What had been a nagging whisper in the back of my head since the beginning of my doctoral program became much more deafening when I started working on my dissertation proposal - my research workflow was a complete, unsustainable mess. Handwritten notes could be found in this pile of papers or that manila folder. Annotated journal articles were mostly filed in my cabinet alphabetically (but apparently not whenever I really needed to find something!). Additional research notes were saved in an endless number of different folders all over my laptop and, perhaps worse, in all kinds of formats. My unwillingness to commit fully to digital tools was further compounded by the fact that I simply didn't like any of the tools I had. Something had to change. The amount of time that I spent just hunting around to see if I even had something, much less if it was actually what I wanted, was staggering and depressing. So I made the conscious decision, for better or worse, to commit to a digital workflow and so, without further ado, here is my research flow as it currently stands.
When I come across a new reference, I begin by adding it to my bibliography manager Sente. By doing this, I'm able to verify from the beginning that it is, in fact, a new reference that I was previously unaware of. Then I assign it a status based on what I need to do with it - typically 'to be read', but when a quick skim makes it obvious that I won't need it for anything, I'll assign it 'done (not central)'. Now why do I use Sente? Honestly, I've tried almost every bibliography manager out there, and while Sente is not perfect, its use of hierarchical tagging to manage collections has been the deciding factor for me. After assigning a status to the reference , I tag it appropriately (usually this entails one for dissertation, one for each relevant topic, and later, one for nvalt once I have notes on it).
If I have a PDF, I will use Adobe Acrobat to clean it up (esp for OCR). Also, if its scanned as double pages, I tend to crop it into single pages with a great little app called Briss, which is not very intuitive, but it is the best one for this job (and its free!). My attachment preferences in Sente are set up so that once I drop the PDF into Sente, the bibliography manager places it into a SkyDrive folder, which is further synced with Goodreader on my iPad. While I have PDF Expert, my comparison trials continue to find that Goodreader comes out on top. For reading on my Mac, I typically use Preview. Yet, while I will highlight important passages, I still write my notes in a composition book before I type them up (more time consuming, but I find the extra opportunity for further analysis and synthesis is worth it).
Note Taking and Writing
One of the biggest hurdles for my workflow has been the note taking process, because I was certainly one of those academics described by Aleh Cherp, who found themselves paralyzed by the fears that note taking would interrupt our work or that we wouldn't be able to find our notes again. Also I have been leery about the long-term consequences of taking notes in proprietary software. Thus, for me, my notes must be easy to take, always easy to find again, and available independent of where I'm at or what software I use.
I tried a wide variety of different tools for note taking, including DEVONthink and Sente, but the best solution that I've come across is nvALT (a fork of Notational Velocity). The combination of its simple interface and my ability to create and store my notes in plain text files in a SkyDrive folder (backed up with Crash Plan) satisfies my note taking guidelines (see also). I could go on and on about all of its great features, but it is worth noting how nvALT's combined smart search/note creation feature means that you should never have two notes with the same name. I'm still developing my file naming conventions, but thus far I try to use "x author, title" for primary sources and "z author, title" for secondary literature. I also tag notes according to research topic (nvALT uses OpenMeta tagging).
So after I'm done taking notes, where do I spend my time writing? nvALT! Why? I simply love writing in it. In fact, almost everything that I write, including important emails, conference abstracts, or my dissertation, is composed in nvALT. And because I love the experience of writing in it, my productively has markedly increased. I think the simple interface also helps me focus more on crafting paragraphs, rather than getting caught up with my page count. That said, once I need to finalize something or send it out, I copy it over to MS Word because, whether I like it or not, that's the standard format for word documents in my world (and Bob Levitus helped me come to terms with reality of needing Word). I know that lots of folks absolutely love Scrivener, but I finally accepted the fact that it isn't for me.
How do I make this all work together? Well, first I take advantage of the multiple desktop feature on my Mac and typically use this set-up:
This set-up brings me to my final innovation, which might seem odd, but it has been the critical key to making this all work. Like most people, I like to peruse my research notes while I write. But this is a bit annoying in nvALT because, if I want to look at a different note, I have to use a new search and, by doing so, leave the file in which I was writing. I additionally find it helpful to sort and group my notes as if they were real index note cards. So what I've done is create a new database within DEVONthink that is synchronized to the SkyDrive folder with all of my nvALT notes. This enables me to organize my notes into a variety of folders (mostly dissertation chapter subsections), replicate notes into multiple folders, even create new smart groups that auto-populate according to their tag (remember that all of your tags in nvALT show up in DT because it uses OpenMeta tagging too). So now, a three-finger swipe back and forth lets me conveniently switch between my dissertation writing in nvALT and my research notes in DT.
Here is another way of looking at my workflow: