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Gaphor is a UML modeling environment written in Python. Gaphor is small and very extensible.
The repository is located at http://github.com/gaphor/gaphor.
DiaCanvas is a library for drawing diagrams. It is completely Model/View/Controller based and has a Visio (DIA) look. The package also contains a Python wrapper for the library.
K3Studio is the universal workbench for 2d/3d modeling, visualization and simulation.
The main topic is simulation and visualization of automata networks, but it can be used for diagram drawing, flowcharting, presentation, as a CAD, GIS,...
RGnome is a gtk based frontend for GNU R, which is a widely used language for statistical computing. It features a fully working R console and an editor with syntax highlighting.