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Organize Your Research With The New Standalone Zotero

Yaara Lancet 09-08-2011

organize your researchEveryone in the world of research, and many people outside of it, knows that a good citation manager and PDF organizer 3 PDF Document Management Tools for Organizing Your Research The web has seen its fair share of research-friendly tools grow over the past years. Let's discuss some tools that help you keep your PDF article library neat and catalogued for use when you have... Read More is a must if you want to keep track of all the papers you’ve read and accumulated. For the past two years, I’ve been using Zotero to organize my research for articles. Zotero is a Firefox add-on in which you can save citations and links to PDFs and access them at any time.


One of Zotero’s biggest cons is that it works only within Firefox. This means you have to be running Firefox and use it to save the articles you find. As long as I was using Firefox, this was not a big issue, but when I switched to Chrome for a while, it became quite cumbersome. Not to speak of the fact that I had to load Firefox every time I wanted to look at my database (which can be a lengthy process at times).

This is why I was delighted to find out that Zotero have come up with Standalone Zotero Alpha (Windows, Mac and Linux) and with Chrome and Safari connectors for it. Note that this project is still in alpha, so it is not perfect by any means. These new versions came out in February, so hopefully we’ll see some updates soon. Now let’s see what it can do to organize your research.

Standalone Zotero

In order to get Standalone Zotero you’d need to head over to the project’s website and download the version of your choice. If you want to connect it to Chrome or Safari, download the relevant connector as well.

organize your research information

After installing, if you’ve used Zotero before, clicking “Yes” will synchronize your Zotero library into the new version, and you’ll have all your articles available immediately.


For those of you who’ve been using Zotero in Firefox, the standalone version will look very familiar. It is pretty much the same thing we’ve been using in Firefox, but it stands for itself. It’s so similar in fact, that it was hard to find the differences. But one big thing is apparent – I don’t have to run Firefox anymore to use Zotero. Hurray!

organize your research information

Browser Integration

But Zotero is not much good if I can’t look for articles in my browser and add them to Zotero from there. I’m disappointed to say that this part of the new project is still in its infancy and is not working very smoothly, but I’m sure things will only get better from the alpha version. So what works and what doesn’t?

I first tried the Chrome connector. This is just another Chrome add-on which you can download from the Zotero homepage.


organize your research information

Differently from the Firefox version, which allowed me to save citations directly from Google Scholar search, in Chrome I had to click individual links and could save them only from there. When I click these links, I got an icon on the right side of my address bar which I could click to save the article in Zotero.

organize research notes

Even this didn’t work all the time, as I kept getting this error:


organize research notes

Even though I got this error every time I saved an item, some of the items did actually get saved, and I could see them and access them from Zotero. This might be a translator issue and will hopefully be fixed soon.This error kept jumping up regardless of whether I was actually trying to save something or not, which soon become quite annoying. If you want to read more about the developments of the Chrome connector, you can look at the Zotero forum.

In Firefox, things became a bit funny. First of all, you cannot run Standlone Zotero and the Firefox Zotero simultaneously. You need to choose, one or the other.

organize research notes


But surprisingly, after disabling the Firefox version and trying to use only the standalone version, I didn’t get the save icons in Firefox at all. When I closed the standalone version and enabled the Firefox version again, everything worked fine. The conclusion – if you’re using Firefox, you might do well sticking to the good old Firefox Zotero for now.

MS Word Integration

One of the most useful features in Zotero is the MS Word integration. I used this to enter citations and created a bibliography for my whole thesis, and I don’t know what I would have done without it. Standalone Zotero comes with the MS Word integration already built in. Previously, you had to load Firefox for the sole purpose of using the Word integration. Not anymore!

organize your research

The add-on itself seems to be unchanged, meaning you can still enter citations, create bibliographies, edit them, etc.

Bottom Line

I was very excited to try this new version of Zotero. This alpha version sure feels like alpha, especially in Chrome, and if you’re new to the business of PDF organizers and you’re not using Firefox, you might want to search elsewhere for now.

