Writing a dissertation has two steps: writing and editing. Writing can be done in DT without any problem. All tools are there. Editing perhaps need an additional software, but I am sure @BLUEFROG has a solution for that as well :). Again, up to the writer!
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Jim are you still working on your Theory of Everything dissertation using DEVONthink? The one that will gain you the Nobel Prize? We’ve been waiting for you to publish.
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Actually, I’m hoping to get the Nobel, an Oscar, a Grammy, and a Tony award for it!
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Jeff Taekman has published a comprehensive workflow for academic writing at his website: Workflows in Personal and Professional Productivity <://wippp.com>.
A lot to chew on, including his use of 15(!) Apple Ecosystem applications including Devonthink 3 and Devonthink To Go, which he uses his webpage to explain.
"Some criticize my workflow for its complexity, but I can assure you that it is amazingly functional once set up. I can’t imagine working any other way.
I’ll start with the “meta” infrastructure programs that make the whole workflow run, including the set-up. I’ll then cover how I collect information . After that, I’ll write about how I read and synthesize the information to help with sense-making. Then, I’ll go over extracting information . Finally, I’ll take you through the writing process , from concept to manuscript/grant submission. I’ve included links to past articles to show how I’ve set up my infrastructure."
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Jeff’s “workflow” (a word that makes me cringe) is really not complex. Reading closely he’s not using all that software for every bit of writing. He’s mainly mentioning how he uses a collection of commonly-used software. (Other than OxMD – and there are other means to get info from PubMed.).
Pay attention to his task groupings: “Infrastructure” (stuff in the background); “Collecting and Extraction” (got to get the documents somehow); “Synthesizing” (got to make senses of a pile of annotations and notes); and “Writing” (the point of all the above). Anyone doing the work discussed in this thread will do the same.
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Not having heard of Paperpile before I have just checked it out. Personally I don’t want to let Google pry into my life any more than it does already. Also a pretty interface for organising etc pdfs when really all that’s needed, at least all I need, is to rename a pdf on arrival and put it it in a folder in Dropbox which is indexed to DT3 where I can further do whatever is enough. Even if not renamed an ocr using DT3 will access the content.
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I think this is good example of why different academic fields (or maybe better termed different readers of academic publications) are adapted best to different workflows.
It sounds as if your work may be such that a scholar in your field can assemble a curated collection that is nearly complete with the classic or seminal articles in the field. The field may grow at a slow enough rate that an active scholar can continue to read and collect new key articles in the field as they are published. In such a field, organizing these classic articles in a reference manager may well be an ideal solution.
But in clinical medicine and many research areas of medicine as well, published knowledge grows so fast with a doubling time measured in months that no scholar or clinician can fully master even small areas of specialty.
As a practical example, suppose I am accessing the literature on knee bracing for cruciate ligament injuries and I want to share with my students or colleagues a few pertinent articles as part of a class lecture or a draft of a paper or presentation or for my own use while writing a draft article. I will typically share such articles via a URL:
Note this link is basically a dynamic website updated regularly which contains not only (a) Full text of the article but also (b) Links to similar articles in the literature, (c ) links to other articles which have cited this article, and (d) links to references cited by this article.
Now contrast that with the classic output of a reference manager which gives simply static references in AMA or MLA format etc:
Now which is more useful for research or teaching or clinical use in medicine - a collection of dynamic URLs (stored in DT3), or a set of formal MLA-styled citations ready for publication (stored in a reference manager)?
Note that if/when you get to the point of actually preparing a manuscript for formal publication, the conversion from URL link to formal citation is easily done. But I suspect even for active publishing scholars in medicine, that represents a minority of cases; the active URL links in DT3 are generally more helpful as a primary means of saving citations.
So that is my dilemma as to why I presently consider DT3 to be my primary repository and reference managers to be secondary. I am interested in learning other approaches to this issue.
(By the way- it is not exactly an either/or situation. It is of course possible to link a URL to a citation in a reference manager, just as it is possible to link a formatted citation to a DT3 record. My main point is that citation manager software excels when your main desired output is a formal list of formatted citations; DT3 excels in almost every other situation.)
What I really hope is that someday academia gets over AMA/MLA/APA/NLM formatting and just accepts URLs as valid citations. That makes so much more sense to me. At that point, I would see no need at all for reference management software; DT3-like or generic bookmark management software will replace it for all.
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Good point. All apps have tradeoffs. At any rate, a reference manager is much more than just rename PDFs. You need it to capture references, cite references using differ styles, read the papers, take notes, keep these notes, etc. in my case, paperpile helped me to capture, manage, read, and cite all kinds of reference without any friction. As always, there are other apps available for testing.
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You present the scenario very well, and the use-case is very clear. Incidentally, you illustrate why DEVONagent is so useful in some disciplines, but not in others. I could never think of a use for it myself.
