Reference Managers

Occasionally I write about or share links to articles about interesting technology that is useful to me or my patients. This post is the first in a series I plan to write addressing common technology-related issues that arise while writing research papers. If you are starting your dissertation, thesis, or other large research paper, there are three thing I think you absolutely must do.

  1. Develop a robust backup routine, and then make it even more redundant.
  2. Learn how to use the styles feature in your preferred word processor.
  3. Start using a reference or citation manager.

Today I want to talk briefly about the third item in the list, using a reference or citation manager. Citation managers are applications that allow you to store and retrieve the sources you cite in your paper and to easily create your reference list or bibliography.

There are a number of different reasons that someone would benefit from using a citation manager . One of the key benefit of using a well-designed reference manager is that it does all the hard work of correctly formatting in-text citations and your list of references using the writing style you’ve selected. When a small change needs to be made (for example, you’ve misspelled the first author’s name throughout the text), the software quickly propagates the change through your document. Or, say you delete all the in-text references from a particular source, the software will remove it from your bibliography for you. Also, say you prefer to write using APA style, but the publication you are submitting to wants MLA, or numbered footnotes, you just select the new style and all your citations are automatically updated to the correct format. Manually making these changes in a 20 page document is hard enough. Now imagine that you are editing your 150 page dissertation. You can see how automating the process would be helpful in reducing time spent checking each citation over and over again. Spending a little time learning how to use your reference manager before you start will save you enormous amounts of time and frustration as your defense approaches.

Another major benefit is that by regularly using a citation manager as you conduct your research, you are better able to organize your sources, you may be able to find other sources that relate to your research topic topic , and you can build a personal library of journal articles, and other references that you can refer back to or share with colleagues .

There are a number of different options when it comes to citation managers, some word processors actually include the feature within their standard feature set. For example, Microsoft’s Word offers a citation source manager that many people find adequate. During my undergraduate program, I tried several different open source offerings, including BibTeX. When I was in graduate school, the current version of Endnote was included in our tuition, and so I used it to write my papers for class, my thesis, and ultimately my dissertation.

I can’t possible discuss every option in a single post, I can’t even remember all the different applications, plugins, and workarounds I’ve tried over the years, fortunately, Wikipedia offers an overview of all of the different options . The important thing is to find one that works for you and your writing workflow, and then to use it consistently.


After finishing graduate school, I started working in a clinical rather than an academic setting. With this significantly reduced budget for research-related costs (read, no budget), I once again looked to open source solutions. One of the options I reviewed was Zotero, an extension for the Firefox browser. I had looked at Zotero years ago, but it wasn’t a robust enough solution at the time and lacked a number of features that I needed. Fortunately, Zotero has matured as a product and has become my citation manager of choice.

Zotero is currently available as an extension for Firefox on mac OS, Windows, or Linux, or as a standalone application for macOS or Windows. The defining feature of Zotero is that you have a browser extension that allows you to clip whatever source you’re looking at to your citation library–even if Firefox isn’t your primary browser.

Zotero is simple to use, and because it is web-based, you have access to your sources anywhere in the world. Additionally, Zotero includes an important add on feature that allows you to “cite while you write” for some (but not all) word processors. When used with Word, for example, a new tab is added to the ribbon interface that lets you easily insert or edit a citation.

There are also a number of plugins and add-ones for Zotero which can greatly enhance its benefit–including a LaTeX plugin for my math friends. The basic Zotero service is free and provides 300 MB of online storage space for any attached files (your actual library data does not count toward your quota), such as PDFs of journal articles. You can upgrade to 2 GB for $20 a year, 6 GB for $60 a year, or Unlimited for $120 a year if you need the extra space.


One of the selling points for Zotero for me was a WordPress plugin call Zotpress that allows me to use my Zotero reference library on my website just like I do when writing a paper in Word. The tool resides in the sidebar and creates a shortcode for in text citations and one for the reference list at the end of the document. These short codes can be used on any post or page, if your theme supports shortcodes. The short code for the reference list at the end of this post looks like this in the editor:

And when rendered by the browser, it appears as you see it below. Any changes I make to citations in the body of the text are automatically added and formatted when the page is rendered. Zotpress is not perfect, you may have noticed that some of my references don’t look quite right, but it is getting better.


phpZoteroWebDAV 2.0

The final Zotero tool I use is phpZoteroWebDAV 2.0 which is a script that creates a simple WebDAV server to sync your library file attachments. Since the free Zotero account only allows 300 MB of attachment storage, and many of us have plenty of space on our own webservers, this allows you to set Zotero to sync your citation metadata (the really important part) to your account with them, while the attachments are synced to your own server space. In addition to creating a space to store the attachments, phpZoteroWebDAV 2.0 also creates a basic HTML interface for your entire Zotero database, so even if you don’t have access to Zotero, you can still browse, find, and download sources that you may need.

One note, when I insalled phpZoteroWebDAV 2.0 on my web server, I ran into an error and the solution was difficult to find. Apparently, WordPress running on an Apache server has a bug (feature?) that when a directory is password protected, instead of asking for the login and password, WordPress throws an error and you end up at a 401, 403, or 404 error page.

The solution was really quite simple to implement, but took a while to find. See the original post here.

Editing the WordPress .htaccess is Simple Solution

The first thing you need to do is locate your WordPress directory. This is often either your www directory or public_html directory. Locate your .htaccess file and open it using any text editor. If you do not see this file you can simply create one using any text editor (such as Notepad on Windows).

Update the .htaccess file before the WordPress information and add the following two lines of code:

ErrorDocument 401 ./error.html
ErrorDocument 403 ./error.html

The finished .htaccess should look like:

ErrorDocument 401 ./error.html
ErrorDocument 403 ./error.html
# BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L] # END WordPress


Make sure your FTP program is set to upload as ASCII. Upload the .htaccess file to your home directory (often public_html or www). You can also upload an error.html to the root directory.

Attempt to access a directory that is password protected will now give you the popup box you were expecting in the first place, so you can enter your login credentials and gain access as normal.

We also learned how to process 401 and 403 errors in the process using Apache’s ErrorDocument directive using .htaccess in the process.

While I’m partial to Zotero, there are other great options. The important thing is to try a few different applications and find what works best for your workflow. Think about how you conduct your research, your writing process, and think about what your future needs might be. Have a favorite already? Share it in the comments below.




Cite this article as:
Robert Allred, "Reference Managers," in Robert P. Allred, PhD, March 23, 2017,


APA 6th:
Allred, R.P. (March 23, 2017). Reference Managers [Weblog post]. Robert P. Allred, PhD. Retrieved June 24, 2017 from

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