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Citation & Paper Management Tools

How to use tools for managing your a collection of citations or journal articles.


Citation & Paper Management Support

Contact Arnold Library
Weintraub Building, B1-010

Learn more about your citation management options!

There are a variety of different citation management tools available to fit almost anyone's preferences. Some things to consider when choosing a citation management tool:

  • Do I need remote access to my reference collection?
  • What kind of system am I running? Mac, Windows?
  • Do I have funds available for purchasing a client-based system?
  • Do I need to share my reference sets with others?

EndNote & EndNote Web

What are EndNote & EndNote Web?

EndNote for Windows and Macintosh is a valuable all-in-one tool that integrates the following tasks into one program:

  • Search bibliographic databases on the Internet
  • Organize references, images, PDFs and other files
  • Watch the bibliography and figure list appear as you write
  • Collaborate using End Note Web, the Web-based research and writing component of EndNote

EndNote Web delivers tools to:

  • Search online resources
  • Save ISI Web of Knowledge records directly to an only library
  • Collect and organize references
  • Format citations and footnotes or a bibliography

Why use EndNote or EndNote Web?

  • EndNote and EndNote Web are both compatible with Mac and Windows OS
  • Cite While You Write is compatible with Microsoft Word, OpenOffice and Apple iPages '09
  • EndNote Web allows video capture from YouTube
  • Integration of EndNote and EndNote web allows access to your database from anywhere

Using EndNote - Getting Started

EndNote is a client-based software program. It is available to Fred Hutch staff via Center IT's Software Licensing Catalog. Additionally, several versions of EndNote for both PC and Mac are available for use in the Shared Resources Computer Lab at the Arnold Library.

EndNote Web is a free, web-based companion to EndNote. To register for an account, visit

Warning Check compatibility and systems requirements to see if your current systems and programs are EndNote-ready.

Refer to the following resources to start working with your EndNote library:

"Find Full Text" Settings for Fred Hutch

Use the Find Full Text command in EndNote to retrieve the full-text articles (PDF) of references already in your EndNote library. By default, this feature will find publicly available or Open Access articles. 

Fred Hutch settings: 

Open URL Path: (check OpenURL if it is not checked by default)

Authenticate with URL:


EndNote & EndNote Web Help & Training


What is Zotero?

Zotero is a free Firefox extension that allows you to collect, manage, cite and share research sources.

  • Collect bibliographic references, pdf's, images, web pages, and sound recordings.
  • Organize collections by project or topic.
  • Tag, append notes, attach files and search your items.
  • Insert citations and create bibliographies in Microsoft Word and OpenOffice.
  • Use Zotero from multiple computers and create groups to share items.

Why use Zotero?

  • It's free, open source, and extensible.
  • Integrated in the web browser so there is no software to install.
  • Ability to easily use and sync your library from multiple computers.
  • Create groups to collaborate with colleagues.

Using Zotero - Getting Started

Zotero is free to download from the Zotero download page. First time users must register for a free account.

Warning To use Zotero with Mircosoft Word and OpenOffice, you will need to first install the word processor plugin for the application you are using.

Refer to the following resources to learn more about building your reference library with Zotero:

Zotero Help & Training


What is Bookends?

Bookends is a Mac-only citation database that allows you to:

  • Do online searches and attach PDFs and images to the citation.
  • Use Reference cross-links which show the relationship between articles and allows you to leave notes/thoughts for later.
  • Syncronize your library between home, work, and group members.

Why use Bookends?

  • Bookends sync feature allows your database to be where you are.
  • Reference linking allows you to make notes and show connections, just like old fashion notecards.
  • Works with several different word processors.

Using Bookends - Getting Started

Bookends is a client-based software program available for purchase via Fred Hutch Purchasing or directly from Sonny Software.

Warning Bookends is only available for MacOS.

Refer to the following resources to start working with Bookends:

Bookends Help & Training


What is Mendeley?

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

  • Automatically generate bibliographies
  • Collaborate easily with other researchers online
  • Easily import papers from other research software
  • Find relevant papers based on what you’re reading
  • Access your papers from anywhere online Read papers on the go, with a new iPhone app
  • And more!

Why use Mendeley?

  • Freely available application that you can install on your desktop or use on the web
  • Ability to sync your library across multiple computers, on the web, and on iPhone/iPad
  • Works on any operating system
  • Read and annotate PDFs
  • Import and organize PDFs stored on your hard drive or other citation management software
  • Collaborate with colleagues and share papers, notes and annotations
  • Export to other citation management software, or create bibliographies instantly in 1000+ citation styles

Using Mendeley - Getting Started

Mendeley is free to download from the Mendeley Download Page. First time users must register a free account at the Mendeley website.

Refer to the following resources to get started working with Mendeley:

Using Mendeley Off-Campus

Unlike other citation management tools, Mendeley does not yet offer integration with institutional proxy servers for access to full text subscriptions off campus, but that function is coming soon!

Until this is available, if you are off campus and want to use Mendeley to view and store full text PDFs from subscription resources, try one of these methods:

  • Use the Fred Hutch WebVPN to establish a remote connection to the center's network. Once connected, you'll have full access to all Arnold Library subscriptions.
  • Use the Arnold Library's Off-Campus Access service to login with your HutchNet ID and password. Once you've logged in, you'll be able to access all Arnold Library subscriptions and resources from your current location as long as your browser is open. If you close your browser, you may need to login again.

Mendeley Help & Training


What is F1000Workspace?

F1000Workspace is an online-only citation database that allows you to:

  • Collect reference lists with your collaborators and share Word documents with editable citations and bibliographies.
  • Find and cite the right references in Word and Google Docs.
  • Log-in, access and use your references & notes from any computer.
  • Set up a 'watch folder' to automatically import PDF references from your computer.
  • Securely annotate and discuss individual articles with collaborators.

Why use F1000Workspace?

  • Access your reference database from any computer
  • Shared reference lists make collaborating easy
  • Save references from the browser with the browser extension.

Using F1000Workspace - Getting Started

F1000Workspace is a web-based program available at no charge to Fred Hutch employees through Arnold Library's F1000Prime subscription. First time users must register a free account at

Refer to the following resources to get started working with F1000Workspace:

F1000Workspace Help & Training