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Is there anything that can be used as a "research notebook"? Specifically, I need to embed graphs/images within the text.

Evernote is pretty good at that. The text can contain inline images, video clips and binary attachments -- the note editor is basically a small word processor.

That's what I currently use. However, the recent HN post about Evernote had paying users complaining about data loss!

You might try looking at iPython Notebook "http://ipython.org/notebook.html". I haven't actually used it (I prefer org-mode) but according to the web site "you can combine code execution, text, mathematics, plots and rich media into a single document".

Check out https://gingkoapp.com . I think they can embed images, not sure about graphs. Overall I find this an interesting way to structure and create documents -- sort of like mind-maps but more textual.

Scrivener's actually an interesting tool for research, depending on your exact needs. Not as cross-platform as it should be though.

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