Using Scrivener for scientific papers. Am I doing it right?

Dear Scrivener Community,

I do not know if I am right in the part of the forum. I am sorry if not.
I also have to admit that my English is my second language. I hope that you understand my vocabulary.

In the last days I tried Scrivener for my papers at university. My idea is to use it for my master thesis which should start the next weeks.

Normally I used Word 2008 for Mac to write my papers. I used footnotes, pictures, build automatically TOCs and picture references. Everything was fine, except that I did not have that fullscreen mode this way of organizing your writing stuff. Before that on the PC I used LaTeX, so I know how to deal with presets and I know how to not use the computer as a typewriter.

But what bothers me with Scrivener (which I really liked so far) is that I have problems formatting my research stuff the way I would like to. I have not found a way to create an index for all the images in there. I was not able to have footnotes while creating a PDF (just endnotes). I had to export it as a Word 2004 format to have footnotes. But then the TOC was not like a TOC in Word, it was just plain, body text. Also all the Headings were just body text. There was no use of any of the stylesheets/presets of Word. That means that if I would use Scrivener as a tool to write all my stuff. I would need to export it to Word and to all the formatting again: Put in the stylesheets. Create TOC, create picture indexes, etc… That would really be some extra work.

So, what is my question now? I would like to ask you: Do I have a wrong understanding of Scrivener? Should I stick to Word (I do not really want to do that!). Is it possible to create documents in Scrivener with image references?

I also had a closer look at the manual and the searched the forum, but I have not found any answer to the questions that came up in the last days.

I really hope that you can help me.

Thanks so far!



I don’t think you’re missing anything, but then again I’m not an academic writer and I don’t have any reason to use TOCs and tables. I know a lot of academic writers like Mellel as it’s very good at that stuff. It also has some powerful outlining and structuring tools.

Scrivener’s not a wordprocessor, it’s about assembling bits of text, images and video and structuring them. Yes, there’s some formatting but it’s only what can be derived from the OS X text system, so it’s not in the same league as Word/Mellel/Pages etc. The word from the Quirkily Gruff One is that final formatting will always have to be done in the best tool for the job - Word, Final Draft, whatever.

I’d guess that your best workflow will be to assemble your papers in Scrivener, export them to Word or rtf format, then pick them up in Word (yes it’s horrible, but can be beaten into submission to do most things and it’s the default format for most people), or Mellel (because it does the kind of stuff you’re after elegantly and quickly).

If you have to do the styling of text as you go, then Scrivener is not going to work for you, since it doesn’t have proper text styles (because it uses a – tweaked – version of Apple’s Cocoa text engine, which does not have them). As you have said, if you style the text in Scrivener you will have to do it again once you export it to a word processor to do the layout. So the best thing to do is to not style the text in Scrivener, or just do so minimally, and do all of that afterwards in the word processor. You have to decide if that way of working is possible for the texts you are producing.

I find it possible – actually liberating – to work this way, and I am an academic. I started using Scrivener when I was about halfway through writing up my PhD a few years ago, and it helped immensely with two things: concentrating on the writing rather than ephemeral stuff like styling, and even more crucially, getting bits of text that I had already written into a workable order.
I used Mellel for the final laying out of the thesis. The combination is far from a perfect workflow, given that styles and cross-references do not carry over from one to the other, but I don’t know of a better one, unless you are willing to look into using Scrivener with Multimarkdown as a front end for LaTeX.
I really do not recommend writing any long structured document in Word. Its style system is a mess and its figure placement a joke, in my opinion, but if you are happy with it and know how to bend it to your will, then you may have more luck there than me. At worst, you may just get frustrated at some point and paste what you have into Scrivener, as I did.

