Software to animate a flow chart?

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I need to create some sort of animation to explain how water flows in a flow diagram under different conditions, and wonder what kind of software would be suitable for creating it? I'm keeping it very simple, like colored lines that are in some way animated to indicate how things flow and work. Any ideas?
 
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You could build it from scratch using the Processing IDE. It comes with many examples and with access to open GL and Java.

processing.org

Yu would define two emthods setup() and draw(). setup() handles initializing variables and graphics
and draw() handles drawing a frame.

The key feature of processing is that it will call draw() once every 1/60 sec and redraw things so itallows you to draw something bump an x,y value and the next call it will draw at the new x,y