I have worked in various fields over a zig-zag life. Most recently in history, psychology, and latterly in counselling/psychotherapy. As you observe, these are disciplines that move rather more slowly than medicine. Historians typically write books that take several years to complete, and often refer to archival material. There is no URL, and I suspect there never will be, for a page in General Rawlinson’s diary (held in the Churchill Archives Centre in Cambridge). I spent long hours photographing the diary, and even longer hours transcribing it. (And were I to write an article about it, I could imagine that it could take twenty years before anybody read it, and maybe a century before anyone wrote another.) Archival research is a marathon, and a very uncertain one. I remember that my professor (not a historian) expressed an interest in going to the National Archives in Kew and researching the use of machine guns during WW1. “Will it be in a box marked ‘machine guns’?” he asked. Sadly, I had to tell him that it could be in any box in the whole damned archive, and any nugget of information could as easily be in the middle of a discourse on women’s petticoats as anywhere else. “Seek and thou shalt find” was not written by an archival researcher.
So, I’m afraid academia as a whole is unlikely to move to URLs as valid citations, because so much material in so many fields will almost certainly never have a URL. Even if every page in all the archives in the world could be digitised and given a URL, that still leaves material in private hands. DEVONthink was very useful to me for storing photos of archival material together with transcriptions of it, but Bookends was better for references, in my work.
As to finding things using DEVONthink’s undoubtedly sophisticated search functions, there were times when it occurred to me that a particular idea (e.g. deportment) expressed in a source work was important, but the word “deportment” never appeared in the text. It was implied, not stated explicitly. That is when human memory, and different tools, like Tinderbox, become useful, because they allow you to map concepts and connections rather better. But I have strayed off topic.
Anyway, I am glad that medicine is moving fast 
. We need it to do that.
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I know this gets off point - but that’s interesting. Do you not see a trend toward having most archival sources digitized? I realize that does not necessarily mean they will be available publicly on the web - but are there really major library collections without a plan to scan and make it accessible remotely?
Indeed - just as you have pondered what the use case is for DevonAgent, I keep pondering the use case for both Tinderbox and for the more recent interest in graphing connections such as Obsidian can do. They are all fascinating pieces of software, but these application depends very much on the nature of the underlying discipline being studied.
Aspirationally, but it’s not easily funded. See e.g.
At the risk of continuing off the point (apologies to all) – a trend – yes, of course. But just to take the case of the Churchill Archives Centre, it has material relating to about 600 people, each of whom has anything from one box to several hundred boxes of material (for Churchill himself, it is about 3,000 boxes). When I was working there I was aware of about three or four staff in attendance. I cannot imagine how many years it would take for them to digitise all the material. I recall that at another archive, when I asked for a photo of a document, it was considered so fragile that it first had to be sewn into a transparent envelope made of an inert material to protect it. It took several days to complete the request. Then again, there are customary practices when working in historical archives that may not be obvious to outsiders – such as preserving the order that the documents are in within a box. It may not be important, but in some cases the order itself is a potentially valuable piece of information about the material. I once showed a professor a box of my own family heirlooms, and I noticed that he was careful to put them back in the box in exactly the same order as he had found them. It was a tell-tale sign of someone used to working in archives. Digitisation would only give us part of the evidence. Indeed, the opportunity to go directly to a document in a database is potentially problematic, because the researcher might miss something from the context – the other documents in the same box. So it is not as simple as it might seem at first.
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I think achieving digital archival of “most sources” is probably never going to happen. For example, the United States government’s archive (NARA) has a goal to digitize 500 million pages out of the 12.5 billion pages it is custodian of by 2024. That would be 4% digitized, if the goal is achieved. At the same time, by their own count, the service receives 100,000 cubic feet of new paper records annually. If NARA could ever catch up with digitization, it would be almost a century away.
It is probably more realistic to assume most archival material will be entered into digital catalogs covering all available digital and analog records.
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Just to trow another idea in here: I use DT for everything PDF (including Print->PDF for webpages), and OneNote for screenshots and handwritten notes.
OneNote is surprisingly underrated, but the one killer feature for me is that it will index my handwriting and make it searchable across all my devices with pretty good hit rate. It does mean you need a Microsoft Office subscription, but a family plan is not too expensive.
I organize my folders using DT, cross-referencing files where applicable; and I organize DT ‘Workspaces’ for special subject writing when I want to have more efficient referencing of main go-to files, including a writing sandbox …
I annotate pdfs with Readdle ‘Documents’, mainly on my iPad, or sometimes on my laptop with ‘Preview’; I import the annotated pdfs into DT and then hit ‘Summarize Highlights’ which damn near instantaneously indexes the annotations and highlights brilliantly. This is so helpful.
I am in the habit of copying my Sandbox writing out into Word or Scrivener but I might try DT for this, given some of the comments here.
