Infinite Loop / The Apple Ecosystem

Minireview: Papers for OS X

Papers is a new app for Mac-using scientists to help organize PDFs in new, …

Working in research isn't all benchwork.  Sure, there's a lot of playing around with enzymes and proteins, gels and nucleic acids, but doing lab work is only half of the equation. The rest of the time is spent reading, reading, and yet more reading.  A decade ago, when I was still an undergraduate, that meant spending a lot of time in the library, digging through dusty stacks and wearing out the department photocopy card (or your bank balance, if you were unlucky). While that might sound like an awful lot of work, even in the early 1990s we were blessed with electronic literature searches like PubMed, prompting lots of comments along the lines of "You don't know you're born," from those scientists who had to pore through printed copies of Index Medicus.

Moving toward the 21st century brought about a change in the way that most of us accessed the literature. Journals started to make use of the internet in a big way, and instead of spending time hunched over a photocopier or filling out an interlibrary loan card, a few mouse clicks was all it took to download the PDF.  So far so good, but this move to electronic copies has brought with it some challenges of its own. The biggest headache has to be what to do with them all once they're downloaded.  I've seen various approaches, from naming each file with the first two authors and the date and simply dumping them all in a central folder all the way to the other end of the spectrum, which involves simply forgetting where you saved it and downloading it all over again each time you want to read it.

The advent of OS X 10.4 made life significantly easier for me with the advent of Spotlight.  Here was a way to search within PDF files for specific words, so if I knew I had the file somewhere on my hard drive, finding it was much easier.  Of course, that still didn't solve the organization problem or having multiple copies of the same PDF.  What we really needed was obvious—iTunes, but for research papers.

Up until iTunes came along, organizing MP3 files was an important job; giving them the right names, storing different albums in different folders, and so on.  But iTunes came along and said "Screw that—you give me your files, and use me to find them, and never mind what the file structure looks like."  Of course, there are still plenty of people who don't want to hand over this control to iTunes, but I'm not one of them, and I've never looked back.  As the mighty Siracusa would say, metadata is key, and once properly tagged, iTunes is all the app you need to access your music.  Which brings me to the point. How great would it be if there was an app like iTunes, but for papers?  The answer is "insanely great!"

That app is called Papers, and it's the work of a pair of talented scientists from the Netherlands (which goes to show that country has even more to offer than decriminalized cannabis, windmills, and mayonnaise on fries).  Alexander Griekspoor and Tom Groothuis, under the guise MekenTosj, were already known to some in the Mac scientific community for their previous work on EnzymeX and 4peaks, the latter of which our very own Dr. Timmer contributed to. Papers is their latest work and, for some of us, the answers to our prayers.

Once you've downloaded and installed Papers, the next thing to do is to fill it up.  In typical Mac fashion, it's as easy as dragging your PDFs onto the window and dropping them. Papers will copy the file into a central library location, at which point you can then delete your original. The file will appear in the library, but without any of the metadata that you need. 

This isn't a problem though.  In the same way that iTunes has the iTunes Store for searching, Papers acts as a front end for PubMed, the NIH's invaluable online literature search.  Simply hit the "match" button and a new tab opens, with the PDF in the middle of the window and a search box on the right.  From here you can highlight text and use it to search PubMed. Then simply find the right result, match it to the PDF and smile when an animation of a scanner beam sweeps across the document.  

You're then returned to your library, and the file in question now has the correct bibliographic information.  If you've got a lot of PDFs this might take some time, but unlike when you're found surfing Infinite Loop, you can tell your boss that you're actually working. Occasionally you'll end up with two copies of the same PDF, and when you go to match the second one, Papers will point this out and ask you if you want to delete the duplicate.

You have other ways of adding your data in addition to dragging and dropping PDFs.  Endnote, RefMan, BibTex and Connotea libraries can be easily imported. For my sins, I'm an Endnote user (or victim), and it was a moment's work to import my library.  The bibliographic information will show up, but there obviously aren't any PDFs attached.  Simply double-click the paper you want and another tab will open to take you to the relevant html page for that article or it's PubMed page, depending upon whether or not it's available as a PDF.  From here you can download it straight into Papers.  You can also export lists of papers back into Endnote or BibTex.

I noticed that there were multiple instances of the same author in the list, but it seems MekandTosj thought of that, and you can combine them into a single instance.  You can also label authors as friends, colleagues, coworkers or competitors, and enter other details about them.  This can be very handy for keeping tabs on your friends or rivals. 

It doesn't stop there though.  As I said, back in 1997 I used to traipse off to the library once a week to catch up on the latest journals.  More recently, it's been possible to have eTOCs emailed direct to my inbox, so I can read the latest developments in the lab, scrolling through e-mails in Entourage and opening interesting-looking articles in Omniweb.  But once Papers knows the address for a given journal, it will fetch the 50 most recent papers published therein, which makes staying abreast like child's play. As with the Author list, sometimes you'll have multiple instances of the same journal, but again, merging them is a button away.  You can edit the entries to include the URLs for each journal's homepage along with their archives to make it even easier to access them. 

Next on the list is the PubMed front end, which remembers past searches and also has the option of a number of predefined search terms.  You can also create groups of papers, much like a playlist in iTunes, and there are smart groups—similar to smart playlists—where any paper in your library will be included that meets certain criteria.

If you prefer using your web browser to read journals, you can still import the articles easily with a little JavaScript bookmarklet that will send the page that you're currently viewing over to Papers' browser.  As for reading PDFs, there's a handy fullscreen function that allows you to concentrate on the article at hand.

Other developers have had similar ideas in the past—iPapers being one, and Yep being another—but none of them in my experience have been as well-rounded or complete.  Although Papers is still in Public Preview, it is stable enough for regular use.  Certain features have yet to be implemented, including the preferences, but in a few short days this application has wowed me in ways I thought I was too jaded to experience.

There are some limitations at present.  Occasionally searching article titles in PubMed doesn't bring back any hits, but I've never not found the right reference searching by author. Currently, PubMed is the only search engine you can use, although a SDK will be forthcoming that will allow users to create their own plugins for other databases, so all you non-life scientists will be able to make as much use of it as I do.  As far as gripes go, that's pretty much it.  Some people might not be happy letting the app handle storing the PDFs, but I'm not one of them; as long as I can read the research, I don't really mind what the PDF's filename is or where on my hard drive it's located.  The functionality is there and, almost as importantly in my opinion, so are the aesthetics, but then you'd expect that from developers who have already won two Apple Design Awards.

Currently the Public Preview will set you back €19 (about $25), which is a tiny price to pay for literature nirvana.  What are you waiting for?

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