Scrivener for PhD thesis

I use Scrivener to write my phd thesis.
I find it flexible in handling bits and pieces around, but I must admint there’s a bottle neck that is giving me troubles: when I have to submit a chapter to my supervisor, I compile the draft as a RTF, then run zotero’s RTF scan to have the bibliography compiled, than send it to him. He sends me back a word file with his punctual comments, bit by bit. Now, how do I integrate these smoothly in my workflow? If I convert his .doc into a .rtf and then import it into scrivener, I save his comments, but not the corrections (added or eliminated words). So currently, I accept or refuse his revisions, and then import the rtf with the comments in Scrivener again. However, the chapter is now a whole, not a compilation of chunks any longer, and this anihilates the advantage of flexibility, which is one of the main reason I use it.
In short, I have a versioning problem. I was wondering if anyone came up with somethin more clever to handle this issue.


There are some suggestions in this thread:


If you search the forums you may find a few others.


I am just beginning to write my dissertation and am wondering how to set the template for the headings and such. The current “APA” template is not compliant with the 6th edition manual. Also, how can I integrate using a citation manager (zotero, endnote, etc.)?


Personally, I never bother with templates. Given that one has to do some reformatting in a word processor after compiling, I usually do all of it at the last moment in Nisus Writer Pro.

Using bibliographic software merely involves pasting temporary citations into the text. You format the bibliography, etc., after you compile to rtf by using Endnote, Bookends or Sente to scan the rtf file.


I wrote my PhD thesis in Scrivener, but I wrote each chapter as a stand alone paper. So I treated each chapter as a separate Scrivener project. My workflow went like this: finish the draft, add the references etc, format it according tot he journal requirements and then hand it to my advisor in Word. She would give me a bunch of comments etc, and I would deal with these comments in Word itself. Unless the chapter needed substantial revision, I would not go back to scrivener. Hope that helps.

I also wrote my thesis in Scrivener, but used almost the complete opposite approach. My entire thesis (including fragments, key references, rejected sections and old drafts) was in Scrivener and I would simply compile to Word whichever chapter I wanted to send to my supervisors (Australian for advisors). When I received their comments, I would import the file back into Scrivener and use split screen to compare their comments and edits with my original, making whatever changes I wanted along the way. I left the full move to Word to as late in the process as I could (entire thesis written, major edits complete, only minor edits and formatting remaining).

I find it hard to imagine using separate projects for each chapter - it seems, to me, to miss some of the strengths of the software. But one of the beauties of Scrivener is it’s flexibility and what seems obvious and natural to one person is counter-intuitive and weird to another. We all write differently.

I’m pretty sure I have documented elsewhere in these forums my use of EndNote & Scrivener.

As for APA style (which I use) I agree with Martin - save that to do near the end in your final document. Keep in mind that much of APA is actually about clarity of language and accurate referencing, the rest is just(!) formatting. So focus on your writing in Scrivener and save teh firmatting for document creation application (like Word or Nisus, etc). To make it easier, you can set up styles (not called that, but I’m not on my mac to check) in Scrivener for your headings, sub-headings, block quotes, etc. However, I suggest not doing these in APA style. Just make sure each one is different from all the others (vary typeface, point size, indents, ect). When you compile to Word, create all the Styles you need (they are called this in Word) then do a search and replace based on formatting. Takes a while (took me a few hours one night) but more than makes up for it in the end. I can’t even begin to estimate how much time and heartache that evening saved over the next few weeks.

It is instructive to see the many different usage patterns for Scrivener. I treated my PhD thesis as a single project. I wrote each chapter in a series of smaller sections which I copied over to Word to test formatting of footnotes (Endnote) and to see the text in a different context. I would copy any changes back to Scrivener and continue to iterate. Once, I was finished with a chapter, I sent the completed text to my advisor in Word. I made any changes in Word arising from comments and copied the changed text back to Scrivener. I treated Scrivener as the master copy for all text. This system worked well for my purposes until the very end, when Word began to suffer serious instability issues when I moved all the chapters into a single Word file.

My suggestion to anyone is to test their workflow early in the process to make sure they have an effective system. For instance, test a chapter but include all the computer generated elements, such as a table of contents, figures, and bibliography to make sure the system works as you expect. The full cycle needs to be tested to ensure there are no last minute glitches that get in the way of finishing the thesis. In the final stages, you should be focusing on content and not deciding formatting and appearance.

Man, that’s such a good idea! I will do so henceforth! I never thought of using split screen.

Heh, I did my PhD in Australia as well.

Wow! I don’t think I ever use Scrivener without the split screen! :smiley:

I came to Scrivener too late to use it for my doctoral thesis, but use it now for another major research project. From my perspective, using different Scrivener projects for each chapter defeats the purpose of Scrivener, as I like to be able to switch between chapters easily and to move text around. Where this system might fall down is attempting to export the entire thesis into a single Word document. Word freaks out when you hit it with massive amounts of text. I would advise exporting each chapter separately, for printing and/or sending to supervisors/readers.


