Successful doctoral thesis using DT

Just wanted to drop a note to say thank you to the DEVONThink team. I have recently successfully completed my DPhil at Oxford, and actually finished somewhat early compared to my deadline. I used DT extensively, and am super happy with its search, ability to work across different formats of documents, and be scripted, all of which I used heavily. Thank you!

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Congratulations!

After years of trying, I’m still struggling to find a way to integrate DEVONthink into my work. Since you are working in the humanities I hope you don’t mind me asking a few questions in order to learn from you.

  1. What was the topic of your dissertation?
  2. How did you use DEVONthink exactly? Just as a repository for your research material? Or did you also write and prepare drafts in it which you would then later give a final formatting in a word processor?
  3. What word processor did you use? And why did you choose that particular word processor?
  4. What reference manager did you use? Did you somehow integrate it with and link it to DEVONthink?
  5. You said you used scripting heavily in DEVONthink. What sort of scripts did you use?

Again, I would be extremely grateful if you could describe in some detail how you used DEVONthink. I’m about to give up. I know it has powerful features, but so does the Finder too.

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Thanks for asking for feedback from @lyndondrake. That will be useful and interesting. Looks like Scrivener with DEVONthink (from the post on the Scivener forum) probably used. That is the same combination I use for my more serious writing, although not for a PhD Thesis. As I approached but did not proceed with a PhD, typewriter and a university mainframe were the tools. :wink:

Meantime, what is it you have tried and am frustrated with? What are the friction points and what are you trying to achieve? My hunch is linking everything with DEVONthink? for what I call “just in case searching”. Yes, linking with reference managers probably has friction, but there has been lots of discussion and suggestions on this forum you can search for. Lots of people here will be willing to assist.

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I am planning to do a few posts giving all the details of what I’ve done over the years. In brief, I did indeed use Scrivener (and Bookends), and I developed a note system in Devonthink as well as ingesting research materials. None of it was perfect or ideal, but it got the job done. I also experimented along the way, pretty seriously, with some other systems too and in terms of my ongoing research career I anticipate working primarily in DT going forward. I’ll post here when I’ve written the longer descriptions of what I did.

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That would be a great contribution. Thanks.

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Congratulations from all of us at DEVONtechnologies! We are humbled to be a part of your accomplishment.
:tada:
:partying_face:

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Congratulations, and eager to know more about your process!

Congratulations! That’s quite an accomplishment.

@rmschne
If lyndondrake used Scrivener, as you say, then there is no need for him to to explain here in detail why he chose that tool. It‘s self-evident. If I were writing a dissertation (in the humanities now) I would choose Scrivener too; and I would use Nisus Writer Pro for the final formatting.

Scrivener has a research folder where one is supposed to store original sources, picts, videos and other research material. It would be particularly interesting to hear from lyndondrake what went into that folder and what went into DEVONthink, …and why.

“As I approached but did not proceed with a PhD, typewriter and a university mainframe were the tools”

Same here. :–).
And file cards, in different colors and sizes, were the ultimate research tool, the best achievable and imaginable of its kind. I still have thousands of those cards just waiting for being digitalized. Most of them are excerpts, but some contain my own thoughts about these excerpts.

“what is it you have tried and am frustrated with? What are the friction points and what are you trying to achieve?”

To be honest, I exaggerated a bit. :–). I did not know that the original poster (OP) was planning more posts with details about how he actually used DEVONthink. I was just trying to encourage him to go into more details and, at least, tell us (1) what his academic discipline is and (2) what topic he was actually dealing with. So bear with me, let’s first wait for lyndondrake, and then I will discuss what I have tried and where my friction points are. :–)

In brief, I used Scrivener for writing the thesis text itself. I had already written quite a bit in Markdown using various text editors, including DT. I used DT for notes, especially reference notes. In terms of scripting, I mostly used it for pulling reference information across from reference managers (Bookends, Zotero). I also indexed all my reference PDFs in DT. I used DT partly to organise my information and thoughts, including idea notes and topic notes with references to other notes (sort-of Roam-like or Zettelkasten), and also to search — I found the search incredibly useful especially at the end when I needed to find hard-to-recall specifics to fill in footnotes or provide detailed justification of a point in my argument. At one stage, I worked hard to build a map between DT notes and other notes in TinderBox, but I never really made much progress with this.

