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VPython is an extension for Python to allow easy, "pythonic" 3D. It is used in education for various purposes, including teaching physics and programming, but it has also been used by research scientists to visualize systems or data in 3D.
Projects using VPython
PyGeo A dynamic geometry laboratory and toolkit by Arthur Siegel.
Matter & Interactions An introductory calculus-based physics curriculum for engineering and science students by Ruth Chabay and Bruce Sherwood (NCSU) that emphasizes a small number of powerful fundamental principles, incorporates the atomic nature of matter throughout, and includes an introduction to computational physics, in which students write programs in VPython to predict motion and to visualize fields. At this URL you'll find a bunch of VPython lecture demo programs useful in teaching introductory physics.
Physics Applications by Rob Salgado. Includes an extensive list of links to projects using VPython.
Earth Science Applications created by Lensyl Urbano and students at the University of Memphis. It includes Educational models (some adapted from Matter & Interactions to add interactivity) as well as, python models that use Vpython for runtime visualization in active research and an introductory, computer modeling class.
This could also be moved to its own page if it grows unwieldy.
VPython video tutorials by Erik Thompson (archived at archive.org)
If you want to try something experimental, check out the "vpython-core2" module from CVS. Objects support transparency by setting color to an rgba 4-tuple, or by setting object.alpha to some value. --2005-02-26 05:57 Jonathan Brandmeyer
Jonathan has now made a beta release. He supports not only transparency but also surface textures and sophisticated lighting.