I am using Scrivener for my PhD thesis too. I write in separate chapters (folders), parts (documents) and sections using multimarkdown syntax and use BibDesk to manage a BibTex database. I have a custom mmd citation template within BibDesk and just drag the citation to the correct position after pressing cmd+y.

After I am finished I compile everything into a file fragment via mmd → LaTeX with no metadata and no LaTeX document class. I take the LaTeX part I have made and add it into a template via an \include statement. The template is already setup with everything I need e.g. styles, meta-data, bibliography style (link to a .bst file downloadable for your target journal e.g. nature or science).

I then typeset the template (which drags the LaTeX part in) using TextMate usually. I have to then run BibTeX and then typeset another 1-2 times before everything is set.

This then outputs a .pdf with nice title page, typography, table of contents, bibliography etc.

Someone at the university has kindly made a LaTeX class that conform to the university/department style :smiley: I will have to give this a go soon- will require some tweaking though.

Awesome Scrivener!

I didn’t use Scrivener for my Ph.D thesis for the most part, because I didn’t feel i knew it well enough and I found the learning curve rather steep (I’m really getting into it now for papers and articles and such, and loving it). The above is correct, but there is a way, at least in the most recent Word for Mac, to have each chapter as a separate doc, but then link them together for printing, etc; you can have the pagination run all the way through, or start new in each section, and the same is true for the footnotes. I’m not a big fan of MS Word, but it’s a handy feature.

Dear thesis writers,
after a long time spent experimenting and “debugging” my workflow I think I finally got a fairly satisfactory solution which I would like to share with you, fellow sufferers :wink:

The end goal is to be able to write in Scrivener, compile, send to my supervisor, who makes changes and comments, efficiently integrate those in my original scrivenings so that I can reiterate the process again if needed and I don’t have to move and stick to Word after the first draft has been compiled. And doing all this using zotero as a references manager.

So, here is how I do:

First off, I’ve organised my binder as follows: Chapter as folders, Sections as documents, Sub-Sections as sub-documents. I use the <$hn> code in front of each section for automatic numebring. Thus:

    1.     I write my chapter sections, usign Zotero RTF-scan syntax for inline citeations {author, year, page}
2.	I create a collection for the current chapter elements only
3.	I sync the collection with an external folder thus creating individual [i]sectionX.rtf[/i] files 
4.	I then compile all the elements in one file [i]chapter-draft.rft[/i]
5.	I run zotero's RTF-scan on it: [i]chapter-draft(scanned).rtf[/i]
    5a.   I copy and paste only the automatically genereated bibliography to the [i]chapter-draft.rtf[/i] in order to avoid losing the inline citation syntax for further iterations of the revision process: I've instructed my supervisor to trust that the { brackets will be replaced by the ( ones in the camera ready version of the file, yet he still has access to the full references list should he want to check some. (I use a similar trick for table and figures refs: I tweak the code $$n:figure:uniqueimagename> instead of <$n:figure:uniqueimagename> to run a simple Find&Replace $$n to <$n when I'm pretty sure the numbering will not change. Or you can handle this in Word in the camera ready version). 
    6.     I send it to my supervisor
7.	I get it back with his tracked changes and comments
8.	I approve changes in Word (normally, one click "Accept all")
9.	I open in Word every single [i]sectionX.rtf[/i] from external sync folder while having the supervisors’ commented [i]chapter-draft.rtf[/i] (or .doc) open - possibly on a second monitor 
10.	I manually copy and paste section by section from it to each individual [i]sectionX.rtf[/i] files, overwriting their content
11.	I save them all
12.	I open my Scrivener Thesis project for syncing: I get notified that documents have been updated and I'm presented with the Updated documents collection automatically, while a snapshot of my original version of the sections is automatically taken, [i]Pre-External File Sync Overwrite[/i]. 
13.	I immediately take snapshots of my supervisor’s version for all the (updated) sections, with title: [i]Spv-Revision_date-sectionX-snapshot[/i]
14.	I proceed to in depth revision using vertically split editors by dragging the relevant snapshot on the heading of the second editor.
    14a. If I haven't made changes since I sent him the compiled draft, the comparison is between his commented version and my [i]Pre-External File Sync Overwrite[/i]. 
    14b. In case I had to make changes in the meanwhile, I damn myself for not being able to stick to sensible deadlines so that I have to grapple with this versioning mess once again, then I roll up my sleeves, I roll back the [i]Pre-External File Sync Overwrite[/i] and I option-drag the [i]Spv-Revision_date-sectionX-snapshot[/i] for tracking changes comparison, taking in account his comments looking at a print out of them, unless you want to rerun the side-by-side comparison between the Pre-sync version and your Supv's snapshot with comments dragging the latter on the editor without the option key pressed once the track changes revision is done.

Morale: don’t touch your scrivenings while you wait for your supv’s feed-back if you can afford to do so.

Now, for this to work, I assume that structurally sections and subsection stay the same, thus the revision is at the content level only. If it changes, you’ll have to redo the section numbering.

I hope it’s useful and if more experienced users have elaborated a smoother way, please advise. Thanks.