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I'm struggling with this problem for a long time, and I'm sure a lot of you out there are having similar problems too: when studying from a e-textbook I read and annotate in one app and make flashcards in another, bookmark interesting sites in my browser, collaborate over e-mail or instant-messaging, jot random notes and ideas in yet another app, keep my bibliographies in yet another app, do calculations different software packages, etc. And over time I start losing track of things.

There are open-source packages for doing all these things, but there isn't a single one that glues them together. Another issue is that many note-taking apps are just too structured and unflexible. For example, you need to manually tag every note, make links between notes, etc. It would be a good thing if such an app had some kind of an underlying semantic engine, so that when you're working on something, the software shows you similar things that you've worked on in the past, or similar things your colleague is working on currently, etc.

I'm thinking of suggesting Computer Science Department at my faculty to start an open-source project for such an app, and I'd like to hear some feature brainstorming.

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I think the question is too vague. Even in your new software you would need a module that does computer algebra and one that does bibliographies. How and why should they be linked? Everything except the semantic search is already there: The glue between the different "apps" is your operating system, for me Linux/text files/Emacs/shell. The semantic engine is tricky and part of ongoing research in computer science, but there are implementations like GnomeShell, MacOS Finder, and they work reasonably well if you keep all your stuff in text. –  Thomas Kahle May 5 '12 at 10:21

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I still find it most convenient to just use a pen and paper for taking notes. My mobile phone has a pen, and can even detect mathematical writing (which works surprisingly well), but the feeling of writing on a flat/glass screen is just not the same like writing on real paper.

When writing on the computer though, Emacs does almost everything I need (Flashcards, Email, Latex Editor, BibTex Manager, Pdf Viewer, Calendar, Instant Messaging, Interface to COQ, Interface to GAP, Sage, ...). More important though is having a good keyboard that is comfortable for typing and especially a US keyboard layout (typing latex code on a non-US keyboard is a pain, for example in my native language I have to either use both hands to type "\" or press 3 keys at the same time).

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