TheBrain is a great tool to use for note taking during and after a course.
 

Recently I took an online course at Coursera, called Model Thinking.

I used TheBrain for taking notes and linking to some of the thoughts I already had in my Brain. (currently just over 10,000 thoughts)

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I used the "Capture Thought Icon" tool to add some screen captures to certain thoughts:

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When you hover over the thought the Image will show (same size as the capture itself)

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 I used the updated link function to give certain links a distinct colour and direction. In this case to point out that Randomness and Random walks do not constitute so-called Markov Models.

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I use TheBrain also to store all the course material. By using different thought types the thoughts get grouped together. In this case I assigned a type of "presentation" to all the presentation files.

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Below you can an exported HTML version of this Brain

Registered users of this site can download a copy of the Brainzip file