Papers

7 September 2007

When journal articles began to appear online in pdf form, I started to collect them on my computer’s hard drive. In theory the pdfs can be accessed very quickly, as opposed to finding a printed article in a filing cabinet. To help find papers more quickly, I devised a filing system with nested folders. Unfortunately, as the file structure became deeper and deeper, it was more and more difficult to find papers: drilling down many folder levels just isn’t efficient. When Spotlight came to the Macintosh, it didn’t help; Spotlight is slow and returns too many hits. In the past years I’ve resorted to printing out copies of important papers, and storing them in strategically placed piles. But this isn’t the way the digital age should work!

I’ve been looking for a solution to the pdf conundrum. I tried Yojimbo, a nice program by Bare Bones Software, the makers of BBEdit (which I use to post to this blog), but it wasn’t designed for the scientific literature. Then this week I stumbled across Papers – written by Alexander Griekspoor (Mek) and Tom Groothuis (Tosj) of mekentosj.com (yes, it’s a play on ‘Macintosh’). These are two fellows who, as Ph.D. students, wrote a number of Mac programs for use in the laboratory. My favorite is EnzymeX, but there are other useful programs as well. These programs leverage the technologies available in OS X, together with visually useful interfaces, to provide solutions to laboratory problems.

Papers is a program for obtaining and organizing scientific articles. I discovered it yesterday, downloaded it today, and after five minutes of using it I’m sold. If you have an existing pdf collection, you can add it to Papers, assign keywords, and organize the paper into categories. The pdfs can be read directly in Papers. You can also search PubMed from within the program, download pdfs, and have them placed into Papers automatically. This description doesn’t even begin to scratch the surface of what Papers can do. I’m sure it will become an important part of my article workflow. If it doesn’t, I’ll let you know.

One problem with pdfs not addressed by Papers is portability. It’s great to have Papers store all my pdfs on my work computer, but what if I want to work on them elsewhere? I could put them on a portable drive, but I don’t want to worry about carrying it around. Better would be to have the pdfs stored online. Yojimbo allows collections to be stored on .Mac – but you have to subscribe to that service from Apple. I’d rather be able to store pdf archives on any WEBDAV server, like those you can store your iCal calendars on. I’m going to suggest to Mek and Tosj to build this ability into future versions of Papers.

  • gsgs

    why are papers in pdf ?
    plain text is much shorter, allows you to easily put everything
    into one big file and quickly search for keywords or several keywords simultaneously.
    When you found what you were looking for, you can still open the pdf with the pictures.

    So I'd convert all pdfs to text and put them in one big file with the names of the
    corresponding pdfs. Then I search the files from commandline for keywords.

    I did the same for the flu-forums (files of > 100MB) and for all posts plus comments
    of this blog.

  • gsgs

    why are papers in pdf ?
    plain text is much shorter, allows you to easily put everything
    into one big file and quickly search for keywords or several keywords simultaneously.
    When you found what you were looking for, you can still open the pdf with the pictures.

    So I'd convert all pdfs to text and put them in one big file with the names of the
    corresponding pdfs. Then I search the files from commandline for keywords.

    I did the same for the flu-forums (files of > 100MB) and for all posts plus comments
    of this blog.