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Blender - Blender is the open source, cross platform suite of tools for 3D creation.
BioBlender - BioBlender is a software package built on the open-source 3D modeling software ...
FreeCAD - An open-source parametric 3D modeler
open3mod - A free, Open-Source 3D Viewer designed to make it all easier. Massive 3D Format support
meshmixer - meshmixer is an experimental 3D modeling tool for making 3D mashups without too much hassle.
Calistry.org - Calistry is an online Chemistry Calculator.