Friday, October 15, 2010

Papers: How to Organize Electronic Journal Articles

I hate journal articles.  I don't hate publishing research.  Journal articles are the standard means of publicly communicating research findings to the rest of the scientific community and I don't hate that either.  What I hate is the fact that I need to keep track of literally hundreds of 10-20 page documents - it's a logistical nightmare.  My undergraduate adviser accomplished this with a pair of 5 drawer filing cabinets.  My current adviser has dozens of boxes of reprints sitting on shelves in our computing lab.  I generally prefer electronic versions for storage purposes, but that becomes a mess when getting papers from ADS, the arXiv, and individual journal websites - all of which use their own convention for filenames.  I hate the piles of papers, either physical or electronic, that result from journal articles.

However I have recently found something that helps with the mess:  a piece of software appropriately entitled Papers.  First a couple of disclaimers - it is not freely available (it costs $25.20 for students, $42 for everyone else), it only works for Mac OS X, and it's really designed for people in biological sciences, so it doesn't integrate as well with the arXiv as I would like.  Also since the software is developed by a small company (6 people, some of whom are also full-time scientists), upgrades and bug-fixes are often unpredictable.

Now that I've got the negative stuff out of the way, let's talk about why I'm writing this post.  The bottom line is that Papers saves me time trying to find papers I want and allows me to effectively carry my entire library of journal articles with me wherever I take my laptop.  On top of that, Papers can extract bibliographic information from PDF files and then export it in BibTex format, allowing me to easily create reference lists for papers.  On top of all that, it provides a nice front-end portal to almost all of the major databases like NASA ADS, the arXiv, Google Scholar, and more to provide useful features.  Let's say, for example, I want to know if one of the leading dynamo theorists and perhaps the most prodigious writers of journal articles in astrophysics (13 peer-reviewed journal articles so far this year) Axel Brandenburg has published anything new.  Papers automatically interfaces with ADS (or another database of your choosing) and downloads the titles and bibliographic references to all of recent entries for all of the authors in my database.  Here's a screen shot to illustrate my example and to generally show how spiffy Papers looks (click to embiggen):
Say what you will about Macs but their GUI's sure are pretty.

The software is also easy to use as a PDF reader with note-taking feature. I regularly use it to read new articles on my bus rides to and from campus. They even have a new version for the iPad that allows you to read and annotate PDF's on Apple's latest wonder. If anyone would like to send me an iPad I'd be happy to write a review on that feature as well.

So if you hate piles of paper on your desk or trying to organized PDF's on your hard drive and happen to use a Mac, check it out. It's not a perfect solution, but it is the best thing I've found to alleviate my hatred of journal articles yet.


  1. For Windows and Linux users, Mendeley is pretty good, and free.

  2. Nick,

    I agree this sounds nice but I was wondering: on a practical level is it really much better then just finding the latest article by (your example) "Axel Brandenburg" using adsabs or spires which also link to both the epring and journal pdfs, let you read abstract and view references citations and will also generate bibtex code for free?

    Again, don't get me wrong as I am sure it is very nice and agree it is pretty looking but I was wondering if it really has significant advantages over adsabs or spires?

    But if people are buying it then I have to concede it must have significant advantages over the free online tools.

  3. Jared*,

    That's funny they have Mendeley for the iPhone/iPad but not the Mac OSX itself. :)

    And what is even more hilarious is the computer they are using in their picture is a Macbook Pro which they evidentially don't support. :)

  4. Joe,
    I use ADS and Papers differently. I use ADS (and the arXiv) to find articles, while I use Papers to store and organize them. I don't use Papers for browsing as much as I use it for storing papers that I actually think I'll want to re-read and reference later. When writing I like to have my sources at hand and Papers is ideal for that.

  5. Great post Nick! I have wrestled with this problem too. Once upon a time (during my MS at BYU) I had piece of software than ran on a linux server. It would serve up papers, bibtex entries, etc. and be a repository for papers. It allowed for collaboration, etc. etc. It wasn't the prettiest though, and now I have no idea what it is called.

    I miss my Mac for reasons like this. I'll have to try out Mendeley.


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