A user’s journey into DEVONthink: Professional academic workflow

Stuart IngramAs my professional role has developed I have become more involved in authoring, reviewing, and submitting academic papers, amongst other activities such as grant and report writing. Prior to DEVONthink Pro Office (DTPO), there was a lot of flicking through numerous PDFs and web pages, whilst trying to keep track of different sections of writing, of which there are always several on the go at once. The main apps in use here are DTPO, Bookends, OmniFocus.

Researching the subject

I suspect that there is a ‘DEVONagent’ sized shadow cast over this section, but for the present if I want to find an academic paper, I use the Bookends online search. This means that everything is teed up for me to import the citation and download the PDF in the most efficient way without getting tangled up in the distractions of the internet.

It searches big, common libraries such as PubMed, Google Scholar, and certain specific institutions, and will drop into a built-in browser for further searching if needed. Any other research is completed via my best friend and yours, Google. Or, in extremis, I might even go to the university library!

Bookends search window

Once I’ve gathered some research material I then use DTPO as a basic outliner. I create a RTF note with a list of main concepts, chapters, and sections and keep this open. Then I run searches in DTPO on each of these, varying the parameters (e.g. using fuzzy search), and checking out the ‘similar words’ sidebar (which pulls up, you guessed it, similar words by spelling and context).

Hyperlinks in DEVONthink Pro Office outline

Usually at this point I will start a new note on each of the sections, which I can then hyperlink back to my original outline note. At top of each note I add a hyperlink to the outline, which has hyperlinks to each of the notes, and this way I can hop between sections at will with DTPO prompting me to save each note as I move on, very handy. To note, the hyperlinks will only work with RTF rather than plain text files.

Writing text

There’s something of an obsession here — I love the process of writing and so naturally I’ve looked quite extensively into the options. I fell in love with Ulysses by The Soulmen, and then fell back out out when I realised it saved text in a propretary format and database. I used Scrivener to draft an academic paper recently, and really liked it’s storage of research documents with the text, and the navigation and display options, especially ‘Scrivenings’ mode. However again, .scriv files are used which is a proprietary format. But with these I still need Apple Pages or (the horror) Microsoft Word to finish the job.

So in fact now all my draft writing is done in RTF files inside a group in DTPO, with hyperlinking as above, so I can reference my research material in the main DTPO window at the same time — a fair approximation of a Scrivener style workflow. Nearly all my current academic writing is collaborative in nature, and at some point (usually not too far after drafting initial sections) that means succumbing to Microsoft Word in order to revise and develop with several colleagues.

Text notes for a familiar blog series

Note: For the future, DTPO has wiki/shared database capabilities (basically you can make part or all of a database available via a web server to others either for reference only, or with editing rights if they use DTPO), for advanced collaboration on large projects, but I haven’t needed to develop this yet.

Handling citations and academic papers

My citation manager of choice is Bookends, because it seems to have the best integration with other applications (and because I actually got quite a long way on the free version of up to 50 references). The normal setup here is to have PDF files stored in the Bookends attachments folder (mine is in my Dropbox).

But I’ve said a few times in this series that I want to keep as much as I can in DTPO, so I looked at the alternatives. Telling Bookends that its ‘attachments’ folder is somewhere within a DTPO database is not supported (or recommended) by DTPO, so the other option seemed to be linking the citation in Bookends to the PDF in DTPO via a hyperlink in a Bookends field. There is a good discussion on this topic here and more thoughts from other users would certainly be welcome!

For now, I’ve settled on indexing the attachment folder of Bookends. Both DTPO and Bookends are set to open PDF files with my editor of choice (Skim), and the annotations are visible in both applications also. There is further integration between the two apps in that DTPO can batch import RTF files detailing each of the citations in Bookends (which also adds an indexed ‘attachments’ folder as above to the database).

Bookends import

In terms of tying all this together I rely on OmniFocus to remember tasks and schedule due dates for submissions and meetings (of course, the minutes go into DTPO). I’ve yet to find any item in DTPO that I can’t copy/paste a hyperlink for into OmniFocus — files, groups, databases, smart groups all work fine, and especially useful is linking to those outline RTF files mentioned earlier, which takes me straight from the task to the project outline.

