In 2007, a talented pair of scientist-programmers called Mekentosj released Papers, a Mac OS X app that did for scientific literature what iTunes did for music. They followed the desktop version with an iOS app that works as a standalone program or in conjunction with your Mac. The combination of Papers with an iPad is pretty good when it comes to catching up on your reading. Still, that was then and this is now, as they say, and a new and rebuilt Papers 2 is here to take over your research management needs.

Yes, new and rebuilt. Papers 2's innards have been redone from the ground up, and as we'll see in a bit, this has resulted in some teething trouble. Despite the internal changes, Papers 2 still has the same great Mac user experience that has won the company both Ars Technica and (several) Apple Design Awards.

Adding papers works in the same way it did before. If you already have a paper, you can drag and drop your PDFs onto the icon or the app. You can also import them from the search function, which works as a front end to a range of databases and repositories, including PubMed, Google Scholar, arXiv, and more. You can also now import directly from a scanner, which is a neat touch. If you're an existing Papers user, you can transfer your current library, and bidirectional syncing with iOS devices will also let you copy over data from your phone or iPad. For new users, Papers 2 will cost you $79, with a 50 percent discount for existing users, as well as price breaks for undergraduates—site licenses are also an option.

Unlike in 2007, Papers is no longer the only game in town in 2011. Probably its closest competitor is the cross-platform Mendeley, which we've looked at in the past—and that's still the best option for those of you who don't use OS X. Mendeley also had some features that Papers didn't; it supported a much wider range of documents than just scientific papers, and has social networking functions that allow you to find and share papers. Thankfully Mekentosj doesn't suffer from not-invented-here syndrome, and Papers 2 has adopted some of these.

In addition to journal or newspaper articles, there is now support for patents, bills, laws, reports, and even media files. Back when I reviewed the first version of Papers, I wouldn't have appreciated how useful this is. Since moving into the field of science policy, however, the expansion of categories has proved invaluable, and gives Papers 2 an appeal to researchers beyond the life sciences.

Another feature that seems inspired by Mendeley is Livfe (pronounced 'life'), which brings social networking features to the app. I can't really comment on how it works as it has been closed to the bulk of Papers 2 users since the app launched a couple of months ago.

Probably the coolest new feature is Magic Manuscripts. You can throw away your copy of Endnote, because Papers 2 now integrates with most Mac OS X word processors (particularly Word and Pages) to let you find references, cite them in your document, and format bibliographies. Manuscripts runs in your menubar, and is activated by a keyboard shortcut that brings up a little search window that floats over your Word or Pages document. Papers will also keep track of different manuscripts you have or are working on, which is a neat touch. It integrates well into your workflow and is probably worth the upgrade price on its own. I'm a giant fan.

Unfortunately, it's not all kittens and sunshine. Because of the completely rewritten back end, lots of functionality from Papers 1 hasn't made the jump yet. For one, there's no way as of yet to merge authors or publications. This is really quite annoying, because JM Gitlin is considered a different author from Jonathan M. Gitlin. Likewise, differences in abbreviations of journals result in multiple entries. This function will be added back, but it cannot come too soon.

Another really neat feature of Papers 1 was the ability to see the most recent 50 publications for each journal, which was a great alternative to subscribing to the journal's mailing list. This is also currently missing, although it too should reappear sooner or later. Being able to save custom searches is also currently missing, but bringing this back (as well as better DOI searching) remains high on the list of things being worked on, according to Alex Griekspoor, one of the original pair behind Mekentosj.

Support for users with multiple computers is still not where I'd like it to be. Mendeley uses a central server to store your database, which means you can keep your home and work computers perfectly synced. My current workaround involves using my iPad to shuttle references from work to home, which works pretty well. In the past, users have put their Papers database in a Dropbox folder, but this is not recommended. As with the features above, multiple computer support is also on the to do list for Mekentosj, and the furious rate of point upgrades—we're already at 2.0.6—tells me that they're not resting on their laurels.

So, should you upgrade? If you'd asked me when the app launched in March, I'd have said not just yet. Now, though, I think that enough functionality has been restored, and the added features are enticing enough, that you should take the plunge.