Jason Shafer is currently a PhD Candidate in English at UC Boulder, he maintains a personal blog over at http://www.jasonshafer.net that is currently chronicling his battles towards perfecting a strategy for digital workflow in academia.

This post is an attempt to persuade graduate students to attempt to create a database of everything that you will read, as well as your thoughts and notes, in a digital form as soon as they begin graduate studies. I’m sure many do this in one way or another, but I am talking about going completely paperless, even for those of us in the humanities. For something so counter-intuitive—to an English major in any case—the reasons for doing so are self-evident: a one-stop shop for every thought, inspiration, musing and annotation of your years of research at your fingertips. Beyond helping immensely when it comes time to write the dissertation, such a database could prove useful throughout your career. I outline here how I managed to go paperless last year. I acknowledge that there are many combinations of software and workflow that can get one to the point of digital nirvana, and I’d be very interested in how others manage it. The majority of this information is aggregated from a few very helpful sites that you will find in the links; my purpose is to condense it all in one place with a few practical pointers. All software is for Mac only, though there is sure to be PC alternatives. I use a combination of Sente and DEVONthink Pro (both have educational discounts and iOS companion apps), though again there are many alternative software options.


The process of going paperless involves collecting, annotating and organizing a vast amount of data into one place and having an intelligent way of sorting through everything. The first step is to amass your treasure trove of digitized information, syllabi, websites, excerpts and books in PDF, manually imported notes, etc. Quite a lot of this is given to your or available digitally—problem solved. For the things that are not one must digitize them and render them in a usable format, for this the flatbed scanners at school are useful. If you are really gung-ho for digital formats you can—with some basic mechanical aptitude—build a non-destructive book scanner at home for less than $100 (I’ve done this, it works, just raid construction site bins for lumber and screws to save some cash). Once scanned and saved as PDFs, you will need to OCR (optical character recognition) your documents to render the PDF image into machine-readable type. For this you can either use the OCR in DEVONthink Pro (if you have the Pro Office version) Adobe Acrobat X, or Google Docs’ automatic OCR for shorter documents. Of course, not everything is digital yet, and if you want to avoid mass scanning you can always manually type shorter, important information into your computer for storage.


Next, it’s time to annotate your files. For this I use Sente, though a budget alternative would be to use Skim (free) along with a bibliographical tool such as Zotero (also free). Sente and Skim allow you to highlight and notate your PDF files. Once this is complete you can use a script to import those notes along with the highlighted text to which they refer, into DEVONthink Pro as individual notecards. The key with annotations is to be selective, highlight and notate with a purpose because the pile of notes that you build up becomes the fuel for the AI engine at the heart of the database program. Excerpt and notate lines or paragraphs instead of chapters; more, smaller notes gives the program a better shot of finding exactly what you are looking for. That means either keeping PDF files organized elsewhere (Sente is a sync-able PDF database, which I use for this reason) or making sure that the DEVONthink Pro AI does not search entire PDF files in your database—and it is fairly easy to exclude them from the search. With your database focused on your research and your thoughts it will operate much more smoothly, and you can go back to the annotated PDFs and dig for more at a whim.


Organizing. Of course you could throw a bunch of your PDFs in a folder on your desktop and a few more notes buried somewhere else on your computer, but once you have a few years worth in there even Mac’s great Spotlight feature isn’t all that helpful. When you really want a shot at organizing all of this data that you begin to accumulate you must use a database program, and that is when the real powerful motivations for using a digital workflow come to light. DEVONthink Pro is a program that reveals its true power only in time. Beyond keeping all of your annotations, books, handouts, and everything else organized (with an automatic organizational system no less) when you start to build up a library of thousands of these notes and excerpts the program helps you not only keep track of them, but, using its powerful AI, it makes connections between notes, forging connections between ideas that you may not have made yourself. You can set up a DEVONthink Pro database easily, using an intuitive nested folder (group) system that belies the organizational complexity of the program (tags, keywords, smart groups, etc) but the ease of importing notes and then cross-indexing with your entire database is by far the most powerful and seductive tool. There are a great deal more reasons to use DEVONthink as a database program to manage your digital academic life,  some of which I am beginning to cover over at my blog, so check it out.

By using Sente as well as DEVONthink Pro, this workflow has some redundancy (DEVONthink Pro can be used as a PDF manager and for taking notes), and yet I prefer the bibliographic and note-taking tools in Sente to those in DEVONthink Pro and therefore use both. After DEVONthink Pro it’s off to Scrivener to write.

Many thanks and much credit goes to Magruder’s Digital Academic Workflow; a lifesaver.

