I’m making a few notes to myself here to document my process for keeping a public research notebook. They might be of interest to you, too.
First, I’m talking here mostly about keeping up with the literature. There are (in my opinion obvious) ethical implications of actually sharing your data on your website. I’ll explore them as I write my proposal, but right now, all I’ve got is other people’s research that I’m reading and writing about, and then I’ll probably have some memos on my own process of preparing for comps and selecting my dissertation topic. Nothing wild.
So, what am I doing? Well, inspired by some writing by Kris Shaffer and Chris Aldrich, and by the fact that I gave a keynote last weekend on Connected Learning and the IndieWeb, I want to share my reading notes on some of the readings I’m doing for comps. It will help me keep track of my most important notes, and maybe it’ll be useful for other people researching similar topics. I tend to pick fairly under-researched areas, and I know it can be frustrating to have to dig up the literature on those, so this is one way I can maybe make it easier for colleagues.
Raul Pacheco-Vega is another inspiration, as he both shares reading notes and has heavily influenced my literature review workflow.
What’s the workflow?

I find the source, as described through one of the various techniques in my literature review workflow, and pull it into Paperpile. If Paperpile can’t find a PDF on its own, then I track a PDF down or, if it’s only available physically, track down a physical copy.
If it’s a PDF, I read it on my Android tablet with Xodo, making highlights and annotations using my Musemee Notier stylus. If it’s a physical text, I take notes on a dedicated COMPS spread in my Bullet Journal (I use a Moleskine large dotted black notebook and a Pilot G2 07).
I create a new Google Doc.
From Paperpile, I copy the citation and paste it into the Google Doc. I name the Google Doc Author Year Article Title. (These are all in a folder called “Synthetic Notes,” nested in a folder named after the literature area.)
I type up a quick synthetic note based on my highlights and annotations.
I use Paperpile to find a link to the source of the original.
Then, I use a bookmarklet with the WordPress Post Kinds plugin to create a new bookmark on my website. (I use the bookmark post kind instead of a read, because I’m only doing an Abstract-Introduction-Conclusion extraction, not a full read of the piece.)
I paste the abstract into the Summary box in the Response Properties box.
I paste the contents of my Google Doc into the WordPress editor and use the “Clear formatting” button to clean up messy GDocs code.
I give the post a tag related to the literature area (e.g., connected-learning) and select the category “Research Notebook,” then publish!

You may have noticed that this workflow leaves out Hypothes.is entirely. This is for a few reasons, but mostly just that right now, Hypothes.is would add several extra steps as I read on my tablet rather than on my laptop. I’d have to open up the PDF on my laptop, re-highlight and annotate using Hypothes.is tools, then use the Hypothes.is aggregator plugin to bring over those to my website. So for now, I’m doing it all manually on my site and not sharing anything there.