My main reasons for switching over to Paperpile were as follows:

1. I didn’t want to pay for an EndNote license (my university doesn’t have a site license).

2. Papers3 for Mac was bought out by ReadCube…and now they are merging both software products into a new framework that is going to be a continual subscription model. I don’t want another recurring software subscription.

3. My Papers3 desktop app was getting infuriatingly clunky and slow (I had 4000 papers in the database before I started clearing them out) - and with the Readcube buyout and impending new software launch, the Papers3 app is no longer being updated or improved.

4. I wanted a citation/reference manager that would work with Google Docs, where I have moved over most of my manuscript and grant writing (save for a few collaborations where co-authors are still using Word docs).

A UCR colleague recommended I check out Paperpile when I arrived on campus a few years ago (Thanks @hyphaltip! You transformed my reference management!). I did, and never looked back. I’ll evangelize Paperpile to anyone who will listen!

A giant list of reasons why I love Paperpile:

• Seamlessly insert references and manage citiations in Google Docs! Inserting a new citation is a quick keyboard shortcut, and basially a Google Scholar search to find the paper you’re looking for (normally quickly typing out a paper’s first author, year, and a few title keywords will bring up the paper you’re looking for at the top of the list - but you can also search using DOI or full title on the off chance you don’t see what you’re looking for).

• Paperpile Pro version is FREE if your university have a site license - which may be the case at your university. Paperpile supports IP address-based and Google Apps for Education site license arrangements

• Supports all journal citation styles, just like EndNote - reformatting is easy if you need to revise/resubmit text with a different refence style.

• You can organize your library using both Tags and Categories (folders). I personally use Tags for manusript- or grant-specific labels (e.g. so I can keep track of what references I cited in different grants/papers), and then I use categories as a more general way to file and organize papers - examples of categories include “Software Papers”, “Nematode Microbiomes”, and “Deep-Sea Habitats”

• You can attach text notes and paper PDFs to references in your library. In fact, Paperpile will automatically downoad all PDFs it has access to when you add a citation to your library - that means if you’re on your university campus or connected to a VPN, it will download PDFs from whatever publishers/jounrals you have access to over your specific internet connection!

• PDFs are synched to a Google Drive (which you can automatically sync and access offline if you set up your Google Drive correctly - )

• Paperpile library is easily exportable in BibTeX format - that includes all notes.

• Library includes a button to automatically search for and merge duplicate papers (which will combine your tags and categories if you’ve added different metadata to duplicate entries)

• You can “star” papers and add color-coded labels to tags (yay for aesthetics and design customization). Starred papers get synched to a separate Google Drive folder for easy access.

• Field codes stay put when you download/export your GDoc text into Word (for the final proposal or manuscript submission that wants a Word doc with line numbers or a stylized document with images and captions). When I’ve had to resubmit or update text I just paste it back into GDocs, update the bibliography, and then replace the Reference list via copy/paste.

What are the downsides of Paperpile? Well not many that I could find, but some things could be improved:

• Your Paperpile library is a text-heavy interface, and not nearly as sleek or nice to browse as Papers3.

• Getting to the PDF documents requires a couple clicks, unlike Papers3 where you have a native inspector to immediately browse the PDF.

• Wildly inserting citations into new GDocs will automatically import them into your library - and if you want things organized you’ll have to go in and categorize/tag references manually. It can be a bit cumbersome and difficult to find “unfiled” references in the Paperpile interface at the moment.

But all these “downsides” are fairly minor and the positives FAR outweight the negatives. Overall Paperpile has significantly reduced the amount of time I spent importing, formatting, and citing references - the efficiency is incredible, and the integration with GDocs is amazingly seemless.