academic use with Yep

Started to use scrivener. Introduction i am a psychiatrist with a lot of teaching to students and residents as well as writing articles. Mostly about RCT’s My workflow is as follows:
brainstorming and gathering information in Devonthink, i have also got Curio but this is more for graphic designers, it is more visual compared to devonthink and devonthink has some advantages already discussed in this forum. Next i create a draft with scrivener for an article, chapter or lesson, wich allas i have to export to word and endnote.
Recently i collect articles in pdf format in yep, yep is a kind of iphoto but for articles, it works with tags and you can categorise the articles also in subprojects, it is a marvelous addition and easy to use. A central place to keep all your articles which can be easily retrived.
You can try it for free!!

To the academics (and any others who have to add footnotes, cross-references, etc. post-Scrivener in a word processor):

I’m interested in what people do in post-processing Scrivener-written articles or books. I’m a bit afraid of what would happen if – after exporting into Mellel (for ex.), adding my footnotes/endnotes from Bookends, and spending time applying formatting – I find out that I have to make considerable changes to the TEXT and its organization itself. How does one ensure that all the “word processing” work is not lost, or that such loss is minimized?

I’m not sure what you are asking here, sorry. Are you wondering if things like italics, bolding, whatever, get transferred from Scr. to Mellel? In my experience, there’s no problem there. What wasn’t clear, though, was that if you are doing all of this post-Scr. work in Mellel, what are you concerned would get lost? I mean, once you’ve got it in Mellel, added footnotes, formatted, then, well, it’s ready to go, right? Where and what are you afraid things would lost in the process?

This is my workflow–to go from Scr. to direct export or to Mellel or Word (if I have to send it to someone who has to have it in Word). Going from Scr. to Mellel is no problem at all, except that I have to convert footnotes to endnotes. Then I polish it up and I’m done (Mellel doesn’t do cross-referencing yet, so that’s not an issue there). Similar with Word. There’s some minor tweaking then it’s done.

Sorry if I’m missing the point. Perhaps if you could explain more fully what your concerns are?


Well, in Mellel (for example), I use the styles to, err, style. In other words, I would never put a book title into italics while typing; I would apply it in the word processor, by applying my style “Book-title”; transliterated words the same. I wouldn’t apply “16-pt” bold to a sub-title; I would apply the semantic style “subtitle”, which I’ve specified to be a 16-pt bold. Footnotes/endnotes are evident. Section or page-breaks likewise.

Some of this might be very obvious to you if you’ve already used Scriv + (word processor) for a long document. I’ve only used it for short pieces and essays, so I’m asking about the longer, more structured documents.

Thanks for any input.

Ah, yes. Well, I think I work differently from you. I know folks who use styles instead of formatting, but I am among the latter. While I might use Apple’s rather primitive styling pallette to create headings, to italicize the name of a book, I would simply use italics on the spot, not styles. Therefore, I never have any problem going back and forth between programs. And I use pretty standard fonts. I understand the logic of using styles, but it’s never been part of my writing practice, personally.

So, sorry I can’t help much here. I write in Scr., transfer it to Mellel or Word for polishing and any modifications to spacing or notes that might be required, then off it goes. This last minute polishing really is pretty minor. Most of what I need I’ve already done in Scr. itself.

The only real work I’m doing in Melle is in writing my dissertation, which, save for part of the first chapter, was written entirely in Mellel, since I hadn’t discovered Scr. way back when. I also needed multiple note streams.

But I have developed and am developing both large and small projects within Scrivener. In some cases, given the export possibilities, I haven’t even needed a ‘word processor.’ I am, in fact, beginning to move away from the idea of a word processor at all.

Sorry if this isn’t helpful.



As usual, your response is quite helpful. But I wonder: as you move away from the concept of a word-processor, as you state, how will you achieve more complex elements of academic writing (for example, multiple note streams, as you mentioned).

I guess my perfect world (here we go again) would be the writing environment of Scrivener (notes, metadata, outliner, hassle-free writing environment), with more robust academic/technical writing features (like those in Mellel, or currently being developed therein).

Hi talazem,

I just do all my structuring in Scrivener so that I can get access to all of the notes, pdf stuff, source materials etc etc.

Then I transfer it all to Word (or Mellel or Nisus) as an rtf.

Then I go through it doing nothing but styles (as you describe it).

The reason is that it instantly generates my table of contents, index, and tables of figures and tables. It also gives me a consistent layout, because I mostly rename word styles to my own style set. For example, Doctoral level work has a PhD style set, articles for publication, and formal conference presentations also have their own style sets. Easy peasy!

Such a simple step after doing all of the real work in Scrivener.

In summary: build your work in Scrivener and rtf it to a proper word processor to finish it off.

