A Digital Workflow to Manage Your Academic Life

Academics, Productivity

Edit 5 May 2014: I have now switched my workflow to iPad. It is very similar in the tools that I use and my post about using the Apple hardware can be found here.

Edit 18 February 2014: Although I tried, I found switching over to the Zotero interface clunky after the sleekness of integration that Mendeley offers, particularly with renaming and filing pdfs.  I am back to utilizing Mendeley. 

Edit 17 September 2013: As I was nearing the end of my time as a graduate student, Mendeley sold themselves to another company. As a result, I, and many other academics have chosen to switch software. I have chosen to begin using the open-source alternative Zotero. Although there is more of a learning curve with Zotero, it has been fantastic at meeting my needs. In the future I will write about the switch.

Awhile back, I wrote a piece for the UC Davis Native American Studies Grad Students blog about workflow automation. Since then, I have continued to add to my digital workflow in an effort to move completely paperless. With my office desktop, Android tablet, and smartphone, I have all the tools I need to help me accomplish a smooth process of researching and writing. The following software and hardware tips are suitable for new and seasoned academics alike. Please feel free to share how you manage your digital space too!

My workflow now includes three pieces of software:

1. Dropbox which I use to sync all my current class, paper, and project files to my desktop, tablet, and smartphone

Dropbox is a cloud computing tool that allows users access to free online space and will sync files across any devices you install on. I currently use the application on my office desktop, tablet, and smartphone. I keep the folder for syncing on my desktop and place all my current project files in it so I have access anywhere since any item in the folder are automatically shared with my other devices. You can also share specific folders with project collaborators while keeping the majority of your files private.

2. Mendeley for syncing all my citation information, reference notes, and automated “cite while you write” (on my smartphone I can search and forward citations to fellow scholars while conversing in the halls or between conference sessions without worrying about forgetting later which is an additional bonus)

I like Mendeley because it has a desktop interface that allows me to use it when I’m not online, yet still synchs all my materials to the online space and all my other devices just like Dropbox. It keeps all my citations up to date. You can store actual copies of references (up to 1 GB) for free, or, use the workflow tips below to keep them organized through your Dropbox and never pay anything!

3. iAnnotate PDF for highlighting and annotating of all those references right on my tablet screen – link takes you to GooglePlay as I own an Android tablet, but the app is available from iTunes as well for Apple users – this free app on my tablet has changed the way I work because now I can get away from my desk and the multiple distractions it provides

Now, my updated workflow from my earlier post simply incorporates my tablet computer. This allows me to work on-the-road or between meetings without finding an office space.


1. Drag a PDF file from the downloads folder into Mendeley desktop (or, if like me you already have folders full of them, you can bulk drag-and-drop). Another option is to use the web importer button for more than 30 different sites to instantly import citations from places like Amazon, Google Books, EBSCO, JSTOR, SAGE, etc.

2. Delete the original file if you used the drag-and-drop method above because the re-named file is already sorted into Dropbox. (More on this later.)

3. Check the reference information for accuracy in Mendeley. The program automatically pulls a variety of meta-data and fills it in for you, but it isn’t always perfect. Make any changes needed, then click the “information is correct” button. Add your tags and sort it into any collection you need. After checking it this once, you never have to enter the information in again.

4a. In the notes tab, I fill in my notes while I read, highlight on the PDF in Mendeley, etc. For books from seminars I copy and paste in my book synopsis papers and then go back and insert additional notes after class discussions. If you take your laptop to class with Mendeley, you can add your notes automatically in the program to any citation.

4b. Alternatively, because the file is in my Dropbox, I can open it on my tablet in iAnnotate PDF. Then, using my GoSmart stylus (the most accurate for fine lines and highlighting that I’ve found, also durable) I can highlight, add comment, handwrite notes, etc. to my heart’s content. Then, using the “email annotations” function, I email all my notes to myself for copying and pasting into the notes tab in Mendeley once I return home. Using this, I can sit by my fireplace and read for hours, read on the plane, or wherever I am that is more comfortable than remaining at my desk all the time. I find I get much more done in reviewing literature using this feature because it gets me out in new locations and keeps me away from the distractions of multiple open windows on my desktop. Since the .pdf files with the annotations are opened through Dropbox, they are automatically synched back to all your other devices. I use the copy-paste function for my notes though so that I have something quick to skim when I am searching through my references while writing.

5. Use the Cite While You Write tool to automatically generate citations in a variety of formats in Word (also works in Open Office, Google Docs). At the end of your document, “insert bibliography” to instantly get a perfectly formatted References list that doesn’t require you to comb through the paper making sure you haven’t missed one.

Check out my previous post on the UCD NAS Grad Student blog in order to walk you through the steps of setting up you Mendeley and Dropbox synch.

Bonus App Suggestion: TextMaker Mobile for your office document needs. This app is not free like the others I’ve talked about but it includes the ability to track changes and add comments, making it one of the best Android device apps for on-the-go work when you don’t want to pack your laptop for your weekend away or out-of-office excursions.

3 thoughts on “A Digital Workflow to Manage Your Academic Life

  1. Hi,
    I stumbled upon your web and found the advice incredibly intuitive. Thanks for that.

    I’m actually fighting the same problem you describe – desktop app to manage references and Android reader to read and annotate on the go. One of the problems some of my friends reported with iAnnotate, though, is that it does not allow exporting of highlighted sections. What’s your experience with this?

    1. Hi Michal – I am glad you find the workflow helpful. In iAnnotate, there is an option to email highlighted sections. I email the highlights to myself and then paste them into the notes section in my desktop citation manager. The article file itself can be saved with the highlights plus the text version of those snippets is then easily accessible. I hope this helps! -Nicole

  2. Thanks for an incredibly useful overview of your workflow. Do you find it convenient to read academic PDFs on a 7 inch tablet or do you prefer a 10 inch?

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