Novel Ideas [57]: Mendeley and My New Workflow

Novel ideas title simple

Last year I wrote about my love for Zotero, a (free) open source citation management system. And while Zotero is still awesome, I’ve been refining my doctoral student workflow and trying different things to find the perfect combination of programs to help me read and write more efficiently as an academic. And I think I finally stumble on a winner: Mendeley.

What Didn’t Work

Zotero worked well enough for my first few semesters, but I found it to be clunky for my purposes of trying to have a “paperless PhD” workflow. So I decided last semester to dive into research for paid options. I finally settled on the combination of Scrivener and Papers3. Both programs let me download and run the full software with a free trial for 30 days, so I tried writing all of my term papers using both. TOTAL. FAIL.


Scrivener is a program designed for fiction writers to brainstorm/research/write novels, but I had seen many academics raving that they made it work well for long research papers. Well…I don’t think it fit very well for my writing style. I’m not writing fiction, so the forcing of the software to work for my purposes was just too intense and not worth the $45+ purchase price. As for Papers3, well, that was a different story. I tried Papers3 because I’d seen soooo many people raving about it, but I really didn’t think I needed a PDF management program. Boy was I wrong! I loved Papers3 and I loved the idea of reading and annotating and tagging my PDFs for use over a 30 year career in academia. However, I became frustrated with a few features of Papers3 and decided that $79 was too much to spend on an imperfect product. I headed back to the internet to search for what I really needed.

What I Needed

My semester of trials and testing revealed that I would much rather use plain ole Microsoft Word for my document writing, as unfancy as that sounds. I don’t want to work on digital corkboards and notecards and outlines and whatnot. I want to work non-linearly on the actual document. As for PDFs and citation management, I learned that I wanted a program that would store my PDFs and let me organize/tag them how I wish. But I also wanted to be able to highlight, add digital sticky notes, and write my own notes in a side panel. Which turned out to be an easy wish to fulfill…

Why I Chose Mendeley

Mendeley is like Papers3, but it’s free. Mendeley is a program that organizes my PDFs and lets me read/annotate them. It also generates citations and works with Word to add citations to working documents. It doesn’t have a lot of crazy bells and whistles, but it does have the one thing I wanted most: a text box where I can write my own notes about what I’m reading. Here’s a screenshot of an article I just finished reading for class (click for a bigger version):


Mendeley, PDF view screen

Mendeley lets the PDF take up most of the screen for easy reading, where I can highlight passages and add sticky notes. Sticky notes show up on the PDF and on the bottom of the right-hand “notes” pane. On the top of the right-hand notes pane, you can see the text box that lets me type my own notes as I read. This is great for class (summarizing articles and writing questions for discussion) and for literature reviews.

Oh, and it syncs to the Mendeley app on my phone and iPad. My iPad is more comfortable for reading long articles, and my phone is a good backup in a pinch.

Screen Shot 2014-03-12 at 8.14.07 PM

Mendeley, library view screen

So far I’m using Mendeley to read PDFs for class discussion and papers, so I’m starting to build my library. I’m still working on using the citation features effectively, and I am spending a lot of time manually putting in citation information for each article. Articles that come from the library databases often have the information automatically, but my PDFs for class posted on Blackboard often do not. Also, I’m still trying to fine tune my tagging and folder systems, which I imagine will be an ongoing process.

Is Mendeley perfect? Well, no. I do wish I could highlight in different colors, free draw on PDFs, and I wish my highlights were saved with my annotations in the note pane (like in Papers3). Overall, though, I’m very impressed with Mendeley and would pick the product even it if weren’t free. That’s a good sign that I’m making the right choice.

As I continue to navigate the various stages of this PhD, I will continue to post how my workflow is adapting to the tasks I must complete. I’m quite fascinated by the idea of individual workflows, so I’d be interested to hear about yours — which programs do you love? Which do you hate? Which can you just NOT live without? What’s your workflow? Share your thoughts!

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7 responses to “Novel Ideas [57]: Mendeley and My New Workflow

  1. I’m only just starting out my Master’s degree (getting stuff together for the proposal now), but Mendeley seems like something I could definitely use. Like you, I really prefer Microsoft Word writing because I’ve grown up with it, know how it works and I feel comfortable with the look and feel of it. I don’t think I could really write comfortably in anything else. For note taking and brainstorming I use Microsoft OneNote. It took me a bit of getting used to, but I found the quicknote function (an annoying little sticky that will stay open on your screen no matter what tab you’re in) very useful. I’m still doing the citations and references manually, though I suppose this won’t last long.

  2. Reblogged this on Ordbilda utbildning and commented:
    Att skriva akademiska uppsatser eller avhandlingar är ofta en besvärlig
    och mycket lång process. Det finns numera många verktyg för att göra skrivandet lättare till exempel organisera alla artiklar som är nedladdade i PDF-format. Tara diskuterar här “Mendeley” som är en Open Source produkt.

  3. Mendeley product manager here :) Thanks for the write-up. We take the time to read any blog post we find about people’s workflows and Mendeley.

    I just wanted to quickly clarify that our software isn’t actually open-source, (though a few things, such as our citation style editor are), but rather we have an open API that allows people to build apps on top of our service.

    I’m currently trying to push internally for all those annotation features you mentioned, so it’s useful to be able to point to sites like this to show people need these core things.

    Cheers, Steve.

    • Thank you for alerting me to my error! I’ve edited out that detail in the post so I won’t mislead my readers.

      The main reason I want to free draw on my PDFs is so I can highlight/underline in PDFs that don’t recognize the text (which, for me, has been about 1 in 5 because my professors uses old copies of book chapters). If I could free draw and choose a thick, yellow pen I could “highlight” or if I just had a thin, black pen I could underline or bracket a key passage. So I would say that it my most desired feature, if that helps you pitch ideas to the Mendeley team. Tell them thank you for a great product!

  4. My math teacher spent a couple classes raving about Zotero last year. I, in contrast, found it to be a rather inefficient software. I had to click a million different things to access my notes and add new ones.
    Microsoft Word is–and, will probably always be–my go-to program for writing of any nature, whether it’s news stories, book reviews, or essays.
    I’ll keep Mendeley in mind when I write my next extensive research essay. Thanks for sharing :)

  5. Reblogged this on Filologia cyfrowa :: Mediewistyka 2.0 and commented:
    Głos oddany na Mendeley. Porównywał różne programy również Emanuel Kulczycki na Warsztacie badacza (wybrał Zotero). Warto poznać i inny punkt widzenia. Nawiasem mówiąc, dojrzewam do zakupu Scrivenera, ale martwi mnie, że na Windowsa jest mniej opcji (a na Maca raczej się nie przesiądę).

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