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Reference Software for Scholarly Articles and Grant Applications

Release Date: January 05, 2015
Category: Scientific Writing Software
Author: Michelle S., Ph.D., E.L.S.

Proper citation of the literature is a critical component of scientific research with practical, intellectual, and ethical challenges. If you are publishing articles and writing grant applications on a regular basis, then you most likely have a body of relevant literature that you need to cite in order to properly justify your work and integrate your findings with the existing body of knowledge. Reference management software can be vastly beneficial toward solving the practical issues surrounding this task. By keeping your citations live and automatically updated while you write your document, this type of software saves you valuable time. If you have your documents professionally edited, this software will save your editor time and, as a result, save you money. If you aren’t yet using reference managing software to assist you, this article will provide some basic information on some options, both paid and freeware, that are available and how to get started using them.

Paid Software


The most popular and widely-used reference management software is EndNote. EndNote is commercially available and considered the industry standard in reference software. The current version of the software is X7 (or 17). Owned and sold by Thomson Reuters, EndNote allows you to build and store a library of references by accessing many different databases, including PubMed, National Library of Medicine, EBSCO-host, and the library catalogs of a large number of universities. EndNote integrates with Microsoft Word such that you can insert citations directly into the text of your manuscript or grant application while you are writing. When a new citation is added to the text, EndNote updates a reference list that is automatically generated at the end of the document. The style of this reference list depends upon your choice (for example: alphabetical vs. order of appearance in the text). EndNote is capable of nearly infinite output styles. Several preset styles are loaded with the program, which also allows you to create your own style according to whatever requirements you have. However, most journals offer output styles, downloadable from their websites, which may be opened and saved in EndNote. This option ensures that your references will be formatted exactly as required by your target journal. Finally, EndNote enables you to share libraries and references between colleagues and collaborators, incorporating social media functionality in the newest version.

EndNote is compatible with Windows and Macintosh. If you are using a Macintosh computer with the Pages word processor, know that EndNote is compatible with Pages, but some functions are not fully supported like they are for Microsoft Word (or Word for Mac). A mobile, iOS-compatible version of EndNote is available within the Apple App Store. The product website has tremendous amount of documentation, tutorials, and videos to help you learn to use the software. The company offers a 30-day free trial. The software is $249.95 for a licensed copy that may be installed on up to three computers. A discounted student version is also available. The software can be purchased in hard copy or as a digital version downloadable from the website.

Papers 3

A second, paid option for reference management software is called Papers. This software was designed by Apple and, while compatible with both Windows and Macintosh versions of Microsoft Office, Papers is designed to work seamlessly with Pages. The current version of Papers is Papers 3 for Mac. Papers 3 can perform all the functions described above for EndNote, including sharing libraries with colleagues using Papers Online. Papers 3 differs from EndNote in one major way. In addition to storing and organizing citations, Papers stores the full-text content of the paper, providing the user with a format to read literature within the software. In this way, Papers 3 offers the citation functionality of EndNote and reading and annotation functionalities of Adobe Reader. Papers 3 is also designed to sync across all Macintosh devices, including iPhone and iPad. If you have the mobile app as well, you can access your Papers library, including full text, from any device.

Papers 3 is available for download from the product website for $79. Like EndNote, this purchase can be installed on three computers. The mobile app is considered a separate purchase, but that single mobile purchase works on both iPhone and iPad. If you are using a Windows computer, be sure to purchase Papers 3 for Windows, which is much-improved from the original Windows version of the software, and has received good reviews of compatibility.

Free Software

If purchasing reference software is not within your budget, there are a number of quality freeware options that provide stiff competition to EndNote and Papers 3 with regards to their functionality and capabilities. This article will summarize the features of two freeware options: Zotero and Mendeley.


Zotero originally began as a widget for the Firefox web browser that could be installed within Firefox and used through the Firefox user interface. Zotero is now stand-alone software with more powerful functions and capability, but it is still free for download from the company’s website. Zotero is available for Windows and Macintosh. Zotero is able to collect, organize, cite, and share research sources and can be integrated with Microsoft Word as an add-in, much like EndNote and Papers. Your library is stored in a cloud-like format, thus it is accessible from any computer; however, the amount of space available for free is limited to 300 MB. Additional space (up to unlimited) can be purchased at a per-year cost. In addition to adding PDFs, you can also save and share images, audio and video files, snapshots of web pages. Zotero indexes the full text of your files, so you can search for a reference using text from the document if that is the only keyword you have. Zotero requires that you create an account on the website in order to create the space on the server for your information.


Mendeley is a free reference manager and academic social network. Mendeley functions much like the other software described here, but one major strength of Mendeley is its focus on being interactive with the academic community. Mendeley allows you to create team plans and private groups. Thus, by working in groups, you can search the libraries that colleagues and collaborators have shared with you and vice versa. Mendeley is available for Windows and Macintosh. Once you have downloaded the software and created a Mendeley account on the website, you can merge your Mendeley account with your Facebook account to increase your Mendeley network using your contacts from Facebook. Like Papers, Mendeley offers the citation functions of EndNote, allowing you to cite as you write, and reader functions like those of Adobe Reader that allow you to read and annotate your PDFs on any device.


All four of the reference managers that have been described here have an export function. This function allows you to create a library file that is readable by other reference managers, making it easier to share your library with a person who uses a difference reference manager. Additionally, if you start using a freeware like Mendeley or Zotero and you decide to purchase EndNote or Papers, the export function allows you to take your library to the new software so that you aren’t starting over from scratch.

If you wish to explore these or additional reference software options, Wikipedia has compiled a very thorough list of reference software options. Using several tables, this page compares the availability of select features within each software option. The site also addresses compatibility with different operating platforms more comprehensively than does this article, which only addresses Windows and OSX compatibility. The comparison site can be reached by clicking here.

Happy citing!

Scientific Writing Workshops

If you like our articles, try our workshops! Our articles are based on the material from our scientific writing workshops, which cover these and many other topics more thoroughly, with more examples and discussion.

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