How should PhD Students/Researchers take notes? When taking notes while studying papers or concepts I'm always torn between 


classic pen &amp; paper approach, which I personally find more productive;
digital approach, will make it easier to find/sort/filter information later


I'm going to be a Computer Science Ph.D student, so I have to be quite productive (solution 1), but also, to work on the long term, so building my own "knowledge database" (sol. 2) makes sense.

I am currently thinking about developing my own tool based on markdown notes, git version &amp; a query tools to find information, to tag/link items as well a generate bibliography etc.

What is considered the most useful way of taking notes, particularly for non-class settings?
In this article, "The Pen is Mightier than the Keyboard," the researchers tested this very issue.  They found that taking notes with pen and paper is more effective... but, that was because students who typed their notes were copying lectures verbatim whereas students who took notes by hand were taking in the information and then writing it in their own words (thus processing the info at a deeper level).

So, the key is the way you process the information, not necessarily the method you use to take notes. But, at the same time, it is noteworthy (no pun intended) that longhand notes tends to lead to that deeper level of processing more so than does taking notes digitally.

Personally, I'm all about taking notes longhand, and I print out articles that are important to me/my work.