Below are screenshots of a system built to experiment with graph visualization in 3D. A pseudo-physical simulation of repulsive and attractive forces automatically produces a layout of the graph. Nodes and edges can be interactively created, dragged, or deleted, as the simulation runs.

The graph visualized below corresponds to my website's structure. Scripts written in Bourne shell and Perl scan my website and produce a plain text description of the corresponding graph. The plain text description can then be read in by the visualization program for viewing.

After creating this prototype, I learned that the ideas it uses are an example of a well established technique known as force-directed layout of graphs. Here are some related references I came across: