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I used to use plain text files. Recently I started using Mendeley because it's so damn convenient and it has a very nice UI, but my problems with Mendeley are (1) comments are private and (2) it's proprietary.

http://www.researchblogging.org/ is a great website that aggregates more long-form posts about papers, but it has a really shitty UI and it doesn't do anything for short comments on random papers by random non-bloggers.

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Let's see what inspiration we can draw from researchblogging.org -- I've read a bunch of data driven / research oriented blogs (or blogs about [understanding] research) and found them helpful.

Research blogging is great, but just to clear up the misunderstanding, comments are only private on Mendeley if you make them in a private group. Public groups are open to the web.

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