[Image by Flickr user Kat G and used under Creative Commons license]


12 Responses to Going Paperless from Day One: Digital Academic Workflow for Grads

  1. Deb says:

    Many thanks for the excellent post – I struggle with taking the final leap into digital as I write and think better on paper but I am all to aware of the potential for a digital database such as you describe. I have been using a site recently that has some excellent articles/reviews/tips on this topic as well & also has some excellent posts/discussions on Sente, DTP & Circus Ponies Notebook – http://www.organizingcreativity.com/2011/07/devonthink-second-impression-and-some-tips/

    (Hopefully the link will work here? One of the main reasons I have not started to use Sente is that there is a software conflict with my OS & Safari that causes sente to crash if I try to use it to search – I have a work computer and cannot update my OS & it is very difficult to ‘downgrade’ safari – at least for me 🙂 I contacted Sente who responded in kind with an ‘oh well .. suck it up’ email which has put me of the company somewhat.

  2. Carla Martin says:

    Thanks so much for this wonderfully informative post! It inspires me to move forward with my own paperless goals. And selling or donating used books is an added bonus. 🙂

  3. I’ll go ahead and plug Papers from Mekentosj… it seems to serve the same purpose as Sente, but it places a little more emphasis on organizing and working with your files than Sente does. I’m in physics and I’ve used it to organize papers for years; I’m really happy with it. (It’s Mac-only, but with companion iPhone/iPad apps.)

  4. Christine says:

    Thank you so much for posting this. I’ve been scouring the web lately for recent posts relating to digital workflows for grad school and just stumbled upon this site and your timely article.

  5. Deb says:

    Hello again
    I have a dumb question re the Sente to DTPO script – I have been able to get it to work no problem – it’s fantastic btw – but I don’t get where to ‘store’ or ‘attach’ the script? In DTPO there is a ‘scripts’ window which you can add scripts to (I think) but there doesn’t seem to be anywhere to do this in Sente? Does this mean storing your script away from the software and ‘running’ it when it is required? I have no experience with scripts so this is all new so i apologise in advance for the basic newbie question!

  6. Kaitlin says:

    After printing out all of my papers for my comprehensive exams, I realized that I wanted to go completely digital for the rest of my degree. For the most part I have been successful; however, copyright issues prevent the digital archiving of older articles or articles unavailable from my institution. Until copyright issues can deal with digital copies of materials, do you think we will ever be able to be completely paperless?

  7. Jason Shafer says:

    Deb: best place for the applescript is the same place devonthink stores its scripts, this way you can access it from the little script menubar icon. This location should be:
    [your hard drive name]/Users/[your user name]/Library/Scripts/DEVONthink Pro

    pop it in there and you won’t have to keep track of it all the time.

    Kaitlin: Copyright issues are a big hoop right now, you can either ignore them and risk death and dismemberment or suffer the inconvenience. I feel your pain.

  8. Brian says:

    This is an interesting article, thank you for writing it. I have a question though. I am about to re-organise my collected PDFs etc using Sente and DTP but I am undecided regarding the directory structure to use ie all in one, a directory for a category eg ethics, or a directory for each PDF to include relevant notes as well. I favour the category allocation but can see sense in just lumping all PDFs in a flat structure as it is possible that a document spans more than one category. Do you have any thoughts from your experience.

    Best Wishes

  9. Arthur says:

    Does this mean that the Digital Academic Workflow nirvana is restricted to Macs ?

    I have to admit I have still to find something that works for me and my PC.

    Being in engineering with a touch of computer science, among the notes I need to add code and versioning systems (Git or SVN) into the mix.

    I really like DevonThink, at least the test drive I conducted on a friend’s Mac, but nothing comes even close in the PC world… 🙁

  10. […] used: make sure you have soft and/or hard copies of your references, and store your references in a digital reference managing system. You can also take a few digital snapshots of paragraphs and images you plan on referring to in the […]

  11. Kate Tang says:

    I’ve been struggling to do the same: with EndNote (for references), Evernote (for taking notes), and iAnnotate (for PDFs).

    In my experience, EndNote doesnt work too well on a mac. So I’ve been tempted to upgrade to Sente. It’s starting to seem like that’s inevitatble.

    Dropbox is a lifesaver too. It syncs with iAnnotate so I’ve been using that for lit. review.

  12. Aaron Seymour says:

    Hi. Thanks for this. I found it very helpful. I’ve been trialling out Sente for annotating and note-taking and DTP for bringing it all together. The brilliant think about this workflow is that you can use your desktop machine or iPad like a kindle and capture all the text you highlight as well as your notes.

    One (major) problem I’m having though is that none of the formatting is kept when this text is captured – e.g. italics are lost in the original text. This seems like it is going to create me a major headache in the future when I have to go back and cross reference everything to add this stuff back in. I’ve been wondering whether I shouldn’t just move to a different app.

    Wondered if this had bothered you and if you’d found a workaround?

    Many thanks!

Leave a Reply

Your email address will not be published. Required fields are marked *

.post-thumb {float: left;}