When I started my master’s program at UdeM (Université de Montréal) this past fall, I decided that I would try to stay a bit more organized than I had during my undergraduate years. Aside from making better use of my time, trying to establish certain routines, and sticking to set task lists for the day, week, month, etc., I’ve tried to develop certain workflows that utilize technology to make my life a bit easier and less chaotic. One such workflow that I’ve really come to rely on involves the management of my digital (and physical, to some extent) library of PDFs with the help of Bookends for OS X by Sonny Software, PDF Expert 5 for iPad by Readdle, and Dropbox.
Before I go any further, I should admit that I am, for the most part, an Apple user, my primary computing hardware being a Mid–2011 13″ MacBook Air, a 4th generation 16GB iPad, and a 16GB iPhone 5. Thus, aside from Dropbox (which is available on almost any desktop or mobile OS at this point), there is an obvious bias toward OS X and iOS apps in this article; however, these apps are merely utilities built on specific platforms. I’m fairly positive that you could find similar utilities on the platform of your choice (Windows, Android, Linux, etc.) and still follow the concept of the workflow I’m laying out here. Also, I should mention that I spent a lot of time doing my own research on various apps and methods of file/data management before settling on what I’m presenting here. In fact, I pieced together a lot of this workflow after reading blog posts and articles on the same subject,1 so I’d suggest that you take what works for you and leave what doesn’t.
Setting Up Bookends for OS X
As Sonny Software puts it, “Bookends is a full-featured and cost-effective bibliography, reference, and information management system for students and professionals.” I looked at, and even tried, quite a few academic reference management applications before settling on Bookends, and I have no regrets about doing so. I easily could go into detail about the features and functionality of Bookends and why I find it so useful, but for the purposes of this post, I’ll just say that it’s a fantastic piece of software. By default Bookends stores both data (the various information relating to each bibliographical reference that you add or import to the application) and file attachments (for example, the full text PDFs that correspond to individual bibliographical references) locally on your computer’s hard drive.
However, I have chosen to store my file attachments on Dropbox, allowing me the benefit of having access to these files both locally and in the cloud via Dropbox. To do this, simply open Bookends, navigate to Bookends » Preferences in the top toolbar, and change the “Default folder” under “Attachments” to a folder within your local Dropbox folder.
As you can see, I’ve created a folder named “Bookends” in my Dropbox root folder with a subfolder named “Attachments” where all my attachments are stored. As a side note, each time you add an attachment to Bookends, you can manually change the location to which the file will be moved or copied (instead of the default location), or you can choose to leave the file where it currently resides on your local hard drive. Simply choose “Move To” or “Copy To” in the first selection area, check the box next to this area (or leave it unchecked to leave the file where it currently is), and choose a folder location from the second selection area or click browse to choose a location not currently listed in this area (which, I believe, will list all subfolders of the default attachments folder).
Typically, I will download files (articles, papers, etc.) or scan physical documents to my Desktop or Downloads folder, attach them to their corresponding bibliographic references, and choose to have them renamed based on the title of the reference and moved to the “Attachments” folder in my Dropbox. As I mentioned, this allows me to view, edit, and usually download all of my attachments from any device with access to Dropbox.
Accessing, Viewing, Editing, and Syncing Bookends Attachments with PDF Expert 5
Similar to my experience with various reference management applications, it took me quite a while to settle on PDF Expert 5 as my iPad PDF viewer of choice. When I bought my first iPad, I used GoodReader for organizing and reading PDFs. However, I found the interface to be a bit dated, and with the release of iOS 7, GoodReader fell behind its competition.2 I started using PDF Expert in its version 4 days, and it served me well all through fall term classes. Readdle’s complete redesign of the app with the release of version 5 in December sealed the deal for me—I now use PDF Expert 5 for almost all PDF viewing and management on my iPad. Although not unique to PDF Expert 5 in terms of iPad PDF apps, I find the Dropbox integration and flow in PDF Expert 5 to be the simplest, most intuitive, and most useful of all the PDF apps I’ve tried. This is integral to my workflow with Bookends and the attachments that I store on my Dropbox. To set up Dropbox in PDF Expert 5, simply open the app and tap on “Dropbox” under “Accounts” in the left toolbar.
