Dissertation writing tools and workflow

Now that my Master’s dissertation is done and submitted (and on its way to a decent mark hopefully!), I’ve been thinking about how my writing workflow has changed so much over the past few years to what is now a pretty organised, logical process that just makes sense. This is due in no small part to advances in technology, but also due to taking some time to figure out what works.

I remember writing academic articles as part of my nursing programme almost 15 years ago now in UCC…and I remember how painful it was. Search for articles, save them in a folder with some kind of descriptive name, likely print them out to read (before the days of tablets!), write the manuscript in Word, add in references manually. I kept a running document with quotes, bullet point summaries and other supporting items with their respective references, and I copied from that as needed (marking them in red when I had used them as below). Then I’d write out each reference manually in my reference list using Modified Harvard style. Don’t forget this was all then saved on a 3.5″ floppy disk…USB sticks were only just coming into vogue. The thought of having to go through this workflow again gives me nightmares.


Skip forward to today. I still use Word, but only for final formatting, and I haven’t changed from that because it just works for me I guess. Now I use Mendeley to organise my references, and Scrivener for writing. Between them, my workflow has completely changed, for the better! There are still a few things on my wishlist, but for now, I’m pretty productive with this process.


An avid EndNote user for a number of years, I made the switch to Mendeley two years ago. There were several reasons for this, mainly though, because Mendeley was free, and promised cross-platform support. I can search within Mendeley for literature, or drop a PDF in my watched folder. I annotate the PDF copy of an article while reading it on a tablet device, which I then attach to the reference record in Mendeley. The free Mendeley web account allows me to access my papers across all of my devices seamlessly. This allows me to search through articles, find the paper, and see my notes with ease. I also arrange papers into folders within Mendeley by type/subject, allowing me to quickly compare related papers. Mendeley also has an MS Word plugin which allows you to insert formatted citations and bibliographies. I’ve since upgraded to a Mendeley premium account, giving me a 5GB web account to store my articles in (4600 articles and counting…)



Scrivener is one of those software programs that I was hesitant to try for a long time. I experimented with it from time-to-time but didn’t commit fully. When I was starting the dissertation I made the leap to complete all my writing within Scrivener. I dedicated 2 days to learning about its features, and then off I went!

Scrivener treats your manuscript as a binder, which can have multiple folders, and within these folders there can be multiple “pages”. The neat thing that this allows you to do, which Word doesn’t, is to work in a non-linear format on your manuscript. Trying to complete one section before progressing to the next is the worst way to write. There were days where I just couldn’t face looking at the literature review section again, and so I focused on my methodology, or introduction. Being able to jump around your structure like this completely changes how you write, and how much you write.


It also lets you move paragraphs, images and tables around without your whole document going crazy.


Scrivener also has some pretty useful tools like word look-up, writing goals (such as words per session) , writing deadline (will tell you how many words per day you need to write to achieve your goal), and the ability to keep regularly referenced research material within the binder for quick reference (this can be in pretty much any format, PDF, DOC, image files). These also include things like Snapshots (rollback to previous versions), automatic backups, progress status per entry, labelling etc. These are all covered in many blog posts by others who also rave about Scrivener (just do a quick search for “Scrivener dissertation” to find more than you ever wanted to read!)

Compiling and formatting

Once you’re done your writing, you can then select sections for export with the Compile option. This can compile your binder as a Word document or many other file formats, allowing you to complete final formatting. You can setup custom compile parameters regarding page breaks, fonts, styles. Once compiled my Word document was over 200MB in size (a recipe for Word crashing if ever there was one!), and it took me about a day and a half to properly format it, align all tables and paragraphs, insert citations and bibliography, and edit all graphs and figures to requirements. Previously when using Word, most of my time was spent addressing these issues while writing, and the writing itself was secondary to figuring out how to stop Word from messing it all up.


Screen real estate

If you haven’t invested yet, I can say there is nothing quite like 2 screens to boost productivity. I have been a 2 screen disciple for years, and cannot imagine working on something as complex as a dissertation without being able to spread information on to additional screens.

