Bridging the Analog – Digital Divide

I was recently listening to the excellent Research in Action Podcast hosted by Dr. Katie Linder. Her discussion with Hannah Gascho Rempel made me think that others might be interested in the system I’ve developed for maintaining both a paper and digital archive of journal articles.

I prefer to read articles that I need to deeply process using a paper copy. I also want to cite these articles in my writing using Bookends, my reference manager.

I have a few 3” binders with about 30 expandable sheet protectors in each. Printed articles are cataloged with the binder where they live, and a number. The printed articles live in the sheet protectors, and their location is recorded in my reference manager. When I need the physical copy, I can put my hands on it in a few seconds. My notes are replicated from the paper copy to the PDF, and also in the reference manager. If I’m writing and don’t have the physical copy handy, the PDF is always in my reference manager.

My workflow is as follows:
1. If an article is really good, I catalog it in Bookends.
2. I open the PDF from Bookends in PDF Expert, my reader of choice.
3. I read the abstract and skim the article to be sure it is worthy of printing.
4. If it is truly meritorious, I assign the next filing location to the paper in Bookends. 1

  1. I switch back to PDF Expert, and use the text annotation tool to mark the top-right corner with its filing location
  2. Now I print the article, read it and mark it up with a pen or (rarely) a highlighter.
  3. I go back to PDF Expert and highlight things that I’ve underlined, add margin notes, etc.
  4. Now I export the annotation from PDF Expert as markdown (you could use text or HTML).
  5. The markdown is opened in Ulysses, and I rewrite the highlights and annotations as coherent sentences and paragraphs. When finished, I copy this to the clipboard.
  6. Back in Bookends, I paste the text into the Notes tab. Thus, the notes are now attached to the paper’s reference.
  7. I file the printed article in a binder in a heavy duty expandable sheet protector.

My binders are color coded, and the location’s first letter tells me the binder color. In this example, K means the black binder. I also number the binders in bookends by prepending a number to the location. This insures the last binder I’ve used is last in the list when sorted by location. For example, this black binder is my fifth binder. The letter for black is K, so it would not be shown last when sorted by location in Bookends. By prepending a 5 to the location (fifth binder), the binders are sorted in the correct order.

While this may seem like a lot of work, I believe it helps me retain the information that is important in the article. Research shows that highlighting alone doesn’t work. By doing the other manipulations of the information — highlighting again in Bookends, then summarizing the notes — the information is processed a couple of more times. All of which help with retention.

When I need to review a paper, I have my notes in Bookends, and can also quickly retrieve the paper copy from a binder.

  1. To get the next location, I click on the Location header in Bookends, which sorts by location. Scroll to the bottom and I can see the last location used. 


Pros and Cons

One of the drawbacks, or pluses, of grad school is the single-minded devotion that is often required of the student. Thus, projects such as this blog languish without updates for years on end. Another side project, pcb-gcode has been languishing for years too, with its last update happening in 2013. This should all be worth it in the end.

For the time being, I just discovered that WordPress supports markdown logo markdown. Maybe more frequent updates will be forthcoming?


Concept / Mind Mapping

A sheet of paper and a pen work quite will for concept mapping, but lack flexibility to rearrange things as one thinks them through. There are a lot of programs for mind mapping, but I find many of them are too restrictive. They want to arrange things for you, or determine what the links look like, etc. Below are a few that I do find helpful.

Scapple, from Literature and Latte, who are the makers of Scrivener.

Tinderbox, a a visual database, concept-mapping, note-taking system. I bought it, but have not used it to its full potential. Scapple is easy, allowing me to get ideas down quickly. Tinderbox would obviously allow more power to manipulate notes and maps.


Writing Software – Scrivener

Scrivener is a pretty amazing piece of software. Its genesis was for writing novels, but it is well suited to academic writing as well. Its reference section and cork board are nice to have, and allow one to view reference material while writing in an adjacent pane of the editor.



Notecards are essentially analog databases. I like the physicality of them – one can carry a concept and reference for that concept around in ones hand.

Luhmann’s Zettelkasten takes this to a whole new level.

Deep Work

Deep work is an elusive, but very productive state of mind. I’ve experienced this state in the past, mostly in the context of writing software, but Cal Newport raised my awareness of what it is and how beneficial it can be. Newport is quite the critique of social media, but maintains a website. So apparently websites aren’t “social media.”