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
level.
The value in this approach is a better viz-environment and a
system for
arriving at unknown associations in datasets.
Nathaniel Bobbitt
Nathaniel
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.
Thanks
Scooter
Nathaniel Bobbitt wrote:
Hello,
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
representations.
I use a porous-solid geometry. I wonder if there are others
with like
interests?
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
science
1. What are the visual barriers in graphic arts for doing
scientific
visualization?
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
http://www.nabslab
.com/aboutus.asp
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