Finding your academic writing workflow mojo Part 2: Reference managers

Updated: Mar 20

Reference managers have to play nice with your writing tools. I think they have to be chosen together and compatibility among them has to be considered before deciding on both. This section follows Part 1 on writing tools. I will take a look at several reference managers that I have tried out and let you know some of my reflections on them. Again, I am a Mac user, so other experiences and options might be better suited for users of other operating systems. Wikipedia keeps an open entry on reference managers that might be of interest to you. Here, I get a bit more specific about requirements useful to social science researchers.

What I look for in a reference manager is ease of use, ability to customise templates for output styles, stability, modification of in-text citations (i.e. author suppression, "see also" prefix or suffix), collaboration, and ability to work well with writing software in a way that does not interrupt my train of thought. Reference management software is developing in a direction that I don't think is that necessary: PDF annotation, which I have yet to find an implementation that I prefer to a regular PDF reader, but there could be some exceptions.

There is one important feature that I have not tested on all reference managers: the ability to search the contents of attachments. I think that several of these applications will do it, but I use a separate application for doing that, which I think has better search algorithms. You could also use Spotlight, built into your Mac OS if you target the folder. I discuss data storage and options in part 4. Another feature to look for, which I don't find useful, but lots of people seem to, is syncing with iPad. Also, make sure you know whether or not there is a fee for the iPad app or for the syncing services.

Importantly, if you like the collaboration features of Word 2016 for Mac, not all reference managers have the functionality to cite while you write in the newest version of Word. I expect this will change shortly.

EndNote (Mac and Windows)

EndNote assumes a somewhat ubiquitous position among reference managers, but has some of the same weaknesses that its strongest ally, Word (at least the older versions of Word) has. It is feature-rich and a lot of other social science authors use it. It is also a standard format for imports and export of references. Using it with Word is very simple, and references can be called from the floating toolbar in Word 2011 for Mac (but not 2016 yet). At the same time, it is fairly bloated, pricey, and difficult to use. Collaboration is possible through EndNoteWeb, but I have not had great luck with this and users get confused about how to use this feature, but collaboration is not EndNote's strong point. A Shared group can be set up in which reference can be placed. I found it cumbersome to set up folders as I couldn't find any "sub-group" function or folders within groups- so organised references have to be assigned sharing permissions group by group. A nine-page description of how to share reveals how complicated this function is. On the plus side, any citation that an author makes will be visible by the other authors in a Word document and the bibliography will sort them all regardless of who added the citation.  I think they call this the travelling library or something like that.

Mendeley (Mac, Linux, Windows)

I tried Mendeley when I was setting up my workflow. I liked the 'social' aspect of it, but ultimately found that things like modifying citations (i.e. suppress Author) were weak as was the ability to customise styles. The basic version is free, so it's worth a shot. As at September 2015, Mendeley has a plug-in that works with Word 2016. I couldn't find any others that did that. In terms of collaboration, the free account only allows a 100MB of shared storage and 2GB of personal storage. Personal plans are a reasonable monthly price, but the team plan allowing for five collaborators is $49/ month. Over a two or three-year research project, paid software might be cheaper.

Zotero (Mac, Linux, Windows)

Zotero is a web-based application with downloadable software. It seems to tick most of my boxes, although I have never really given it a good run, mostly because the collaborative feature is limited by free storage of only 300MB. Additional storage is available for a reasonable fee. If online storage is not an issue for you, or you want to get into monthly subscriptions, it might make sent to try this out.

Sente (Mac)

Sente is my reference manager of choice with Mellel, my favourite word processor. It also works with Word 2013 for Mac, but I have not used it that way. The advantages of Sente are its super-flexible customisation of formatting styles and its excellent in-text citation modifiers (although it cannot suppress a year, only the author, so if you want to say "Smith (2000) theorised that...", you have to write "Smith" manually, but the reference year will still show up with author suppressed). Another missing feature is allowing associated edited book chapter entries. As it is, references are not related to one another, which is inconvenient when I want to reference a chapter of a book. First, I have to make the book entry, where the PDF is stored if there is one, then duplicate that entry, modify it as a chapter of a book with accompanying author information, then duplicate that file for any other chapters I want to use. The main problem is that when I want to read that chapter, I have to hunt for the entry that holds the PDF. Sente has an active user forum and a great tagging system to easily find your references later. Sente has a PDF annotation feature, but I have never used it, preferring to use my PDF reader for reasons that I explain in Part 3. Annotations in PDFs are stored as notes, which is quite handy for searching later. There are no collaboration features in Sente and even e-mailing a reference is a bit of a process. The website states it works with Word 2016 for Mac and Windows. Note that if you want to search the text of attachments, I suggest that you set Sente to save PDFs outside of Sente, in a designated folder. This way, you can use the files in other applications.

Bookends (Mac)

Bookends can be bought as a bundle with Mellel. It has a vibrant development team and user forum and a lot of customisable features. It is quite easy to use and stable. Collaboration is a bit lacking, but it is probably a great choice if you are planning on using Mellel. Bookends has some very cool features like cross-referencing references in addition to normal tagging. Annotations in PDFs are stored as notes, which is quite handy for searching later. I suggest that Bookends vs Sente is a toss-up with Mellel and there are lots of lively debates on that if you want to search for them. One of the things that bookends does beautifully is allowing chapters of a book to be associated with the book reference, in which the PDF could be stored. In the end, they are both great applications. As of summer 2015, Bookends has more developer engagement with users than Sente, but that could change.

