Use paperpile

How to use paperpile.com

Paperpile is a great tool to keep track of all the papers you have read and an easy way to store citations. You can access the lab's account on Basecamp on the Lab Passwords page.

Getting Started

First thing's first — you'll want to add some papers to your new library to learn how to organize your papers and work effectively with Paperpile. Read on for some tips on how to quickly make the most out of Paperpile.

Add papers

The first thing to do with an empty library is to fill it up with papers relevant to your work. Paperpile make this easy with three ways to find and add articles from the web:

  • Click Add papers button to search online directly from Paperpile or upload PDFs from your hard drive.

    Tip: to quickly upload PDFs, just drag and drop from your file manager into the Paperpile window.

  • Use your browser to search for articles on Google Scholar, PubMed or ArXiv and click the import buttons Import button.

  • Click the Paperpile button Paperpile toolbar button in your browser toolbar to import from hundreds of supported publishers' sites. A green arrow appears on the button when you're viewing a supported site (For an example visit doi.org/10.1038/nature10530).

Get organized

Next, add some folders and labels to help keep things tidy. Click the New Folder button Paperpile new folder button to add a new folder. You can rearrange your folders by dragging (labels are sorted automatically).

Drag a paper into a folder using the drag handle Drag handle on the left side of the paper, or use the toolbar buttons Folders and labels toolbar buttons to organize many papers at once.

Cite, copy, paste

You can quickly copy and paste formatted citations using the copy button Copy toolbar button. Choose between copying the plain citation string, a rich-text version with abstract & links (good for emailing), or the Bibtex data for manuscript preparation.

What's next

Where to go from here? You can learn about some of Paperpile's other unique features by viewing our guides on how to Write papers in Google Docs and Sync your files with Google Drive.

But more importantly, Paperpile makes reference management easy so your next step can be to get back to doing what you do best — research!

Write papers in Google Docs

Paperpile's Google Docs integration is so simple that most users need no introduction — just create a new document and start writing! For those who like to be prepared, here is an overview of the main features and tips for collaborating on academic documents with Paperpile and Google Docs. If you are having trouble with the Docs plug-in, visit the troubleshooting page for tips on how to solve the most common issues.

Inserting a citation

To insert a citation, either click the Paperpile button Google Docs Paperpile button in the toolbar or use the keyboard shortcut Shift-⌘-P (on Linux or Windows use Ctrl-Alt-P ) to open the citation window:

Google Docs Paperpile insert citation dialog

Start typing to search within your library. Paperpile will search within the title, keywords, abstract, etc. of all papers in your library, the same as when you search from the main Paperpile interface (example). Choose a result to add it to the current citation:

Google Docs citation added

To add another item just start searching again. Or, click on any of the citation tags Google Docs Paperpile citation tag to edit advanced options (see Advanced options for citations below). When you have finished creating a citation, click Add citation to add it to your document.

The citation is inserted into the Google document as a link with placeholder text, e.g. Google docs citation text. Note that this is not the final formatted citation; see below for instructions on Formatting a bibliography.

Advanced options for citations

Clicking directly on a citation tag opens up a panel with details and more advanced options:

Google Docs citation details

The upper part of the panel shows a familiar overview of the citation metadata with a link to open the item in Paperpile.

Below that are three advanced citation options:

  • Location / page numbers: choose from a range of location types (see a partial list) to use when citing a specifc page, chapter, or book from within a larger work. Example: Google Docs citation location.

  • Prefix / suffix: Add arbitrary text to be included before or after the inline citation. Examples: Google Docs citation prefix and Google Docs citation suffix.

  • Suppress author: this option causes citation styles to not display the author name within inline citations. When using a parenthetical citation style, this allows you to include just the year in parentheses. Example: Google Docs citation hide author instead of the usual Google docs citation default.

Formatting a bibliography

After adding or editing a citation, Paperpile can reformat your document and generate the bibliography with one click. Simply choose Paperpile > Format citations to proceed. (Note: you will need to give permission to the plug-in the first time you format a document. This will only happen once.)

To choose a different citation style, open the citation style window with Paperpile > Citation style...:

Bibliography style dialog

Search for the journal or publisher whose style you would like to use, and a preview will show in the bottom of the window. Click Update to update the citation style and reformat the document to see the changes.

Collaborative editing

You can edit a Paperpile-enhanced Google document with any number of collaborators, whether or not they already use Paperpile. Just click the Share button in the upper-right corner of the screen and choose who to share your document with.

If you share the document with collaborators using Paperpile, they will be able to add new citations and reformat the document without trouble (see our FAQ entry on how collaborative citations work). For anyone not using Paperpile, citations and bibliography items will link to a web-based view where you can edit or update the data for a given item.

Important: Citing a document from your personal Paperpile library will create a local copy specific to the Google Document. This copy will be updated if you update the original copy in your library. However, as soon you or someone else edits the local copy of a Google Document any subsequent changes you make to the original copy in your library will not update (and thus overwrite) the local changes. Also, changes made to the local copy by yourself or a collaborator will never propagate back to your library.

Citation styles

Paperpile supports the popular "citation style language" CSL with more then 8,000 citation styles available from citationstyles.org. We regularly update the citation styles in Paperpile so that you always get the newest styles and updates.

To change the citation style in a Google Document go to Paperpile > Citation styles and search for the name of your style.

If you can't find your style you have two options: (i) find an identical or very similar style or (ii) create your own style. In both cases you can use the citation style editor available at editor.citationstyles.org. This free web-tool allows you to find styles and to modify existing styles to your needs.

If you have create your own CSL style, download the CSL file to your harddisk and upload it to Paperpile in Settings > Citation styles. You can then select this style in your Google document as described before.

DOIs and URLs in your citations

For most reference types Paperpile lets the citation style control how to display DOIs and URLs.

However, for print articles Paperpile does not show DOIs or URLs by default. More precisely, citations of types "Journal article" and "News article" with the field "pages" set will not include DOIs or URLs.

To override this behavior, activate the option "Always include DOI and URLs". This option will show DOIs as specified by the citation style. Note, that some citation styles don't support DOIs and this option (despite its name) cannot change that. You may need to adapt the behaviour of the citation style by editing the CSL file (see above).

You can store multiple URLs in the field "URLs". Paperpile will always use the first in citations.

Known issues

  • You can only use the Google docs plugin with the same Google account from which you signed up to Paperpile. If you have documents owned by your non-Paperpile Google Account, share and edit them with your Paperpile-linked account.

  • It is nice to be able to collaborate and ask other people in the lab to add papers to the paperpile account for you. If someone ELSE adds the reference to the shared folder, you have to take one more step to be able to cite in google docs: go into the shared folder, select every paper, and then click the "add to library" button that appears.