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