5 Reasons why Paperpile is my new reference manager of choice

Those of you who may have been following this blog for some time will realise that I am a bit of a reference manager geek. I have used pretty much every platform available including Endnote, Mendeley, Papers 3, Sente and Readcube whilst writing posts on my previous tools of choice, Zotero and Papership. For the past six months I have been using Paperpile, a relatively new entrant to the market whose differentiating feature is that it works entirely online using Google Chrome and Google Docs (other platforms are in development). I thought that I would set out the main reasons why Paperpile has in my view become the tool to beat in what is increasingly a crowded market. You can get an overview of Paperpile by watching the promotional video below, then read on to find out why I rate it so highly…

1. Paperpile works entirely online.

For many this may seem a bad thing, but as I have already written about here and here, I favour the light, fast and responsive approach that online browser based tools provide over the large, clunky and often over complicated desktop application that of more traditional tools. Paperpile lives in Google Chrome and stores your library in Google Docs and so as long as you have access to a computer with the browser installed, your entire library is with you and you can begin writing immediately.

2. Deep Google Docs integration

For me online, cloud based applications are the future of work and at the moment Google Docs is my tool of choice. All of my recent academic journal and conference papers have been written entirely in Google Docs (I will post an account of this soon) using Paperpile to manage citations. You can seamlessly collaborate with other Paperpile users on a single document, adding citations and seeing each others’ changes in real time. Even if they do not use Paperpile, they can still help edit the manuscript and view a document’s citations. Because all references are stored in a central library, there’s no need to worry about keeping everyone’s personal libraries in sync — it just works. I have successfully persuaded a number of my collaborating authors to take the plunge and work with me using this system.

3. Deep Google Scholar Integration

Whist there are perhaps some who have issues with using Google Scholar for undertaking literature searches, for many of us it is an invaluable resource. Paperpile’s deep integration with Scholar means that it only takes one click to add new papers to your library. Paperpile also shows you when you have already added a source as you can see fro the screenshot below.

Screenshot 2015-04-15 21.27.08


Of course you can also add papers to your library using the Paperpile extension in Google Chrome from any database you care use!

4. It. Just. Works!

I can’t emphasise enough how frustrated I have been over the years with reference managers that have corrupted my entire library or documents I have been working on (thanks Endnote), or ones that crash constantly when attempting to import my PDFs (Papers 2 and 3). So far I have found Paperpile to be the most stable of all the apps I have ever used. It dealt with importing my close to 1500 document library speedily and without issue. It supports nearly every citation standard I have ever come across and Paperpile uses the Citation Style Language (CSL) to format citations and If there is no style for a particular journal, chances are that there are identical or very similar styles you can use.

5. Responsive staff

Paperpile was founded in 2012 by three computational biologists — Stefan, Greg and Andreas — who share a passion for exceptional software and scientific papers. They are academics themselves and so really understand the specific needs of their users. They are always present and super helpful on the forums responding to issues very quickly. Paperpile is still in active development and there are some interesting future plans such as mobile apps and integration into other online platforms such as Microsoft Word online and other browsers.

I encourage you to give Paperpile a try to see for yourself if the workflow works for you. Let me know how you get on in the comments!

11 comments on “5 Reasons why Paperpile is my new reference manager of choice
  1. A group of enthusiastic staff at University of York conviced a receptive IT team to obtain a site licence. Very happy about this. I have used Endnote, Mendely, Papers, Papers & Zotero, but nothing as simple and simply powerful. To me it has been designed by researchers, not for researchers.

    • Hi Matthew

      Yes, we were discussing this on Twitter last night – very encouraging. Unfortunately my experience of the IT team at my institution is rather less positive. We are already restricted from using systems such as Dropbox or Gmail for work and Chrome is not installed on any of the staff/student computers (although as of last month staff can request that IT install Chrome on their office machines). The result is that many of us end up using our own machines or purchasing a laptop as soon as we bring in any funding to get around these restrictions.

      Perhaps I will take another run at them to see what the likelihood of adopting a system like Paperpile would be…Ill report back 😉

  2. (Feel free to delete this message)

    I’m certain that you mean “manager” instead of “manger” (in the title and second line of the post).

    • Ha! Thanks Luisa and well spotted… Must have been WordPress’s auto spell. Good lesson there about the value of proofreading!

      Thanks for the heads up 😉


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  5. It’s really simple to do the job! It has great options to categorize the articles and do the cite in action. I’ve used Mendeley and Papers. The deep integration with google docs made me change my workflow. Now all papers are done in the Google Docs/Drive/Paperpile world.

  6. We used PaperPile for a while until our pdf library size became larger than 1 TB and still growing. Unfortunately clouds are too expensive for us now and we consider switching to an on-premise solution like Daminion Server or similar and pay nothing for an extra disk space.

  7. Could anyone make a detailed comparison between ReadCube and PaperPile? I though PaperPile lives on internet and Google could be a problem: how if no internet access? How if you have to travel to a place where Google is banned-eg China?

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