Question: I have finished my M.Sc. in Applied Mathematics in 2016. I wish to pursue a PhD. Currently I am preparing for GATE (Graduate Aptitude Test in Engineering, a master’s-level national entrance exam in India). In this respect, I have a few questions. 

1. If I only have a valid GATE score but no CSIR-JRF NET qualification, will I be eligible for the 25 k funding?
2. If yes to above, is this funding available for any NAAC-accredited university (public or private) in India?
3. Is there any written statement from the government which validates this?

Answer: 
When it comes to knowledge I make the (admittedly vague) distinction between general knowledge anyone in the field would have and specific knowledge that an expert probably would need to look up.  

For the first kind I use pen and paper. Pen and paper is better for learning things by heart and for this kind of knowledge there usually are plenty of textbooks to look it up if necessary.  

For the second kind of knowledge it is usually enough to get the gist of it. That is why I write my notes on my computer. Here it is less important to know it by heart and more important to clearly record a reference for potential future use. Searching through a file directory is easier than trying to find a random piece of paper I might have thrown out. 

Of course given the time, writing a draft on paper and then a final version on your computer is best. However who in academia has time to spare for that?
I used and still use pen and paper, although for my discipline, I bought engineering paper so that I put graphs on the left page and content on the right page. That is what I used for lectures and presentations. There are limitations on a digital format unless you turn it into a glorified writing pad. You cannot mark arrows easily, you cannot easily link text to graphs and you cannot write marginalia as easily, unless you are typing in LaTeX.

Outside of lecture, I use highlighters. Although I keep a digital copy of articles, you cannot markup a pdf from a publisher. I maintain four inch binders that are organized in a manner that is useful for me. I have my own Dewey system. Electronically, I store the articles using tags as names such as serial\_correlation\_explosive\_roots or mvue\_cauchy\_trimmed\_mean. I also depend a lot upon memory. The difficulty of using a markup system is that you do not know what will be important in three years.

When you read an article it may be that keywords a, b, and c were what was important to you, but the article contained a seemingly uninteresting reference to keyword d, which is not a keyword because you don't care at this point in time. The keywords do not hurt, but if they cause you to commit less to memory because you say "I can search it," then you actually have lost retrievable data. Of course in an ideal world you would have built a search using the contents of the pdfs.

Pre-built bibliographic tools exist. BibTex is very useful, though not ideal. For continuity I use BibTex though if I were starting today, I may not. I maintain a unified bibliography for everything I have ever used or done. BibTex is part of LaTeX. If you are going to do professional writing, you should probably learn LaTeX. Download something like MikTex and then use something like TexStudio as a wrapper so you do not have to type out all of the commands. It isn't bad to learn on MikTex, but it is slower than TexStudio since TexStudio will guess what you are trying to do and autocomplete.