PhD workflow setup - help!

Hi guys. I’ve just started my PhD journey and after a lot of research, bought DEVONthink pro and DEVONthink to go. I have read a few different workflows here and feel the following software works well:

What advice would you give to a new starter like myself to setup a simple workflow that allows me to add papers I need to read in DEVONthink pro which get synced across all my devices so I can read on the go and annotate? The more workflows I read about, the more I get confused as some of them are quite advanced! I’m watching all the tutorials and enjoying tinkering with the software so will appreciate any advice you guys can give me.


Tinkering is one way to figure out the best way to work. Takes a long time. Helps with avoiding real work.

A better way, especially with a research effort you wish to start, is to discuss the concepts with your colleagues – especially ones farther down the path in your field than you are – and see what worked for them. Might be software, might be something else that succeeded for them. Good researchers learn from good researchers – and it’s usually not about software so much as disciplined behavior.

Your question is good but very broad and vague. Maybe you could specify some more? Like “I am studying amyloid aggregation-induced cell degeneration in elasmobranch fish, with four months focused on a literature review, two months for specifying the experimental framework for this phase of my research, and between three and six months of alternating lab and field work. So I need to aggregate the research and compile annotations and bibliography; document my experimental protocol; and then document my lab and field phases.”

Something like that might help others suggest options and methods, with software or other tools, that helped them.


I might offer two points of general advice:

  • Annotate in only one app, not in multiple apps. Either Bookends or DevonThink or GoodNotes support doing annotations. Bookends and DevonThink play nicely together. I cannot speak for GoodNotes in the mix (although I can testify for the good behavior of PDFExpert in the mix).

  • Annotate on the iPadOS (hopefully NOT using iOS). With Scribbles support under iOS14, the translation to go from hand notes to text notes on an iPad with a Pencil2 is now to a standard that Steve Jobs must have been dying to have so that he would finally roll over and support an iPad with a stylus. Were he still alive, he would be in heaven to know that this feature has been robustly implemented. (Yep!)



Not sure what that means?

Give yourself the opportunity to do this, at least. One way to make that happen is to keep the PDFs and the metadata of your literature separate. (Bookends and other apps like it allow for the whole process to be managed within a single app, of course.) So I run Zotero which contains the bibl data of a few thousand sources, but no PDFs, and I’ve never used it to annotate anything. My PDFs instead live in DT (named broadly as Zotero names files: ‘author - year - title’; and in two huge folders, one for ‘primary’, one for ‘secondary’ lit, a division which may make sense only depending on your academic discipline!). I open them from there and annotate as I see fit. Sometimes underlining/highlightng from the Mac, or mostly, reading them on DTTG and annotating there in the native DTTG edit mode, or in another iOS application that supports the file system (PDFExpert, indeed).

Zotero of course comes with a Web Clipper that downloads the metadata and the PDF as attachments from repositories at a single click. I tend to use that; then open the PDF attachment (in Preview) and manually push it to DT with the ‘share’ extension. If you would be downloading 10s or 100s of PDFs at the same time you may want to automate that process. I’ve never felt the need, since I never get more than a handful at any one time.

I write long form in Scrivener, too – but rarely import PDFs into it. I am aware it can act as a project container, but ultimately it won’t scale as DT will, so once more, I write there only, and refer to the PDFs from DT.

Keep it simple indeed, and review your system every now and then. Good luck with the PhD!


I finished a PhD about ten years ago, and the combination of Bookends, DEVONthink and Scrivener served me very well. I would agree with what korm says. But I would add that in my view the workflow that is going to work best for you is the one you devise for yourself. Different fields have very different requirements, and studies within the same discipline may also be very different. There is also the argument that devising your own workflow is a useful way of getting to know your material and how to make use of it. Good luck!


Just suggesting that iPhones are not the most ideal place to do annotation work when compared to iPads.


Good points, @mbbntu – just as all the advice about how to take notes does not generally do better than one’s own attempts. My notes are incomprehensible to anyone but me.

I can’t overemphasize this point. I use Bibdesk not Bookends but the idea is the same - the reference manager has the canonical citation and links to everything else (PDFs, eBooks, DT databases, unconverted WordPerfect files with notes I took in grad school, etc.).