Thanks nicka and spinningdoc for your good explanations. Right now I am doing a paper with Word again which I planned doing it in Scrivener, but I think I will definitely switch to Scrivener with the next papers. Word crashed repeatedly on my girlfriends Mac in the last days (had to reinstall office 2008). Today it began to add pages (on its own while writing) to my Word doc. It ended up with a thousands of pages. Luckily I was able to copy and paste it into another doc. I do not want that to happen with my Master thesis. Therefore I will give Scrivener another try. And I will also look up that MultiMarkDown with LaTeX.

Thank you very much.


That sounds like a corrupt Word document. Perhaps you know this (and it’s a bit off-topic here) but it’s often best to paste everything except the final paragraph mark from the corrupt document into a new one. The experts on the Mac Word mailinglist call it ‘Doing a Maggie’.

I agree with what was said so far. On my own Ph.D. experience, Scrivener was perfect: I ended up being much more writing productive than I ever was because I liked the environment in which I was working on.

For final editing I used, not Mellel (which I had, but never managed to pass the learning curve), but Nisus Writer Pro (less stable, but very easy to use). In NWP I formatted most of the writing, included headings and TOCs, images and tables (that I made into images, since I don’t like the Mac kind of basic tables), header and footer, and bibliography (via Sente).

This workflow worked out quite well and I still use it for papers and reports.

– MJ

I don’t know about doing it “right” but Scrivener is the best thing for scientific papers since the invention of academic prose (maybe better, on second thought).

First, you have to disabuse yourself of the idea that scrivener does form. It doesn’t, it does content. So, any tables, footnotes, etc, will have to be added later. Having said that, it’s useful to keep in mind that there are two forms of scientific footnoting: bibliographical (history, PolSci, IR, most of the hard sciences) in which your footnotes include bibliographical information (and the awkward op cit, ibid, and their relatives), and substantive, in which references are embedded in the body of the paper, there is a bibliography at the end of the paper, and footnotes are kept for substantive comments (anthropology, sociology, psychology). I prefer the latter, it has to be said. I find Scrivener works better on substantive footnotes, because it does not handle footnotes too well, or, at least in the same way a dedicated word processor does.

All the above was really an aside. I think ThomasA’s question is really about workflow. Since I have now written at least two major (90-100pg) reports and several articles as well as parts of two novels on Scrivener, I have some experience of how to make the work flow easier.

a. start with your template (or just start a project).
b. I usually collect and import all (or as much as possible) of the relevant literature if possible in electronic format. For example, every time I read an article, I make notes, these, as well as any pdfs are added to the research binder, which I subdivide into relevant themes.
c. write an outline (I use a word processor for that, or simple write it out as a flat text file in Scrivener). Import the outline so that each chapter is a folder, and each section is a document within that folder. The thing to keep in mind is that you can reverse b. and c. if you prefer, AND given the flexibility of Scrivener, you can change the order, merge, delete, etc with no problem. However you do it, it helps to eliminate duplication. If you do the outline part first, then you can make the folders in the research binder the same name as your outline, but I don’t like doing that since of course you use references multiple times.
d. Once everything is set up (takes from 30 minutes to a few hours) you can then write each section. I have started color marking each section as “First draft” “2nd draft”, “Revision after review by outsiders”, etc. You can merge, split, promote, delete sections as you will and as the ms develops. The trick here is LABEL EACH SECTION FULLY. Think of it as a container: the parsimonious way to write scientifically is to ensure that each container contains one ‘thing’, that is, major subject of interest. Since I use MLA/Chicago referencing, I also have a file at the end called REFERENCES (since I use Bookends, which plays very nicely with Scrivener, this is not strictly necessary, but I am old fashioned).
e. Once the MS is to your satisfaction, compile and export it to your word processor. This is where you do the formatting: tables, figures and captions, headings, TOC, etc.

I find (and my experience includes six academic books, over ten novels, and numerous papers) that working that way cuts around 40% of the writing time of a scholarly work. To add to that, I have the feeling (though can’t substantiate it) that it also improves the quality: the references are there for immediate consultation, arguments can be structured in a logical flow, and redundancies are eliminated.

Have fun
per ardua ad astra