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Portable Annotations and Automation

In the previous blog post, I explained key elements of my academic workflow: easy capturing of references, file storage on the cloud, portable annotations produced while reading, automation, and collaborative writing at one place. I made a screencast to share my workflow involving elements of capturing, storing, and collaborative writing in Google Docs.

In preparation for this post, I recorded another video focusing on elements related to portable annotations and the automation of piecing information together for later retrieval. More detailed information about the R scripts and web hosting I mentioned in the video could be found on this page. The workflow could be further automated and optimized when Paperpile provides public APIs, which seems possible in the future.

“Open” Workflow

I hope this video could offer my two cents on academic workflow. However, you may find the practice of putting notes online bizarre. That’s totally expected as safeguarding ideas and avoiding embarrassments are norms in most settings including academia. Why would one put such rough notes online anyway? Wouldn’t it be embarrassing in case of half-baked (or pre-baked) commentaries? How they might be useful at all for other people? Wouldn’t it be enough if I try to publish in Open Access journals or make various forms of my research “products” openly accessible? Those are all fair questions.

My choice of putting notes online was inspired by Dr. Stian Håklev, a close friend of mine at OISE and a strong advocate for Open Access, Open Education, and Open Scholarship. He was one of the original co-founders of Peer2Peer University and studied Chinese National Top Level Courses (equivalent to MIT Courseware) for his master’s thesis. As part of his commitment to Open Access, he wrote a bunch of Ruby scripts to power a wiki-based citation management system, in addition to his ambition to only publish in OA journals. The idea of opening up the process or “immature” artifacts – instead of the final products (e.g., journal articles) – is attractive to me, and inspired me to settle on the current workflow/practice I’m following.

It was a while ago when I noticed a LifeHacker article citing a note I shared about Steven Johnson’s book while I was still manually taking notes from readings in Mendeley.1

Following the attribution link, the author of the LifeHacker article actually borrowed much information from a post on 99U, which originally cited my note.

Information travels. I was even more surprised that the LifeHacker article has been reblogged for dozens of times, and has also been spread on social media (Google+, Twitter and alike). And I had no idea things would unfold like this at the first place of posting the notes. There are other examples that I’ll not mention here.

Such an example may sound trivial but at least points out a possible way of public engagement for academics. Can you tweet your way to tenure? Maybe not, or not too soon. But publishing the final articles in the most prestigious journals should not be the only way. More openness with various stages of the academic workflow may catalyze public engagement. As Philip Cohen, a professor of sociology at the University of Maryland at College Park puts:

It’s important to value and reward openness in our routine work… Public engagement does not need to mean separate activities and products, but can mean taking a public-facing stance in our existing work.

Finally, if you are interested in promoting openness in academia – in whatever area – check out this year’s International Open Access Week during October 24 - 30, 2016. Go to a local event, or engage in a conversation online.

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

  1. Credits should go to Steven Johnson as the quotation was actually from his book.

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Bodong Chen



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Bodong Chen, University of Minnesota

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