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Personally, I think that drag and drop is a really bad UI for doing this sort of thing. I think that the lack of an effective means of editing graph based information has been a big reason. I think that the seccond reason, is that all of these tools have used their own, complicated serialization format, rather than using something more unixy that you could build a real ecosystem around.

I'm trying to solve these problems with textgraph: http://thobbs.cz/tg/tg.html and while the ecosystem is still in daipers, I am finding that using a simple and LIMITED file format, that can do nothing more than use text based edge lables and text based vertex contents, makes development of the ecosystem much faster than if I were to go crazy with having ecosystem features like edge collors, box vertex and arrow shapes ect.

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