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I also have a 3rd portable screen that I use in portrait mode for reading PDFs at my desk. I actually used this screen along with my laptop to prepare my dissertation draft while travelling across Canada for two months – a very picturesque office! Below is my office one day while in Fort Liard, NWT.

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Using Scrivener stretched across two screens, with its built in split screen option, allowed for easy navigation through two sections of the document for the purposes of creating table of contents, comparing Table and Figure numbers and more. So if you can, I recommend getting a second screen, it will make life easier!

The cloud

Being able to save in the cloud has really changed my workflow also. Now I have safe, secure access to my drafts and research across all devices, my Mendeley web account keeps all my research articles together, I have automatic backups of Scrivener manuscripts to the cloud, and I can collaborate in real-time with other authors using Google Docs without risking version conflicts. Be paranoid and keep backups of data across several different cloud providers. I think I had 9 cloud accounts on last count…you probably don’t need that many.


The end result is a 175 page document that was actually a joy to write (the data collection was another story!), is easy to navigate, looks professional and will hopefully do well. I cannot recommend using Scrivener and Mendeley enough. Give them a try, and I guarantee you they will change how you write. There is a learning curve associated with using each of the programmes, but there are countless online resources provided by both vendors and users that it is easy to learn how to use them or troubleshoot them.


  1. Hi Alan

    I’m trying to set myself up to use scrivener as I move into thesis writing next year, so i want to get everything bedded down properly! Have you got a workflow for how you manage citations? This is the bit that holds me back the most. I have been trying to use zotero, but the method i’m using seems to always miss one or two. Would appreciate some insight as to how you manage this!


    1. Hi Mike,
      This is unfortunately the part where it gets a bit messy. I personally put a placeholder like this [Author, Year, Journal] in the text itself. Once I export to MS Word, then I go through the document replacing all of these placeholders with the Cite While You Write feature, ensuring it gets added to the reference list correctly. I attempted the Zotero rote, but found this just quicker, and it ensures that I proofread the manuscript in a bit more detail also. If you come up with another solution I’d love to hear it!

      1. Of course, my dream would be a Mendeley plugin for Scrivener – I have contacted both companies about the possibility of making this happen, but I doubt that there’s much of a demand for it, so I won’t hold my breath!

        1. Thanks for the quick reply! I think your method is the only really viable path forward at this point. It’s such a shame that there isn’t an appetite to give scrivener a proper citation solution 🙁

          I imagine that the other place where it gets a little messy is incorporating changes and comments from supervisors etc. Is this where you use google docs as an intermediary before the final compile into Microsoft Word?

          1. I agree, who knows, maybe they’ll be willing to work on something – it would be a killer feature if they could make it happen!

            Yep, I copy in the document to Google Docs (I don’t do the proper citations at this point, just the placeholders), solicit feedback and changes, then make the changes in Scrivener, and re-export. Once all changes are made and comments addressed, then the final export is when the citations are dealt with. Scrivener can roll back to previous snapshots too, and you can easily compare versions of a section to see the changes (revisions show up in different colours).

            It takes some getting used to, but it actually worked pretty seamlessly in the end!

  2. i have a similar workflow with Mendeley and Scrivener, the biggest issue, (references inclusion appart) is integrating the feedback form my supervisor, his comments and changes. Putting them back in scrivener means copy pasting several sections, and the track change then disappear…

    Thus so far my workflow is: Draft chapter in scrivener (type in placeholders + paste formated references from mendeley in a references section)> clean up in word MS> get feedback > review and other rounds of feedback> Get the chapter validated > Paste back final version in Scrivener; Move to the next chapter.
    I am still experimenting, suggestions and tips are welcome !

    A mendeley plugin for Scrivener would indeed be ideal and make our lives easier !

  3. Likewise I adore both scrivener and Mendeley but until there is a Mendeley plugin I’m sticking with word. I’m nowhere near organised enough to manually go through and put in my references after the fact….

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