But if, like me, you already have everything in Zotero and enjoy using it, this new version is a sparkle of new hope, which already provides some very much needed improvements. I can’t wait to see future versions and to have the Chrome integration working better.

What do you think of the new Zotero? Think it’s worth a spin to organize your research? Tell us in the comments.

Related topics: Organization Software, Study Tips.

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  1. Guest
    August 11, 2011 at 11:10 am

    Another of Zotero's major drawbacks is that it is impossible to delete your account if you so choose. Especially if someone is working on a sensitive project (not talking Wikileaks or anything of the sort!), s/he might want to remove all data from their servers (or in any case if someone may have compromised your login information)! 

    Also, if you just find you don't use the account anymore there's no method of cancelling. IMHO that's just not good business practice to keep user data on file despite requests to be removed. This is a topic of frequent discussion on their message boards; I myself tried it, found the extension buggy and unreliable, and promptly uninstalled the Word and OpenOffice plugins as well as the Firefox extension. The few documents I was able to upload/link to, I deleted (after a backup, of course).Myself, I'm a bit old fashioned, but I find a good solid three-ring binder (or more than one), to be much more reliable and trustworthy than these cloud services just yet, even if they are bulky and awkward and pinch your fingers from time to time. Gone are the days when "collaboration" meant a study buddy at the library or coffee house after hours. It concerns me that services like Zotero (and the Internet in general) seem to operate on a Vegas-like business model of "what happens here, stays here." (More like a Vegas tattoo parlor if you ask me!) ^_^

    • Tina
      August 11, 2011 at 10:28 pm

      Dear Guest,

      you are losing out by not providing a proper email address when commenting on MakeUseOf. And I don't mean on spam. ;) I have noticed your comments and that's all I will say.

      • Shy Commenter nee Guest
        August 20, 2011 at 3:24 am

        Hi Tina,

        I hope you don't think I'm spamming :) I really like MUO but am quite a bit paranoid, if paradoxically so (otherwise I would be a passive observer rather than a commenter). I don't mind healthy discourse but operate more on the "confessional booth" style of social networking, where neither the Internet (nor the priest) knows you're a dog.

        If you must know, though, I am actually a duckbill platypus. ;-)

    • Yaara
      August 12, 2011 at 7:54 am

      I totally agree about cancelling the account. There should be a way. As for binders, I see the pros in using them, I just can't imagine printing out each and every article. :)

  2. Roni Tibon
    August 11, 2011 at 7:36 am

    As a standalone version, I like Mendeley much better. I with those Zotero dudes will stop being lazy though, and will develop a decent Chrome version.. 

    • Yaara
      August 12, 2011 at 7:51 am

      I never used Mendeley, but I heard it's good. After I started with Zotero it just seemed like such a hassle to start using something else.. maybe I should try it sometime, though. A fresh start.

  3. Anonymous
    August 10, 2011 at 5:42 am

    Being a firefox user, I have to stay away from Zotero Standalone as yet. But I would like them to trim down current firefox addon to a 'Firefox-Connector' only. If that happens, one would independently start and exit zotero standlone as needed. In its current form, zotero addon is a major cause of firefox sluggishness, particularly when its library gets larger.

  4. J. Simon van der Walt
    August 10, 2011 at 5:32 am

    That's a really useful article, thanks. I use Zotero and recommend it to my students, didn't know about the standalone version though…

    • Yaara
      August 10, 2011 at 6:40 am

      I wouldn't recommend it to all of them just yet (some people are uncomfortable with unstable versions), but it's definitely a step in the right direction.
      And if you have some computer savvy students, I'm sure they'd be happy to give it a spin!

  5. Mike
    August 10, 2011 at 1:54 am

    Besides Evernote I'm been using  Memonic in Chrome & it works nice & is fast & easy.

    • Yaara
      August 10, 2011 at 6:38 am

      Memonic looks interesting! Thanks for sharing!

  6. Anonymous
    August 10, 2011 at 12:13 am

    cool love it