Sorting and Reading All Those Papers

By Laura Zirbel

Last month, I wrote about how to get and read papers from the arXiv in Google Reader. Now that we have all these papers, and have filtered out the ones we want to read, how do we go about it? Assuming I’m not printing every paper that passes my way, I’m breaking this question down into two parts:

  • How do you sort and store your papers?
  • How do you read your papers?

Ideally, I would love to have a program that does both (and does both well)… alas, I haven’t found the holy grail.


Papers – The major drawback is that it’s not free. Papers costs 79$ (one time). You can try it for 30 days for free though. Also, while it has a built in reader with highlighting feature, I didn’t like it as much as Skim. On the plus side, it looks and feels like itunes, so the UI familiar. And it’s designed for science and medicine, so less specializing is needed. And you can “open with” Skim, so it is somewhat compatible with other readers.

Itunes – So I haven’t tried this, but LifeHacker has a how-to on using itunes for pdf storage. But I use itunes all day and I’m worried about messing up my stuff.

Evernote – This looked really cool, and it can do a lot more than sort pdfs. But the software seems to be laggy and uncooperative with opening pdfs. There’s no also no preview of the pdf, just a pdf icon with the name. It’s initially free, like dropbox, and may be a good way to back stuff up, but I wouldn’t want to use it everyday.

Folders – This is probably the most obvious. You make a “papers” folder, and put all of your folders in there. I have 300+ papers though, and need a better way to sort.

Yep – Again, the major drawback is that it’s not free. But there’s a ten day trial, and then a 39$ one time fee. I’m still in my ten day trial, but this is the winner so far. Another drawback is that, as far as I can tell, you can’t “open with” Skim, you can only open in preview. In Yep, you tag your files, so a paper can belong to the “background” group and the “pivot method” group, without having two separate copies in two folders, or messing around with shortcuts. The interface is drag and drop and very user friendly.


Preview – The good news is that you already use it (or something very similar.) This is the standard pdf reader for macs, and it can do a lot. It can highlight (only yellow), underline, and you can add notes. It doesn’t highlight double column articles well. (Does anything?) It’s easy to use, and for most of us it open automatically when we click on a pdf.

Skim – This is my favorite. Beside being free, it gives you all the colors you could ask for. I like color coding my highlighting (blue is stuff to verify, green is potentially useful, yellow is important, etc.) and Skim gives you as many colors as you like, and notes. It’s also bad at double column highlighting, but it is better than preview at highlighting math well.

Perhaps this is all just procrastinating actually reading these papers.

I think I may switch back to preview if Yep works out and I decide to get it. What do you use to sort your pdfs? Does anyone know of a good free alternative to Yep or a better pdf reader?

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