometry at play. This helps understand 
sequence variation, symmetry, and truncation.

I am ready to work with...experimental data collection (spectroscopy) and 
the computational problem of identifying feature space that is how 
parameters and features are shared/hybridized...within the representational 

The value in this approach is a better viz-environment and a system for 
arriving at unknown associations in datasets.

Nathaniel Bobbitt


I am working on 3D visualization for protein structure prediction as part of 
my dissertation. Base platform for modeling is X3D which provides support 
for rigid body physics in the model. The goal is to allow the Human Expert 
to take an amino acid sequence and based on homology, mutual information for 
co-evolving pairs and generally accepted structural rules manipulate the 
structure for a proposed tertiary model. Current data for the mutual 
information of my research can be found at http://www.proteinx3d.com

Visualization will play a huge role in future discoveries and it typically 
beyond the scope of the average biologist/programmer writing code in Python 
or Perl.

Add me to your email list if you get anything of research interest.



Nathaniel Bobbitt wrote:

I am looking for researchers interested in simulation and modeling 
techniques that revise our basic understanding of 3-D and geometry in life 
sciences: 1. protein visualization,  2. diagrams of cellular and biochemical 

I use a porous-solid geometry. I wonder if there are others with like 

My work is geared towards the representation of: 1. folding, docking, 2. 
intramolecular relationships 3. practices for the collection and 
visualization of screening techniques.

I am looking for academics or 3-d party software developers to collaobrate 
with. Please let me know if you or others might be interested in the review 
of a position paper based on three poster papers:

Expressivity: Steps for the optical transformation of the envisioning of 

1. What are the visual barriers in graphic arts for doing scientific 

2. How can optical behaviors improve the expressiveness of a visualization?

Computation: Physical steps toward the envisioning of science

1. How can numerical control, shape a boundary system while still showing 
the visualization of complex relationships?

2. Why trap complexity before being given datasets?

Plasticity: Trapping Geometric motives in a 4-D Fractal Space

1. What would a 4-D fractal space mean in the mapping of: barriers, hidden, 
and emergent patterns in organic forms: folded, twisted and coiling?

2. Where to go to find new geometric primitives for 3-D fractals?

I look forward to your reply.

Nathaniel Bobbitt


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