There are myriad good articles on academic workflows out there (https://macademise.wordpress.com and https://macademic.org to name two), and innumerable ways to combine the various apps which may or may not simplify things. I’ve tried to keep things really simple here and there is probably room for improvement, however I’m really keen not to overcomplicate things in this area.

Next in this short series: Personal usage. 

8 Responses to “A user’s journey into DEVONthink: Professional academic workflow”

  1. Daniel says:

    Hi, great to read! two comments:
    – regarding text editing in an open format: I highly recommend Nisus Writer Pro. I’ve written my master thesis in it, found it a great writing support and got a great result.
    Nisus Writer Pro offers integrates very well with DT Pro, has excellent text handling, and is more stable and much better to use than Word (e.g. handling of tables, graphs, etc. which is a big hassle in Word).
    – it would be great to read some user stories of professionals (non-academic, office workers) or people who use DT Pro for their home filing (I guess the next instalment covers part of that 🙂
    best, Daniel

  2. Adam Smith says:

    Hi Eric

    I’m enjoying the series, do keep it up!

    +1 for Nisus Writer Pro, it’s a great word processor and better than Pages. Like Daniel, I have used it for dissertations and it’s rock solid. But if you need to collaborate with others, you’ll inevitably end up in the dreaded Word.

    I also like Ulysses for writing and have no problem with the fact that it stores its text in iCloud not in DTPO. I can always copy chunks into the DTPO group when I’m finished but Ulysses as a drafting tool is great.

    Unlike you, I’m using DT itself for annotating PDFs (on my iPad and/or Mac). It seems to do this well, and the sync works fine. I haven’t needed to use a separate editor like Skim.

    However, I’m struggling with bibliographies. I need to look again at Papers 3 and see if I can make it work with DT.

    Good luck with the blog!


  3. Devin says:

    Hi Stuart,

    I’m also enjoying this series. I’ve been using DTPO for 2+ years (feels like longer!) but am finding plenty to learn from your thougtful posts. So, thank you!

    I’ve heard good things about Nisus Writer Pro, but wanted to recommend that you also check out Mellel. It’s a beautiful and solid app, with a styles feature that makes much more sense than any other word processor I’ve used, and an outliner that is very useful too. And all sorts of other magical features. I especially recommend it to you because it works so smoothly with Bookends, offering a “Live Bibliography” that I don’t think you can get with any other reference manager / word processor combo.

    I think both Nisus Writer Pro and Mellel offer demo versions, so you can see what you feel comfortable with.

    Good luck with your MSc coursework and other projects!

    – Devin

  4. Stuart says:

    Thanks everyone for the positive comments, good to know people are finding this interesting, and enjoying reading as much as I am writing.
    Adam – since writing this I’ve also started annotating PDFs in DTPO. For some reason skim refuses to save a separate skim notes file for me anymore, which was the main reason I had for using it.
    All – yes I’ll check out Nisus! Unfortunately constant collaboration (and therefore Word) is a fact of life for me pretty soon after the ‘scribbled draft’ stage so I don’t think I can esacape it!

  5. I’m continuing to enjoy this series but one little niggle (maybe not down to you, Stuart) but where a screenprint from DTPO is included, could you make sure the image is clickable to enlarge? In this latest post they (mostly) are but they do help to illustrate what’s being said (written).

  6. jneumann says:

    If there is a linked resource, we will endeavor to link to it.

  7. @ David R Parker: My fault, I missed to click the right button. Changed.

  8. John Johnson says:

    Thanks for the posts. I look forward to hearing your Mac Power Users interview.
    For document creation, I recommend investing some time to learn LaTeX. The best editor I’ve found for LaTeX is Texpad – it has great features that simplify the process, a nice preview screen, etc. Once in the (LaTeX) mindset of thinking separately about your document’s content and its presentation, it is really hard to go back.
    For collaboration, try sharelatex.com, if your coauthors are LaTeX savvy.