Good luck … it’s worth figuring out an efficient workflow for sure.
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What is the goal? If you are talking about just writing your thesis, then I suggest working backwards. Are you going to be using Word, Mellel, Scrivener, LaTeX, Lyx? When you say your “journey”, that potentially covers everything from lab notes, to equations, statistics, and both original and source material. The setup that I use a legal scholar is not going handle the demands of a bio-physics researcher.
Whatever you do, do it consistently and in as few programs as possible. One thing that I like about DevonThink is that it doesn’t modify imported data (although this can be a problem if you are trying to save databases as some services like Box won’t work). This is important for two reasons: company going out of business and database corruption.
While DevonThink has been around for quite a while and seems to be a stable company, you should always have a plan for what do to if the service you use suddenly goes out of business. I came to DevonThink years ago when CircusPonies Notebook went out of business and have been very pleased.
In terms of database, Bookends gives you multiple naming options for saved PDFs. I have had problems over the years where I have had to relink PDFs to the entry in Bookends. This does not happen in DevonThink because of the nature of the program.
Best of luck in your research!
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I think you meant to reply to the original poster?
This assumes you use a Mac or ios.
You must give Hook.app a try. Linking documents and recording their sources.
Another is LiquidText.app for taking notes from PDFs.
I hope this helps.
There’s a lot of good advice in this thread. Sorry if I repeat some of it.
The answer does probably depend on what discipline you are in and if you search for “academic workflow” you will find pages where people describe workflows that work in different disciplines. There was, for example, a really interesting one for historians that I found a while ago (I forget the authors’s names). I did not adopt it because I realised that, although it would have made sense to start with it, it did not make sense to switch mid-project because so much of my data was already in the system that jumping over to a better system would have been a lot of work. So it is worth sorting out a system at the beginning.
Like some others in the thread, I do historical research involving archive, and DTP3 is brilliant at processing the photos I take of documents into searchable (mostly) PDFs. Somewhere in the forum is a macro for merging and renaming PDFs that I use routinely and which has saved me hours of work. I then catalog them in Bookends. There are methods on the forum for linking items in DT to their equivalents in Bookends, so that you can go quickly from one to the other. I also search in DT, though that is more limited because my documents do not always OCR into coherent text. The OCR works better with modern printed material than with ancient carbon copies that have had plenty of time for the ink to fade and the paper to go brown, Or those purple duplicated documents where the colour eventually disappears pretty much completely.
A key point that I don’t think anyone has mentioned is you need to make a decision about how and where your documents are stored so that both DT and Bookends can access them, and whether you have a single copy or a copy for each app, ideally with links. DT does not like other software doing things to files stored in its databases (potential disaster awaits if that happens) and Bookends needs to know where attachments are, so you don’t want to move Bookends attachments when you are in another app. This is where you need to decide whether you are going to store documents inside DT databases, and then copy them to the BE attachments folder (or vice versa), creating a link, or store them in a folder where both BE and DT can link to them.
I may have misunderstood, but I am not clear why you should want to add a second reference manager to the mix (Zotero was mentioned). DT should be good for notes if you don’t want to do notes in Bookends. If I were starting from scratch, I would do a lot more note-keeping iand creation of metadata n DT.
I do not store PDFs in Scrivener. It may work for some people but does not for me. Scrivener is brilliant for writing and organising the final thesis/book and is great for storing drafts and editing them into the final manuscript. The merit of using Bookends and Scrivener together is that you can have a document open in Bookends, and be typing something in Scrivener. When you want to cite a reference, Cmnd-Y, Cmnd-Y and a code for the currently selected reference is inserted into Scrivener, just like that. Add the page number or whatever else you need, and when you later scan the document you will have a perfectly formatted reference.
I arrange stuff in DT to mimic the way it is organised in the archives I have got it from, including the order in which documents occur (the position of a document in the file might tell me the date or other context of an undated piece of paper), but as I have already got a lot of Groups set up in Bookends, corresponding to my subject matter, I often find myself going back and forth between Bookends (organised by author or whatever) and DT, where they are organised as in the archive, depending on how I want to think about my material.
One thing to note is that DT and Bookends, along with Tinderbox (that would complicate the mix!) have the best support I have ever encountered. Seriously good support. Scrivener is good too, though I have less experience of that.
Good luck.
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I’m a year + into PhD , you must become a virtuoso with whatever Apps you select.
Scrivener - advantages (that sold me) i) outlining (via the Binder) and ii) almost impossible to loose/ delete anything; disadvantages = learning curve. Solution = same
BE: works really well with Scrivener (and Word, and Mellel (don’t bother there)
again; a learning curve
Still working out how to integrate DTP into things - its great for archiving (and probably history - DON’T buy the “training” videos by the history people - hopeless for our work)
DTP great for OCR and strong and finding
good luck
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