Finding your academic writing workflow mojo Part 1: Writing tools

There are a lot of choices out there when it comes to finding software to help you with your writing. The most obvious of these is your word processor, but there are a couple of other types of software that can influence the efficiency of your academic writing. In this post, I review five types of software and outline the ways in which they can be assembled to make an academic workflow. These five types are: 1) word processors and writing tools 2) reference managers 3) PDF annotators and 4) databases and organising your notes 5) drawing and image processing. Fair warning: I am an Apple user, so some of these could be different for Windows or Linux. I also have a social science perspective, which might be different for some disciplines.

1. Writing tools

There are lots of debates on various websites about which is the "best" word processor. My reflection on it is, it depends on what you are writing, and has a lot to do with your process and objective. I will also say that the decision about your writing application has to be made together with the reference manager as they do not all play well together equally.

Microsoft Word (Mac & Windows)

Lots of people use Word and are perfectly happy with it. I find my self frustrated using it as I don't feel like I have full control over the way things are formatted, that formatting changes without my consent, and that it is unstable, especially for for larger documents, say over 50,000 words or with lots of tracked changes and cross references (at least on Mac, but also on the last version of Windows 7, which was the last version that I had to use in the office. I don't know about newer versions). Word is effective for collaboration though as other users can easily add to and comment on your draft, especially when linked with OneDrive, Dropbox or other shared folder service. There are some great collaboration features in Word 2016 for Mac and the web version of Word, which I have yet to fully test drive, but I like the new commenting features. Note that Word 2016 for Mac and Windows are currently compatible with Mendeley, but other reference managers are not yet working at the time of writing. Now that Word 2016 for Windows is out, maybe that development will speed up for reference managers. Also, I cannot see and have not yet tested collaboration between Word 2016 for Mac and Windows, but it seems that it will work.

Google Docs (Mac, Linux & Windows)

Google docs has a lot fewer features than Word, but is very stable and quite capable for limited formatting. Its real advantage is in collaboration. If co-authoring a paper, multiple authors can work on the same document at the same time without getting conflicted copies that desktop applications have using a shared drive like Dropbox, Box, or whatever. You can even use google docs offline. What I don't like in Google Docs is that basically I need to format the document once it is finished in another application and that automatic numbering for tables, figures etc is not possible, nor is creating cross-references like you can do in a full word processor. So, that makes it nice to a co-authored journal article, but not ideal for a thesis or book. Google Docs works with two reference managers with which I am familiar: ProQuest Flow and PaperPile. Anything else, you would have to use 'curly references' (coded placeholders in curly brackets) and export to another word processor for finishing and bibliography creation.

Scrivener (Mac & Windows)

Scrivener has been getting a lot of attention in my circles. It is decidedly not a word processor in that its function is not to finish formatting, although it has the basic features to do some of this. Scrivener is great for organising writing. Basically, you can write in chunks (a sentence, paragraph or section) and not worry too much about the flow of your work. It is really easy to move these chunks of text around, or bin the bits you don't know what to do with but don't want to lose. I have used it on several occasions to deconstruct my writing and put it back together in a way that makes better sense. Scrivener is not that great at auto-numbering and cross-referencing, like Google Docs, but it is possible using the <$n:type:name> formula in your text (basically <$n:h1:First_Heading_Name> would be your first heading and the fist subheading would be <$n:h1:First_Heading_Name>.<$n:h2:Second_Heading_Name>. Similarly, you could refer to <$n:figure:Figure_Name>. When you export to a word processor, they will all number nicely, but they are hard to keep track of and you have to make them all manually). I know some people who use Scrivener to store and organise all their notes as well, but I have never used it this way. Also, if you work with complex tables, Scrivener might not be the best for you. If you are the kind of person who likes a finished format as you go, as I am, you will need to break away from Scrivener at some point. You can use any reference manager that works with a word processor, put in 'curly references' and when you export to the word processor, you can scan the document and your references will format and bibliography will be produced.

Mellel (Mac)

Mellel is by far my favourite word processor for sole-authored work. It is rock-solid, has great formatting flexibility and is designed specifically for academics. I really love the control I have over formatting (through styles) and cross-referencing, and find that it does tables quite well. It integrates with some specific reference managers (Sente and Bookends), so that you can reference your literature without leaving your writing application. That is quite handy. It also, very conveniently, opens to the last place you were in the document rather than at the beginning... this makes it very easy to remember where you left off. My only complaints about Mellel are that it can get hard to find the cross-reference I am looking for on a very large document (when I have hundreds), captions cannot be anchored to images for text wrap-around (a minor formatting issue really, rendering problems for briefs but not really for full manuscripts or journal articles), and there is no indexing feature (which is not available on that many applications). It uses a proprietary format, so it is not the best for collaborating with non-Mellel users. Its PDF export is great (especially since they added the bookmarks in the PDF) and Word export is imperfect formatting-wise, but workable... then the changes have to be manually inputted into Mellel.

Pages (Mac)

I used to just make a mention of Pages in this article, but now I am elevating it because Apple has added collaboration. Pages is a solid all-round word processor and works with several of the major reference managers. It is still not as feature rich as Word, but in my experience, it has been much more stable. I have mentioned already that I do almost all of my current work in Google Docs because of collaboration (across platforms). I don't see that changing really because Pages requires all collaborators to have a Mac, but if your team is running all Mac, then Pages could be a good option for a larger document, like a book or something, that requires collaboration but is too big or requires too much formatting for Google Docs. As I have mentioned, if I were writing a book I would definitely go to Mellel first, but they have not integrated collaboration yet so that only works for sole-authored. Pages works with EndNote, Mendeley, and another of reference managers, although note really with my favourite two as I showed in Part 2.


There are lots of others that I have looked at, but never really tested, or decided on in favour of some of the above. They include word processor alternatives like OpenOffice (which I use extensively for drawing, but not writing), InDesign (nice for formatting, but I prefer not to do this as a separate step) Ulysses, Nisus Writer Pro and a lot of others, as well as collaborative writing online software, like Authorea (getting other authors onboard was a challenge and some LaTeX knowledge is required, but has a basic built-in reference manager) and Overleaf. I also like the control that LaTeX seems to offer, and have worked with it a bit, but I haven't found the time to let that learning curve go yet.

I intentionally made Part 1 about writing. Although it is not the first step in the workflow, it is it the decision that I think has to be made first and the other applications have to be compatible. Along with the reference manager (Part 2), your writing application is the most intimate in a way, and has the most influence on fostering or inhibiting creativity.

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