Mind maps vs flow charts ... can't say that I have a preference for one or the other. I find that there are times were mind maps are more appropriate for the through processes that I am going through than flow charts, and vice versa.
For this thing, I looked at flowchart.com and mindmeister. I found both to be simple to use and intuitive enough to learn. However, for me, I personally like an app. that I have been using for the past year called MindNode. It is very similar to mindmeister, but allows you to convert your mind map into a flow chart.
For class, I find mind maps to be the better choice, because I don't feel as constrained when I am putting together a lesson. Typically I will create a mind map first, then upon reflection of it, convert it to a flow chart before I make a final draft of my notes for a class. I find the flow chart to be a more organized form of my charts than the mind map.
With my students, often times I will have them take a small section of notes or chapter of the text book and create a mind map of the ideas presented. I like to to this before I lecture or discuss the content with them, because it exposes them to the terms and they are able to see for themselves how ideas and concepts are connected and related. I recently did this with the rock cycle, and then had them expand it with each of the rock types.
I don't know how useful I personally find each of the tools in this exercise, but I can see their potential from a collaborative standpoint. For me, I tend to fall back to the old pencil and paper mind map. I just like the feel of it. If I know it will be too big for notebook paper, then I will use my MindNode app.

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