I did all my formatting in Markdown/LaTeX. I have used Nisus Writer Pro extensively in the past, and would use that (perhaps with Adobe InDesign for final layout), but the problem in my field (Biblical Studies) is that the main style guide for formatting citations is almost impossible to adhere too outside of BibLaTeX and the biblatex-sbl package. Hence I decided to stick with LaTeX for layout/formatting.

I do have hopes that as Zotero, and hence CSL-based processors and in particular pandoc-citeproc, make progress towards more complex style implementation, I will one day abandon LaTeX altogether, so my main investment is in pandoc-flavoured Markdown. Scrivener compiles easily to Markdown, DT works well with Markdown, and I can always edit in a text editor, so it feels like a plausible long-term investment.

The biggest change I am planning in the immediate future is around citations. As you can see from the scripts I’ve posted in the past, I always struggled with the gap between my reference manager (Zotero for a long time, and Bookends) and DT. I only really need a reference manager to generate the citation entries, at the moment in BibLaTeX format, and perhaps also in JSON for CSL formatting. I would much rather work with my PDFs, EPUBs, random docxs, and all my literature notes in one app, namely DT. It is not too hard with custom fields to add the reference information (a bit clunky, but then Bookends and Zotero are both clunky in different ways too). Then it’s just a matter of scripting the generation of the appropriate BibLaTeX code fragments for each reference. Funnily enough I have a fair idea of that code because in both Bookends and Zotero, the demands of the SBL style meant that I had to customise the output pretty heavily anyway.

Once I’ve done that the reference manager piece goes away, and I’ll be working almost exclusively in two apps: DT and Scrivener, with pandoc and LaTeX behind the scenes doing the formatting.

Hope this gives some idea of what I’ve done.

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To whom? self-evident is reflexive, so indeed maybe it it evident to yourself. This does not mean it’s also evident to anyone else, myself included. Also, there are other applications and avenues @lyndondrake could have taken. Scrivener may be good but it’s not the only solution for everyone.

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Congratulations on completing your PhD! I am glad to hear that DT was useful for you. Thank you to everyone in this thread (and others over the years) for sharing details about how they have used DT for research. For my own research projects, some tools have worked better than others, but I think it is safe to say that DT has been at the top of the list as part of everything (articles, books, PhD, presentations, teaching, and so forth).

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Thanks for a complete explanation! Very useful.

Sort of off topic, but perhaps of interest to those reading.

FYI, while I have never attempted to format output from Scrivener into a PhD thesis format (which I presume the university has specific rules), I have good success using Scrivener’s built-in LaTeX compile formats, with a few tweaks added over the years, where a TXT file formatted for a LaTeX compiler is the interim output. I use the “memoir” Document Class. Any/most LaTeX tool apparently works, but I’ve been using “texmaker” to do that hard work. I like how Scrivener facilitates automatic TOC, Index, etc. into well-formatted document (which I print to paper and/or PDF). Never found need for Markdown and/or pandoc to be involved, but for complex stuff I can imagine these may be helpful.

So … DEVONthink in a window on the left for research, copy/paste notes, etc. and Scrivener in a window on the right for writing, with macOS as the integration “app”.

The pair of these apps fruitful and valuable (profitable) for me for a long time.

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I am pretty much where you are. I use Bookends somewhat, I even have some pdfs in there. Like you it is for formating and citations in principle, though I use it slightly differently now.

I have to say I am happy with my current set up. Bookends DEVONthink 3 and a writing app. I also have LaTeX but don’t use it much now.

I wish Bookends was searchable via Finder, but you know, I just put a print out of the current state of Bookends into DEVONthink 3 and everything is searchable from there. At least you know you have it so to speak, it is easy enough to find it in Bookends if one needs?
I did used to import references just to search them. There is probably better ways of linking Bookends and DEVONthink 3: I await the experts!!

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Oxford’s rules are thankfully not too horrible, but yes, I ended up writing my own LaTeX template for Pandoc. I also ran into a slightly fiddly interaction between pandoc’s idea of what should happen to citations inside footnotes and my own, but with some help from the pandoc-discuss list I have a filter that produces the LaTeX output I need.

And yep, I’ve got two external monitors, one for Scrivener and one for DEVONThink, more or less.

