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Problem 1

I have been struggling coming out an efficient way to take notes while reading papers, one commonly-used way is annotate the paper while reading, but some issues include

  • These notes are hard to organize since they are distributed through the text.
  • There notes usually could not include mathematical formula. However, it is the major part of my notes.
  • When paper is lost in thousands of papers, it is impossible to recover them.

Therefore, I tried to use stand-alone notes written in markdown, but problem 2 arises.

Problem 2

As mentioned in problem 1, there are so many papers (and notes) I need to keep and it is just not feasible to keep hierarchy of folders, which could have up to 5 or even 10 hierarchy. Even though problem 1 is resolved, an effective and easy way to search and retrieve previous papers and notes is still needed.

Finally, any input about your solutions is appreciated.

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I highly recommend OneNote for note-taking. I really can't figure out how my life would be without it. You can categorize pages in different levels: section group, section, and subpage. You can also categorize your ideas within a page in different headings. You can even collapse or expand the headings as you wish.

It doesn't support LaTeX, but you can add math formulas with pseudo-LaTeX code in it. See Is there any way to get LaTeX in OneNote? in TeX SE.

It also seems that full LaTeX support is also available: https://blogs.msdn.microsoft.com/murrays/2017/07/30/latex-math-in-office/

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I like taking notes separately in an infinitely zoomable online outliner and include hyperlinks there to the papers in question. Dynalist supports KaTeX and Markdown, and there's a MathJax Chrome extension for WorkFlowy called MathFlowy, although it's broken right now since WorkFlowy redesigned. WorkFlowy and Dynalist also have a lot of user-defined tweaks on Stylish. There's a zillion other outliner options, both online and offline, but I personally like these two.

Since you can hyperlink to other items in the outline and tag individual items, it's easier to keep stuff both organized and connected. It's also possible to export portions of the outline to plain text or RTF.

EDIT: I forgot to mention Gingko, which supports both Markdown and MathJax and has a variety of export formats. I haven't used it in a while, but it's an interesting UI which is especially useful for organizing projects and long notes. The dev also recently released a desktop version if you prefer something that works offline.

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I am a huge fan of Emacs org mode for note-taking. There is somewhat of a learning curve, however. To use org mode, one must first install and learn to use Emacs.

Among the many benefits of org mode are the abilities to export to many different formats, such as ascii, latex, or html.

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  • it's more about organizing notes rather than researching notes, isn't it? Because the two kinds of notes are hugely different – Ooker Feb 24 '19 at 12:38
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    Org-mode plugins exists for other editors as well. I am a fan of Sublime Text 3 and I use the orgmode plugin. I like how I can link different notes and move between them in Sublime. – bytesinflight Feb 24 '19 at 19:15
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    @Ooker org-mode can do basically anything. – henning -- reinstate Monica Feb 24 '19 at 20:01
  • @henning I think research notes need rich formatting, hyperlinks, web and mobile synchronization, etc. Can org-mode have these? – Ooker Feb 25 '19 at 2:06
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    It has a markup for formatting and tables, it has all kinds of links, and it has mobile-org for synchronization. And that's just the tip of the iceberg. – henning -- reinstate Monica Feb 25 '19 at 8:04
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I would say it is very complicated to find an approach that satisfies all your needs. Nevertheless, and if you can forget about LateX I would recommend you to use Papers3 or readcube, since they easily allow to organize all your notes and papers. Main drawback is perhaps the price, but you need to decide if you are willing to solve your problem or not, and what is the price you are willing to pay.

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