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It was the beginning of this new school year when I started to “revamp” my academic workflow, which has been very digital since the dawn of my dissertation research. There are tons of articles you can find online about digital workflow for academics, e.g., this post, this one, this post involving LaTeX, etc. For me, there are a few essential things I want to achieve in my workflow:

  • Capture: Easily capture references from the Web, including Google Scholar, journal webpages, and my university library, into my personal reference library. More efficient ways of importing PDF files will be sweet.
  • Storage on the cloud: Store both bibliographic information (i.e., metadata) and the PDF files on the cloud for ubiquitous access.
  • Read (everywhere) + portable annotations: I wish to read on my Mac, iPad, and iPhone, even though I mostly read on my Mac. More importantly, I do not want my annotations to the documents to be locked in closed ecosystems (e.g., Adobe Reader, Mendeley’s PDF annotator). I want all my annotations to be portable. A fancier way to say this is to give annotations their own independent lives as conceptual artifacts open to be connected with other artifacts.
  • Automation: I wish to automate steps of my workflow as much as possible, while spending minimal time to engineer automation by myself. For example, I wish to piece together annotations and bibliographic information together into annotated bibliographies.
  • Collaborative writing at one place: Writing collaboratively is essential to me. Writing in LaTeX does not work for me because colleagues in my field(s) typically do not use it. Writing using Markdown and Scrivener is also fine, but again, more appropriate for individual writing tasks. Writing in MS Word is a pain, especially when comments explode after a few exchanges; and that’s when it crashes on my Mac.

Before this semester, I was using a pretty sophisticated workflow depending on Mendeley (for biblio capturing & storage), Dropbox (for storage), Skim + PDFExpert (for reading and annotation), and some R scripts (for automation). Theses tools support my efforts to ‘publish’ some of my raw notes online, just as an integrated component as my workflow. However, I struggled when writing collaboratively with colleagues. I was either stuck with MS Word and ended with a file name like this. Or, I need to insert reference after-the-fact when writing in Google Docs.

Things have improved after trying Paperpile, a fairly new tool for reference management. It comes with MetaPDF, which allows you to read & annotate PDFs in browsers and, more importantly, exporting annotations into various formats. For storage, Paperpile integrates with Google Drive, so that your PDF files are all synced through Drive. In addition, it integrates with Google Docs through an add-on! The whole design seems very intuitive to me and reflects much thinking to make our life easier.

Below is a 9-min video I made for colleagues in a faculty writing group. It describes three things: (1) basic interface; (2) capturing references from the Web; and (3) inserting citations into Google Docs. More tutorials may follow…

Disclaimer: I am not affiliated with Paperpile in what-so-ever manner.

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Bodong Chen


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Bodong Chen, University of Minnesota

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