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FWIW, this is what I do, on both the Mac and the iPad. (Although the Apple Pencil has brought GoodNotes into the iPad mix.) I’ve found that closer integration doesn’t really provide enough benefit to make up for the added friction. (Although I’m writing mostly feature length articles, not theses, so the reference management load is significantly smaller.)

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@lyndondrake

“Hope this gives some idea of what I’ve done.”
Well, actually … not really.

Your field is Biblical Studies and you used LaTeX because in Bookends you couldn’t create the style your supervisor demanded. Right?

You said: “the problem in my field (Biblical Studies) is that the main style guide for formatting citations is almost impossible to adhere to outside of BibLaTeX”

Could you give an example? And by that I mean a demonstration of style elements you need that can’t be reproduced in Bookends?

Also, what do you mean by “the main style guide”??? What style guide are you talking about? And where can I access that style guide? Please be a bit more specific.

I already have “The SBL Handbook of Style. For Biblical Studies and Related Disciplines,” and there is no need for LaTeX there, as far as I can see.
I assume you already checked this out with Jon, the developer of Bookends. Nevertheless, I would love to see some concrete examples.

“At one stage, I worked hard to build a map between DT notes and other notes in TinderBox”
I have only superficial knowledge of TinderBox. TinderBox reminds me pretty much of the old HyperCard. Therefore my question: What sort of notes would you not store in DEVONthink but rather in TinderBox? And why?

And finally, do you use DT for areas which are clearly outside Biblical studies and your academic interests, …such as daily news (help you grasp the Russo-Ukrainian War, for example), computer and software related stuff, finances, etc.? Or do you use the Finder for that?

And as to Zotero, it only fully works if you are using MS Word, LibreOffice and GoogleDocs (not sure about LaTeX though). See:
https://nisus.com/forum/viewtopic.php?p=38466

@BLUEFROG
„Scrivener may be good but it’s not the only solution for everyone.“

Thank you, BLUEFROG, for you comment. You are absolutely right. Thanks for correcting me.

The reason why I said this is based on my personal experience. The biggest problem I’ve always had (in the past) is how much existing knowledge I can take for granted by my readers. If I want the following points in an article or a book to come across (a, b, c, d), I often soon realized that if the reader is ever going to understand b, he or she must first have understood d. Scrivener makes it easy to “correct such mistakes” by shuffling whole chapters around as well as displaying only a limited number of files in one single window for concentrated work.

I assumed @lyndondrake’s field was literature, history, philosophy or a similar field where people usually don’t need mathematical formulas and a large number of images; and for those subjects Scrivener seems a good choice. I didn’t know that his university or his supervisor demanded a reference style which – apparently – can only be rendered in LaTeX.

The problem I had in the past (which I mentioned earlier) has now been resolved by the Internet: If someone doesn’t know what Njála or Njáls saga is, he or she can google it! If the reader is too lazy to do that, then it’s his or her own fault if (s)he doesn’t understand the article.

@tudoreynon
„Bookends […] is for format[t]ing and citations in principle, though I use it slightly differently now."

“though I use it slightly differently now” … What do you mean by that?? Please explain.

I have started to store some pdfs in it. Hard to explain what the criteria are; it is like those we used for ‘piles’ of Xeroxes in the old days! One sort of knew where things were…
I really use those bibliography programs historically to format, so that I can just copy and paste a citation properly without fiddling as it were.
Though in practice I found one is always messing with them for one reason or another. I try to use the style recommended by The Linguistic Society of America now. It is neat and highly adaptable with little trouble for say, podcasts and the newer ones you need. The number of styles is ridiculous out there and I feel there should be more standardization.

It turns out the Bookends attachments folder, unlike Bookends biblio lists themselves, are searchable with Houdah Spot since they are kept in a folder in Mac Documents. I don’t really understand it.
Though the Bookends citations themselves can’t be searched, I assume Finder will search the attachments though too, since Houdah works through that. I think I have some papers in both Bookends and DEVONthink 3 as well and really, for me, space is now now problem.

Some PDFs and papers are more closely tied to the citation than others in my mind, I can’t explain beyond that. It is very much a system that is more than a sum of its parts though that I have. It would not make sense outside DEVONthink 3. I hardly use Groups in DEVONthink 3 anymore and I think that affected my workflow outside it somewhat.