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Thank you all for your helpful replies. Let me be a bit more specific about my goals. My research pertains to elucidating the causes of fibrosis when biomaterials are implanted into the body. It is of interest to me as I am also a urologist-in-training. Up until now, my system of research was extremely haphazard. After starting PhD, I realised I need to have a simple system that captures relevant works in the field efficiently and I need to switch from a paper based setup to a digital setup. When I stumbled upon this forum, I ended up buying into the apple ecosystem to get access to these apps. What I am trying to set up is a system where I have separate databases for Urology research and my PhD research. From what I gather from the above replies, I should import all the relevant PDF’s to DTP and references into a separate system (Bookends/Bibdesk).

During my reading phase, I download all the relevant literature to a “To be read” folder in google drive so it is accessible across all systems. Is there a way to automate this on a Mac so when I download it to a folder on my desktop, the citation gets sent to the reference manager and the pdf to a folder in Devonthink?

Yes, with Hazel. I have an incoming folder with a Hazel script that sorts files into those with DOIs (which BD can import usually without intervention) and those without DOIs (which I’ll need to look up). See


I am a fellow physician and while I do not have a PhD and I only occasionally publish professionally, I do frequently cite medical literature in my consulting work.

In general I believe your workflow should and will evolve to be unique to you. Asking “What should my workflow be” is like asking “What type of house should I buy and how should I set up my home office” - you can get lots of great ideas from those who offer examples, but your solution will be individual.

That said, I would discourage having separate databases for “Urology Research” and “PhD Research.” I believe one of the best habits you can establish early in your career is to establish a single source to archive and search all of your medical/biological citations/publications. Inevitably you will come to be interested in all sorts of subtopics in medicine and biology either intentionally or by happenstance. Some of these will overlap between PhD research, Urology research, and Urology practice; some will apply to only one; and others will be in unrelated fields.

While it is very helpful to use groups and/or tags in DT3 to organize references, I suspect over time you will conclude that the search capability of DT3 renders such categorization less important than you first think; it also makes it much more helpful to keep all citations in one database.

There is one question I still have not fully resolved myself - is my main database of references DT3 and I link to my reference manager when needed, or is my main database my reference manager and I link to DT3 when needed. I started with the latter approach but increasingly I am trending toward the former. I suspect that for an active publishing scholar/professor it is more important to use the reference manager as the primary database because many such scholars routinely need to reference large lists of references in a very precise format. But when accessing the medical literature I find it is more typical to reference a small number of key publications at a time and the exact format of the reference is not nearly as important; in fact, increasingly a simple URL is just fine in medicine for any purpose other than final publication in a printed journal, and thus the reference manager is much less important in medicine than other academic fields.


Interesting. But if the OP is going to be writing a thesis, they are going to need to cite quite a bit. I would therefore suggest that at this point they need to see the reference manager as the hub and starting point of everything they are doing. You do not want to be accused of plagiarism, nor do you want to find yourself hunting around for the source of something when you have a deadline to meet.

If I were the OP, I would put everything in Bookends, allow Bookends to manage and rename all the PDFs etc, and index the attachments folder with DEVONthink. I would tag the PDFs as a way of categorising and organising the material. (I suppose I should say that I use this method myself, and it has usually worked pretty well.) I find that tagging files is more flexible than putting items into static folders or groups, and it goes well with smart folders/groups. And of course tags are visible across the system and appear in the Finder as well. For some time now I have used a system of tagging devised by Macdrifter which consists of merely doubling the initial letter of any word you use as a tag: so instead of Freud the tag is ffreud. This makes it very easy to search for tags. Back in the days when I was doing my PhD I might have had a PDF that was tagged with cchapter_1, ffreud, ddefence_mechanisms and so forth.

But as I said before, devising your own system is advisable, in my view.


For sure I agree there!

My point is I find it easier to locate a pertinent reference with Devonthink’s search feature than using the search capability of most reference managers.

And I think it is fine during the writing/editing phase of almost anything in medicine to use a web URL link or a Devonthink Item Link as the reference.

At least for me, this makes my writing process much more efficient to find the relevant publication, and it assures that I do not plagiarize. If something is going to publication or some other very formal work product, I simply need to convert the URLs and/or X-item links to the exact MLA format or whatever format is needed. Sometimes a reference manager is not even needed at all in medicine since most medically related citations are on PubMed and PubMed has pretty good support for creating a bibliography in the necessary format.

Most notably, we have just given an excellent example of how a workflow that works for one person may not work for another. Just think of each person’s use case as an example and then mix/match ideas from those examples to come up with your own workflow.

And I suppose my point is that if you have everything well organised in Bookends, you don’t need to search in DEVONthink :slight_smile:

I bow to your greater knowledge of the field – but what if the OP decides to develop the academic side of their career (is taking a PhD a sign of this?) rather than the practising medical side?

