Civilization advances by extending the number of important operations which we can perform without thinking about them.

– Afred North Whitehead

Have you been annoyed at writing a bibliography? Or wanted to keep track of interesting academic papers or your annotations for them? The video above and this post will make retrieving, importing, annotating, and referencing academic articles (or other sources) a breeze, and showcase a few other small tools!  

When writing papers alone or in groups, I'm sure you have run into the same hair–ripping problems I have:

  • Your group members seem to have no understanding of what a proper academic reference style looks like and just paste a URL
  • You've numbered a bunch of citations in your paper but then realize you missed one or want to add another, so you either don't add it (and drop an argument) or renumber everything
  • You're writing a paper for a publication and are asked to change your reference style to an entirely different one
  • You're relying on Word's built-in citation manager but are working on another project with many similar citations and don't want to do them all over again
  • You are currently typing in references manually

If these issues still plague your writing process, you are living in the dark ages!

Please allow me to introduce to you the immense power of a reference manager. I've heard one of my professors refer to computer modelling as a way of extending our brains, and I see this as the same. Perhaps you've already heard about this from a librarian before, but there might still be something new for you here. In the embedded video above, I go over the following topics:

  • What a reference manager is – a personal library that you can index, search, organize, and easily export as citations on your clipboard or into common writing tools
  • How Mendeley allows you to annotate PDFs and synchronize those annotations and any of your notes to other devices (spoiler: it relies on a proprietary cloud, which I've now found an open–source but horribly outdated alternative to called Docear... let me know if there are others out there!)
  • Big drawbacks to Mendeley and why I still use it – essentially, synced PDF annotation is a big feature for me (I want to annotate on both my computer and my tablet), and it has two big features built-in: PDF file management and Bib(La)TeX file exporting, which can both be done in the open–source Zotero, but require some massaging to set up correctly
  • A demonstration of how Mendeley makes citing papers easy in Word, LaTeX compiled locally, Overleaf, and in groups (I don't show this for Google Docs because I now refuse to do any serious writing there, but it is possible; see post about why I avoid internet–based writing tools)
  • Some unique ways of finding literature: AI-powered search engines (a good one I miss is wizdom.ai), conditional search terms, and network analysis on literature

Below is a full list of topics and hyperlinked timestamps for your convenience:

00:00 Overview
01:05 Downloading and importing PDF articles into a reference manager
03:48 Powerful Mendeley features
07:35 Integrating reference manager with local LaTeX, Word (10:00), Overleaf – and shared Mendeley groups (13:44)
15:48 Quick VS Code demo
19:10 Mendeley PDF naming and folder management
20:46 Annotated PDF syncing discussion
21:56 Adding manual entries
23:17 Copy citations directly (for various citation styles)
23:53 Extra citation styles
25:00 Cool AI-based search engine: Semantic Scholar
27:30 Search terms with conditionals (helpful for improving your search game!)
28:34 Citation as Networks with CitationGecko (32:45 for the super cool part)
34:01 Accessing papers remotely (See more at https://jrwang.ca/2016/06/13/connecti...)
37:24 LaTeX and plots

Finally, some caveats about my workflow (an FAQ, so to speak):

  • I know Mendeley and Zotero have browser plug-ins to make importing references easier too, but I don't like browser extensions (I run a lot of tabs in my browsers and extensions hog scarce resources, and it's a lot of bloat!), especially because it's usually a hit-or-miss on getting PDFs properly.
  • I would love to switch to only Zotero and open-source options, but annotating on my tablet is really important to me

If you'd like to see my full setup, see my post below:

Compiling LaTeX Locally on macOS with VS Code and Git (How I’m Writing My Thesis)
Introduction In the past few months, I’ve finally learned to use LaTeX properly in an attempt to make my eventual thesis-writing life easier. Additionally, it seemed difficult to help all my group members get some collaborative writing platform working together (and we all avoid Google Docs because …

Edit 2020-02-14: P.S. Nerd me just found out that the IPCC AR6 WGI is using Mendeley for their collaborative writing. Here's their guide for working together.

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I'm an engineering student living in the future. I care about dreaming big, finding truths, and building equity into our society.