Mr Lightning,

Thanks for your response. That does seem natural and apparent enough. My questions revolves around two cognate issues:

  1. what to do if – after spending time styling as you mentioned – you have to go back and make alterations to the text? I mean, if they are just small typos, etc., then you can just fix them there, and go back to the Scrivener manuscript and do the same. But what if they are more significant? On the Scriv side, all would be fine; but wouldn’t it take a lot to do the smaw again in the word processor? Styles, footnote alteration, bibliographic entries scanned from Bib programs like Bookends, headers/footers, etc.?

  2. Sometimes academic writing requires that one avail oneself of tools like multiple note streams, or bibliographic info, while writing. For example, I might cite a book, but also want to add a comment to the citation – this is part of the writing process effectively, and not just post-writing processing.

I am just wondering out loud. It might be that the more severe of these issues might very well have solutions, like just learning to use the Bookends mark-up (for example) for citations while writing, and adding any needed comments right into the curly brackets. But how about the other issues?

Thanks for your input.

Ah, yes, well you refer here to one of the times I do and would use Mellel! Complex note streams. My dissertation is utilizing this feature and there is no other wp that I know of that does this so well. And with Mellel’s outlining feature, it’s definitely not a negative experience to work in the program!

Of course, eventually (at least that’s the claim), Mellel will do indexing and cross-referencing, etc., in other words, more complex tasks than Scr. is capable. And it works with Bookends to do citations, which is something I never bothered to master, but a lot of folks use that feature extensively.

So, I say ‘moving away’ from a word processor and not discarded altogether! I have come to think a different way about all this, however. I used to wish for one single program to do it all. I mean, I still use DT Pro and MacJournal in addition to Scr., and other small programs that aid my workflow. What I’ve come to over my years of experimenting and searching is that it’s just fine to have a ‘suite’ of programs rather than one that does everything. I seriously doubt Scr. could have the flexibility and elegant interface it has and have everything packed into it each of us could possibly want in one program. I’ve concluded that each program I use needs to do what it does really well and play well with others. So Dt does really well what Dt is designed to do and fulfills that need, and Scr. does what it is supposed to do really well, etc. That includes Mellel for the most part, though I’d happily abandon it for a wp that does what it can do AND has an easy-to-use interface!

I guess what I was trying to say earlier is that, for me, since I’m moving more away from strictly academic writing, Mellel won’t fill a need so much any more. It won’t be required and Scr. can fill the bill for most of what I do. But if you are doing a lot of heavily academic work, and if I ever do again as well, then I don’t see how we/I could truly move away completely from using such a program. In such a case, I’d either write my draft in Scr. and then add the more complex elements in Mellel or, if that wasn’t practical (which would be sad because I love writing in Scr.), I’d just do the whole thing in Mellel.

Does that make sense? That all said, I can definitely understand your wish to meld the powerful writing environments Scrivener and Mellel offer. To have all the flexibility of Scr. and the more robust wp features you need in academic writing, yes, I can definitely see wanting that!


Well may be all that different software programs could be made in different modules. Reviewing some discussions from academic writing one could argue that scr* could be one of the modules; the other being brainstorm and database module and the last module in the workflow would be wordprocesssor and a bibliographic program. This would mean cooperation between different software developers, is that possible or should i keep dreaming?
Regards walter

I come to this product after years using Notabene on PC’s. I’m happy to be moving away from Windows, finally, and was motivated partly by discovering Scrivener.

Anyway, I publish occasionally in academia, and I plan to do this:

  1. Work in Scrivener, jotting down notes and bits of text. I will use Markdown for formatting, since I detest having to move my fingers off the keyboard touch-typing position when I want to make something italic. It’s much easier just to do this.

  2. Input citation information into Bookends. Then I can copy the citation into Scrivener, inside of {}'s.

  3. Export the MMD into RTF, and import it into Mellel. From there, I can scan the file, making properly formatted citations and bibliographies, and fine-tune the formatting.

If I ever need to revise my text, I can go back to 1 & 2. Step 3 is trivial, at least if I use Markdown, since the formatting will mostly involve font selection, and Mellel is good at that sort of thing.

Even with all three pieces of software, it’s still cheap.

Hi byzkarl,

I think a number of academic users would be interested in your workflow, as it is something that comes up often. If you have the time, it would be great if you would start a separate thread in the Tips & Tricks forum to elaborate on this workflow, as it could be really helpful to those who want to integrate bookends and citations etc into their work.

Thanks and all the best,

I second this request. The thread would make a convenient reference point for those of us performing similar tasks using these applications.

I still have to look into MMD and how it is used both in Scrivener and after export to other WP programs such as Word, Mellel or NeoOffice.</MMD Newb>


MMD simply exports a structurally sound XHTML file. If your favourite word processor can understand this and transfer XHTML headers into header styles, thus injecting them into whatever outline it uses – then it should be an excellent solution.

There was talk of the possibility for creating an XSLT which would convert XHTML to the XML formats that some of these word processors use – to establish a minimum level of structure in their native format – but I have not heard of anyone who has done such a thing yet. If that were created, one could simply add it to the Scrivener MMD Export settings and automatically create a Mellel document (for example), right out of Scrivener.