Dropbox authentication should only take a few seconds, after which you will have complete access to the contents of your Dropbox account. If you set up your Bookends as outlined in the previous section, you should be able to navigate to your attachments folder and view all of your Bookends attachments.
Tapping on any file will download that file in PDF Expert 5 and store the file on your iPad’s local storage. By default, PDF Expert 5 creates a Downloads folder in your Documents where all downloaded files are sent (this can be customized in the app’s settings).
Once you the file has downloaded, you can tap on it to open the PDF. This is where some of the more powerful aspects of PDF Expert 5 come into play, especially if you’re using the app for research reading. Using the toolbar at the top of the screen, you can add various annotations to the PDF. I’ve added a couple small annotations to a document to demonstrate how they will transfer when the PDF is uploaded back to Dropbox.
Once the file has been successfully uploaded to Dropbox, I would advise that you delete it from PDF Expert’s local storage (as long as you don’t plan on annotating it again any time soon), as locally stored PDFs can quickly eat up valuable iPad storage.
Back to Bookends: Viewing Annotated PDFs in OS X
To wrap this up, the final element of this workflow is viewing the annotated PDF in OS X. I like to take as little to class with me as possible. Unless I have a physical copy of the reading for the day, all you’ll see in front of me is my MacBook Air and a thermos filled with hot coffee. Thus, it helps to have all of my readings with annotations accessible from OS X. Using the example of the Schiller text that I annotated with PDF Expert 5 in the previous section, let’s take a look at how the annotated PDFs make it back to home base (my laptop). Dropbox sync is almost instantaneous these days, so as soon as you upload an annotated or updated PDF from PDF Expert to Dropbox, you should see a notification in OS X that a file has been added to or updated in your Dropbox folder. Looking in Finder, I can see that Letters Upon The Aesthetic Education of Man was last updated today at 10:14, which is when I uploaded the annotated copy of the text from PDF Expert.
If I open the PDF in preview, I can view and even edit the annotations made in PDF Expert, which is very useful when viewing the PDF in class and wanting to add an additional note here and there.
Also, as far as I know, annotations added in Preview should show up in PDF Expert, were you to download the file once again from Dropbox within PDF Expert. Of course, an even easier way to access your Bookends attachments is from within the Bookends app itself. Using the search bar in the upper right hand corner, I can quickly search for “letters” to find the Schiller text. Because Bookends recognizes the attachment as existing in the attachments folder within my Dropbox folder, anytime a file is updated via Dropbox, its corresponding attachment in the Bookends app will be updated as well. You can quickly open Bookends attachments in Preview by double clicking them. Right clicking anywhere on the attachment will display other available actions, such as “Reveal Attachment in Finder.”
So, there you have it—a relatively simple workflow that connects the OS X reference management app Bookends with the powerful iPad viewing, annotating, and management app PDF Expert 5 via the ever useful Dropbox cloud service. As a caveat, I feel that this way of doing things may be more conducive to disciplines within the humanities than those in other realms of study. However, even if you don’t follow this guide step by step, there may be bits and pieces worth implementing within your own reference and PDF management system.
- Endnote vs …. well, everything else
- Managing your research literature: Sente versus Bookends
- Sente vs. Papers: What is the best PDF management system?
 While writing this, I took a look at GoodReader’s website and discovered that they recently released an update to their app with a complete redesign à la iOS 7. As much as I’d like to give the new app a try, I’ve invested too much time and energy into PDF Reader 5 to justify making another switch. However, I’d definitely suggest taking a look if this is your first venture into the world of PDF management on the iPad.