Michael Behr has an interesting post on his scientific writing workflow. The post isn’t really about how he writes his papers but rather how he organizes and curates his research materials. As you’d expect, he uses an Org file to store links to research papers and take notes on them. If you’re an Org mode user you won’t have any difficulty imagining what this looks like.
What’s interesting about his workflow is that he use Zotero to capture and store copies of the papers he needs for his research. I used Zotero long ago when I was still using Vim and Zotero existed solely as a Firefox plugin. These days, it’s available as a standalone application as well so even if you’re not a Firefox user, you can still take advantage of it. One very nice aspect of Zotero is that it has Emacs integration so that you can interact with it from within Emacs. Behr’s post describes how this works and how he uses it.
I’m not sure how necessary Zotero is if you want a similar workflow. You can easily store the papers and link to them from within Org files without a separate application. You could, for example, use the org-attach command (see this video for an excellent introduction) to store and associate copies of the papers with an Org file. It appears that Zotero does make it a bit easier to retrieve papers but I’m pretty sure that a bit of Elisp could easily duplicate its capabilities. On the other hand, Zotero is already available and has nice integration so if you don’t mind the separate utility, it’s a good solution.
If you’re a student or researcher who needs to keep tract of papers, be sure to take a look at Behr’s post. His workflow is interesting and may give you some ideas.