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I think mindmaps are a start and usually not an end in themselves. I use two primarily but have looked at others. Those are Freemind(http://freemind.sourceforge.net/wiki/index.php/Main_Page) and iThoughtsHD (http://toketaware.com/ithoughts-new-home/). I use both for brainstorming and taking notes from books/papers. Sometimes also for the start of new ...

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