On the organisational front, Papers 2 allows you to create folders of journal articles called "Collections," which can either be manually curated or a "Smart Collection" based on a search query like author name, title, or anything else contained within the metadata of each paper. In this way it's really easy to keep track of papers by species, methodology, results or even particular authors.
Speaking of keeping track of authors, Papers 2 can also keep track of your own published work. After you've imported your world changing/sure for a Nobel Prize this year articles into Papers 2 you can drag and drop them into a smart collection called "My Papers" under "My Research." It keeps track of the various journal articles you've authored and allows you to share your work via email, instantly creating a PDF, HTML, RTF or Word document summary from all or just some of your manuscripts.
Papers 2 also includes a kind of social network for science, called Papers Livfe [sic], which allows you to share what you're reading, view what's popular and share your ratings of papers.
In a very Mac-like way, Search is an incredibly important and useful part of the Papers 2 experience. It allows you to search much more than just the author and the title within your journal library -- it takes the search into the article text itself. In effect, once you have a big enough library, you can just search for a gene, a topic, a process or anything else you're looking for and Papers 2 will do the legwork for you, pinpointing which articles have the keywords you're looking for, how many times they're mentioned and where in the article they are. With one search you can separate the wheat from the chaff and get down to the real information you need. It's time saving, allows you to be more comprehensive and most importantly, gets you the information you need fast.
Managing and allowing you to read articles on the screen is all very well, but if you can't get that citation out into the paper, thesis, or grant application you're writing what good is it? Thankfully, Papers 2 can either work in harmony with your citation manager of choice, be it Endnote or its ilk, or can completely replace it with its own citation manager called "Magic Manuscripts."
It runs as a little menu bar app that can be invoked using a customisable global shortcut, ready to paste a reference in the style of your choice into just about any text field as you can see above. If you prefer to use a citation manager like Endnote that has a built-in "cite-while-you-write" add-in for your word processor of choice you can easily export a single paper, a group of papers, a collection or two, or even you whole library to BibTex, Endnote, Reference Manager, Bookends or to any program that'll read the fairly standard RIS file format. From there you can paste your citations into your documents using your established workflow. Indeed maintaining a concurrent library across both Papers 2 and a citation manager is easy, as Papers 2 will import citations and any PDF files you have attached to them from Endnote and many others, meaning that you never have to start your Papers 2 library from scratch.
On the go
That's great, Papers 2 makes managing, searching and importing journal articles easy on your Mac. But wait, I haven't gotten to the best bit yet -- iPad integration.
Using Papers for iOS, which runs great on both the iPhone and the iPad, you can sync your journal library back and forth with your portable device. It's handy to have your entire journal library on your person at all times if you have an iPhone, just in case you need to quickly import a new paper or show someone something, but when you slap it on your iPad you get so much more.
I've been looking for a way to ditch paper copies of journal articles for years, and Papers for the iPad combined with Papers 2 on the Mac finally makes it possible. Syncing over WiFi, you can read any and all of your journal articles on the iPad anywhere you go without having to lug that stack of paper with you. You can either read full screen in landscape or portrait, or zoom in to get a closer look.
The interface is intuitive and makes blazing through those papers easy. Once you've found something interesting you can highlight it, annotate it with a dropped pin, or simply attach a note to the whole article. It makes the traditional process of printing, highlighting and scribbling notes in the margin totally obsolete and saves trees and time too. About the only thing Papers for iOS is missing is text search within the articles themselves, but everything else I could think of is there.
With Papers 2 on your Mac, and Papers for iOS on your iPad, you really have the ultimate in journal organising, reading and annotating, all without paper, all without fuss. If you're starting a new academic year, or just looking for a better way to do things, then Papers 2 is certainly worth a look. If you're a Mac user, you're going to love it, and if you're not, well it might be the push that gets you to switch.
Papers 2 for the Mac is available for US$79/€59 directly from the developers at Mekentosj.com (group and student discounts, as well as a 30-day free trial are available), while Papers for iOS is available as a universal app for $14.99/€11.99 from the App Store.