In any case, it often seems to happen to me that what helps in finding material is my own memory. I will have a vague recollection of some form of words, a theme, an idea, a subject, and then it doesn’t matter what program I happen to be in. I will be hunting inside my own head as much as anywhere else. But perhaps that is different from medicine, too. And perhaps I am an oddity in that I don’t find DEVONthink’s sophisticated search all that useful, and rarely use it – perhaps because I am looking for themes or ideas more often than words.


I am also a fellow physician and finished my PhD last year. Like many I used a combination of Bookends (for managing the citations), DEVONthink (for making links, searching for references and organising notes), Curio (for brainstorming and planning my thesis) and Scrivener (for writing). I kept two seperate databases in DEVONthink - one for my literature (the indexed Bookends folder) and notes and a project database where I kept all of the organisational material related to my PhD e.g. ethics documentation, data, emails, supervision minutes etc. A lot of what I did I have written about, including the various scripts that I wrote to automate many components of the PhD.


Regarding one database / multiple databases, I suggest it doesn’t matter so much with DEVONthink 3. The “how many databases” question is really a meta question about “how do I organize my materials”. Of course the answer depends on personal skills, but it is not something that needs to be answered definitively up front.

I usually recommend initially having one database. I like hierarchical folders (“groups”), others like tags or hierarchical tags, others like strict file naming conventions, others not. Just don’t lock into a set method up front unless it is a method that worked for you in the past. A beauty of DEVONthink (easier than Finder) is that reorganization is relatively “easy” – of course that ease diminishes as the collection grows, so do not wait too long to settle into a method.

Do not forget the DEVONthink AI “see also” and “classify” features. “Classify” can be helpful for organizing some kinds of documents. It works best when there are a lot of grouped documents in the database(s) so it takes a bit of growth in the database before the value of “classify” kicks in.

My own preference: Start with one database. Do organize with groups or tags or both. Do not dump everything into one group – that has a lot of downsides with any database, especially a research database. Take advantage of Smart Groups and Smart Rules.

@sanadsaad I haven’t seen much in this discussion about document annotation and how it relates to your note taking, and later on to organizing and drafting your dissertation. What is your experience – what has worked for you in the past? That will influence the choice of tools and method.


@sanadsaad. Here is my workflow:

  1. All pdfs are captured, renamed, and organized in Paperpile. Paperpile is a powerful reference manager, simple to use, and can be used in both desktop and iPad.
  2. All pdfs are stored in Google Drive (this is how Paperpile works). You can also index them in DT to have the best of the two worlds.
  3. I read, add comments and highlighted the pdfs using Paperpile on iPad. Everything you do will be synced, and you will have all your work available on many platforms, including DT.
  4. Then, I export all comments and highlights to a markdown document (yes, you can do that in Paperpile) and index the markdown document in DT.
  5. I process the markdown document by writing permanent notes using the Zettelkasten approach (there is a book on how to do that in DT, including how to make links, etc.). When the markdown document is processed, I delete it.
  6. I use markdown for my permanent notes, keep them in a Dropbox file, and index them in DT. You can always import them to DT if you want.
  7. When writing a paper, I search all the relevant notes in DT, export them to Scrivener, create an outline, and then write the article.
  8. When I fell the first draft is good enough, I export it to MS Word (because journals ask an MS document), add the references using the Paperpile plugin, and complete my task.

Some additional thoughts:

  1. You do not need Scrivener to write your paper. You can do everything in DT.
  2. You can use Bookends instead of Paperpile, but after testing both apps a lot, I found Paperpile easier to learn, maintain, etc. Besides, reading pdfs on the iPad with the Paperpile app is an excellent experience.
  3. By following this workflow, you will increase your productivity. Do not waste too much time overthinking how to organize your permanent notes. Just set a time everyday to process your pdfs, write your permanent notes, and link your notes in meaningful networks. You will build a knowledge system that will help with your dissertation.
  4. DT has everything you need to be successful. Good luck!

Well, given these are two completely different products with different purposes/features … I would never try to write a thesis with DT only. Scrivener highest priority, with Word/Pages/WhateverWordProcessor next. Possible in DEVONthink? Yes, but why?


I would never try to write a thesis with DT only. Scrivener highest priority, with Word/Pages/WhateverWordProcessor next. Possible in DEVONthink? Yes, but why?

I would - just to prove it can be done efficiently :wink: :stuck_out_tongue: