The scientist's toolbox 1: reading science

My favourite way to read scientific articles or books is... on paper. Not that I don't use digital versions, they have the advantage that I can pack a bunch of documents on an IPhone or IPad and bring them with me in the strangest place in case I have to check something. But there are many things that I cannot do easily: taking notes in the text or margn, drawing on it, easily access references, equations (the navigation in a digital document is rather limited). There are some tools like Zotero which try to add these functionnalities but the experience is far from being natural. The PDF format remains my favourite for the moment: the management of equations and pictures with the different ebook formats is, in my opinion not convincing. Generally speaking, Iam rather disappointed by what the  document readers offer or, more precisely, by what they do not offer: I would like far more interactivity on the content: to be able to watch the content of a document in a reference, check the significance of a symbol, acronym or word, to change the units in figures ad calculations, and so on. 
Up to know, I have not found a single reader that allows this while keeping the quality of a Latex output.
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