For the purposes of reading, managing, and citing journal articles, I use the software package Papers. It’s been very useful to me by helping me keep track of the myriad of research that comes out every day. Also, it is quite beneficial when writing articles owing to its handy applet that can insert citations and can format journal-specific bibliographies. The one obvious downside to Papers is that it costs money ($50 for students - ask your advisor to buy a group license!), but you certainly get what you pay for.

When I started graduate school, I used Mendeley mainly because it was free and it served its purpose well (at the time). However, I started looking for alternatives when Mendeley was bought over by academic corporate giants Elsevier, who had a vested interest in its users’ data. In this process, I was turned on to Papers by the Mac-centric lab that I belong to around a year and half ago. I had recently bit the Apple bug myself, so to say.

At the time, Papers2 was the latest version of Papers. Papers2 was fantastic: great design and interface, browser capabilities, multiple user tweaks, ‘smart’ collections, social media connections, a citation applet, offline support, and the in-app ability to search for supplemental information. Mendeley offered some of these functionalities but Papers far outweighed the latter with its elegant design and importantly, stability.

Fast forward to Feb. 2014, Papers3 was announced. I was quite kicked to try it out and I switched as soon as I could: it was awful.

On first glance, there were plusses: The GUI was completely different; certainly more modern, minimal looking - and it did look better than Papers2. There was a browser below the library, and there was a separate ‘window’ for reading papers, where multiple tabs could be accrued. It was similar to the aesthetic jump from IOS 6 to 7. The interface seemed more functional as well. Quite exciting!

Although, under a couple hours of use, I began to get really frustrated. Here’s where it failed miserably: stability, on multiple counts. Firstly, when importing your previous Papers2 library into Papers3, the metadata for hundreds of papers was lost and Papers3 would hang when trying to update those. Major suck. Second, more importantly, it would not allow me to keep my database of pdfs attached to the papers without renaming all the files or making an extra copy (I have my own way of categorizing/naming these pdfs). When I tried to work around this, Papers3 would crash. Next, it had a very difficult time handling pdfs where images were large or weren’t flattened (Papers2 did as well) which would lead Papers3 to crash. Sense the theme? It would crash many times and the users were stripped of the tweaks they had in Papers2. So… I did what a good scientist does: give this new thing its due time, get frustrated, and then revert to something I was familiar with - Papers2.

Two weeks ago, on whim, I decided to revisit Papers3 because the large pdf-issue and the iOS6-like design of Papers2 was getting to me. I thought, "there must have been some improvements made…” After all, I had felt that Papers3 was released too hastily and prematurely, so surely after a year and more testing improvements should be on the cards.

And well, I was pleasantly surprised! There have been improvements:

The library transition is now seamless from Papers2 to Papers3.
I am allowed to keep pdfs named whatever I want
The stability has increased ten-fold from last year (I haven’t had a single crash over the last two weeks)
It is less buggy (browser/applet etc.)
Features such as in-app addition of supplemental information works smoothly

Full disclosure, I don’t know if there has been a lot of work done on Papers3 since last time I used it, but I do know the problem was non-unique to me. There still are some gripes (for example, ‘My Papers’ is buggy: nothing shows up) and I don’t think they have the best structured online support community. However, I am digging the new interface and design (like last time) with a slight improvement on the features of Papers2 (unlike last time).

If you are looking out for a paper management software and are serious about it, I would recommend Papers3. If you were a Papers3 deserter like me, I would suggest you give it another stab.