Papers (Mac & Windows)

Papers looks great. There, I got that out. Aesthetically, it is very pretty and has some cool bells and whistles like a world map of the authors of the papers. Unfortunately, I found it unstable and difficult to customise, but ultimately, I abandoned it because I decided to use Mellel as my main word processor for sole-authored work and papers and Mellel don't interact that well together. If you use something like Word, you might like to give Papers a try although I couldn't get Magic Citations to work with Word 2016 for Mac. There is a new "Papers Online" feature that boasts collaboration, but I found it a bit unstable. For example, I shared a collection and the PDF on the shared computer was the wrong one or could not be found. The other thing on collaboration is that Papers 3 is a bit like Endnote in that there are no sub-folders in a shared collection. I will say that chapters of an edited book is executed well in Papers (chapters of an edited book by different authors can be linked together). Papers 3 has the ability to search for text within attachments, which means you don't have to leave to another application to search for content.

Colwiz (Mac, Linux & Windows)

Colwiz gets special mention for its commitment to being a free reference manager with excellent collaboration features. It gets a bit into project management with shared calendars and assigned tasks. The collaboration allows users to share references, but not the PDF of the file (well, it can be shared in their 'Drive' but Drive is not available offline, and the file is not linked to the reference entry). Some entries, without a DOI, are automatically marked "private", making it especially difficult to share grey literature, which is irritating. That is a letdown, as one of the things I would like in a collaborative reference manager is the ability to annotate the same PDF with my team. I also have an issue with the lack of ability to modify in-text citations to, for example, suppress author. UPDATE: Colwiz has a Google Docs add-on now, meaning it can be used for cite-while-you-write.

Proquest Flow (Chrome on Mac, Linux & Windows)

Flow is one of the three reference managers designed for use with Google Docs. It is free for those with academic institutional e-mail addresses. It is web-based so there is no software to install, although you can link it to DropBox to store your own PDFs for offline reading. You have to install an "Add-On" in Google Docs and open a Flow account. Once you have done this, you can simply open the Add-on and a sidebar appears in Google Docs that you can use to reference, and modify your citations. It is basic, but seems to do what I need it to do. The best part is that you can share the references with other users, so you all pull from the same on-line reference database when writing together in Google Docs, which is a strong collaborative writing tool. You can increase storage by linking your account to Facebook and LinkedIn and the more users that share a folder, the bigger the storage will be (or just use your DropBox allocation). There is no way to customise file naming, which is a bit inconvenient since the default is by document title rather than year or author. Note that depending on your institutional settings, you can only see your own PDFs in Dropbox, therefore, collaboration is severely limited. Flow does not have the ability to search for text within attachments. You will have to use another application for that, but if you store the attachments locally, that shouldn't be a problem.

Paperpile (Chrome on Mac, Linux & Windows)

Paperpile only works with Google Docs (for now). It is monthly subscription software for a reasonable rate (about $3 per month). Although it is web-based, it syncs with Google Drive, so you can save all your PDFs there for offline reading, which is nice. Paperpile is built for collaboration and it is easy to share your folders, and all references (and their PDFs in read-only) with your co-authors. Collaborative annotation is possible through Google Drive, but a bit tricky. For the most part, shared references and their PDFs are read-only directly within Paperpile. Offline storage is a bit chaotic as the attachment gets stored in the user's Google Drive who uploaded the reference, so it means if you want others to be able to comment on that file, you have to also share permissions in Google Drive. Collaborative annotation aside, it is easy to copy shared references and attachments into each user's personal library for editing and annotation. The intergeneration with Google Docs is great and easy. Author suppression, adding page numbers, prefixes and suffixes are all there, which makes this a favourite of mine. I like the Labels feature which allows for easy drag and drop tagging clouds. I think that customisation of citation formats is still tricky, but it, like others, pulls from so it will be pretty solid. You can make your own style, but you have to use CSL formatting which is a bit beyond my level of interest. Paperpile does not have the ability to search for text within attachments in the general search, but once in individual documents, the PaperPile PDF viewer works well. You will have to use another application for searching across PDFs, but if you store the attachments locally, that shouldn't be a problem. UPDATE: PaperPile is testing MS Word integration, as well as Android and iOS versions.


There are lots of other reference managers out there, along with hybrid applications like Docear that is also a literature annotation and writing planning tool. It looks powerful, but is quite convoluted to use, at least on first glance. LaTeX users might prefer to use something like BibDesk, which I have never used.

It is important to choose your reference manager and writing tools together. I have used the EndNote-Word (for a collaboration, but it didn't work that well) and Sente-Mellel (sole-authored- love it) combinations extensively for different types of projects. Now I use Google Docs and Paperpile for a collaborative project and it works well for me. Uptake of something other than Word/Endnote for collaborators seems a bit of challenge though, so although it works for me, I end up translating manual citations to Paperpile a lot for papers I lead.

The next posting in this series will be on PDF readers and annotation, followed by data management.

UPDATE: After using PaperPile for about six months I find myself seldom using my desktop-based reference manager and consequently my favourite word processor as PaperPile only works with Google Docs. Although I was doing this only for collaboration, I find keeping two reference managers cumbersome, and so I am now doing sole-authored work in Google Docs mostly. See the link at the top of this page for my review of word processors.

This article was originally posted to the author's LinkedIn page.