Category Archives: Grad School

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?



Thursday, March 13, 2014 was an exceptional day. When I returned home, a letter was waiting for me, and my girlfriend was quite excited. The letter was from The Georgia Institute of Technology. I made a point of sitting down first, then opened the letter. The first three words were, I am pleased. This was one of the happiest days of my life. I have been accepted to earn a PhD in Applied Physiology with a focus in Prosthetics and Orthotics. With those three words, I knew that the past five years of hard work had paid off, and the next step is now before me.

I will work to create an implantable interface to allow two-way communication from the wearer’s nervous system to a prosthetic limb. This will allow control of the limb, but more importantly will give the wearer a sense of touch. This sense of touch will result in the prosthetic becoming incorporated into the wearer’s body scheme – they will come to think of the limb as their limb, not just a machine attached to their body. This will improve satisfaction with and the utility of prosthetic limbs, thus improving the amputee’s quality of life.

I can’t wait to get started.