A happier scientific writing: Putting a plug in for Paperpile (+Google Docs)

A couple of years now, I discovered Paperpile reference manager and I thought it was awesome. Although there were decent free managers like Mendeley (which I actually liked) or Endnote (which I didn’t), there was nothing really effective. My other concern was that I wanted to use Google Docs, as it would allow me to work with colleagues as well as to seemingly move writing from my Mac and Linux box (or any other computer).

I shared the document below with my colleagues at the Max Planck Institute for Dev. Biology, and Google Docs + Paperpile ended up being the default writing combo for our department (and I think is permeating to the whole institute).

 


[Written in 2016 with minor editions. Some features might have improved]

I had to share this awesome discovery with all you guys! If you are too often annoyed with your regular reference manager … keep reading.

So far I have worked with Mendeley (+2 years) and Endnote (6 months) and I haven’t been fully satisfied until one month ago that found Paperpile (https://paperpile.com/). It is a private reference manager that works online and is fully integrated with Google Drive, Google Docs, Google Scholar, etc …

Below I explain the pros and cons and attach some screenshots showing how it works.

PROS

  • No need to install anything, it runs in Google chrome browser as an extension. This means no incompatibility with your operating system! Mac, Windows and Linux can use it.
  • Since it is integrated with Google search engine, you can add a paper to your reference library (including pdf) with just one click (see screenshots below).
  • Super-accurate metadata recognition. It gets the details of the paper with basically no errors, because you import it directly from the journal web page or from a reference database and search engine (Mendeley tried to do this but most of the time I had to edit it manually).
  • With your gmail account (and the free 15 G of space in Google Drive), you can synchronize all the pdfs of your papers and you can have them in your desktop (to fill it up you probably need over 10.000 papers).
  • Online high quality integrated pdf editor. You can highlight, add notes, etc.
  • The annotations are also synchronized. That means that online annotations appear in your pdfs, but also the edits in your pdf appear also in the online pdf editor (for instance if you are editing with Preview software in Mac).
  • Perfectly renamed pdfs.
  • It is INTEGRATED WITH GOOGLE DOCS! Now, we can write entire papers in Google Docs.
  • [UPDATE 2017] I just learned that you can download a Google Doc (with citations inserted with Paperpile) into an office word document, modify text, and re-upload it into Google Docs without any loss of information (the Paperpile citations are kept even after the two transformations as long as you do not remove the hyper links in the text)
  • Easy import/export Paperpile<->Endnote. Not only the reference database, but also you can transform a Google Doc with Paperpile citations into a word document with endnote citations.
  • You can edit citations collaboratively in Google Docs (that is, two people can add citations in the Google Doc, even if they do not have a Paperpile library. It is done via Google scholar search in the Google Doc screen).
    • So far Google Dosc could be used to write papers collaboratively, with comments, suggestions, edits. But the citations were the last step and had to be edited by a single individual. Now several people with their Paperpile accounts (or maybe a shared account of a lab), can add independently citations to the Google docs.
    • If you click in a citation from another person, you get the citation information and, if that person had the PDF, also view it.
  • Paperpile has shared folders. This might be particularly useful for labs, where the supervisor can share his/her library and all students can search for important references there.
    • You can also share a single paper you like with somebody only with two clicks: >click share >type email > click ok  (instead of finding the pdf or copy the journal url and attach them to an email).
  • NO LEARNING CURVE. I think Mendeley and Endnote are more difficult to use (particularly the second). With Paperpile, I basically didn’t have to learn anything, just uploaded my library file (from Mendeley or Endnote) and started using it. Now I mainly add papers with one click when I see them in internet.
  • It will soon support microsoft word online.
  • [UPDATE 2017] So far Google Docs missed the feature of putting line numbering into a document. This is 100% required for submitting to a journal, so we had to download the paper written in Google Docs and import it to MS word to put the lines. Now there is a Google chrome extension that allows putting line numbers in gdocs. Make sure you scroll throughout the document and that you export it as “print->save as pdf”.

CONS

  • I can only think about a big one: Paperpile works exclusively ONLINE. .
    • Still, Google Docs does work offline, so when writing a paper in a plane or the countryside, you just need to put a comment to remember to add a reference later.
    • Because your papers are stored as pdfs in your Google Drive (which can be sync in your computer), you can actually keep reading them and annotating with another editor (preview or adobe … ) offline.
  • Private software. You have 1 month trial for free, then you have to pay. However, it is only 2.9 $ / month = 32 euros per year. I think that is something more affordable than other options ( Endnote X7 $249.95). I tried 1 month and it was awesome, so I paid it. Of course, they offer shared licences for Universities or Institutions (some affiliated institutions are Berkeley, Max Planck, MIT, Cambridge… )

 

======================================================================

Screenshots

The Paperpile interface. It is just in a Google chrome tab. Folders in the left, the papers in the middle, and some statistics of all your library in the right

When you click in one of these papers, it opens it in another tab with this pdf editor. You can search, annotate in 4 colors, jump between annotations, see the sections outline…

All the pdfs are renamed and sorted in your Google Drive automatically, so you can edit outside Paperpile, or search directly in a folder …

Many ways to import to your library. My favourite is just click the button in the upper right of your browser when you are in the page of a journal, like this paper of Science. When you click add to your Paperpile, it gets all the metadata and also downloads the pdf for you.

When you are searching in Google scholar or even just Google,  a small button of “Paperpile” appears when there is a paper or a book. If you click on it, it will add it to your library, if it is already there it appears in green, and if you also have the pdf, there is a little blue icon in the side.

[Update 2018] —

screen shot 2019-01-18 at 11.31.37 am

You can add papers to Paperpile directly in Google scholar profiles!

— [end update]

You can import stuff in Paperpile platform. As I mentioned, different uploading formats are available: PDFs, bibtex, or RIS (one of the formats of your Endnote library) …

…. or you can just search in reference engines from inside Paperpile, and add with the +.

Add the Google docs plugin (2 clicks). Adding a citation is as easy as to search in the right hand Paperpile bar. Find the paper and click on it.

image2016-3-28 20_13_14

Citation appears in the format you want, and at the end of the document a bibliography is appended when you click update bibliography. Each cite is actually a link to the paper, so if somebody else (e.g. working collaboratively in the paper) clicks on the link, it opens a tab with the full citation and the pdf ! The opposite also holds. If somebody is reviewing your paper and does not have Paperpile, is OK. If there is one reference missing, you can also add it searching in the right bar. This time it goes to google scholar and when you pick a reference, it cites it in the same way. Now if the first author wants, can click on the link and add it to his personal library (that is pretty cool … I tested it with a different account).

image2016-3-28 20_14_42.png

In the same bar there is a button and you can export the whole document into a word.docx file and a endnote.RIS file . I tried and it works.

image2016-3-28 20_15_30.png

 

ENJOY !

 

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