Monthly Archives: November 2011

Managing Citations in Word Using Zotero

I am a LaTeX user. However, the unfortunate reality is that Microsoft Word is in very common use and if you’re collaborating with other people, one of your collaborators is going to insist on using Word. The EUSES group at Oregon State University has traditionally used Word on most of their projects.

BibDesk Screenshot


One thing that I like about LaTeX is that its citation management is quite good – it’s easy to add references, move them around, and have the Bibliography build properly. Right now, I use BibDesk for much of my reference management. It’s extremely lightweight, stores data in BibTeX format, and is quite portable across systems.

The Need to Keep Files

One of the limitations of BibDesk is that it doesn’t handle files very well. You have to often add them manually to each entry, and it doesn’t keep them organized nicely on the file system. One may wonder – why keep files at all? Can’t you just grab them from the ACM Digital Library when you need them?

Well, yes, but I like files. If I have them, I can work offline. I can use Spotlight (rather than Google) to look for files on my hard drive. I also need files so I can transfer them to my iPad and iPhone. There are also a number of references that simply aren’t on the digital library and have taken a bit of effort to acquire, so I’d rather not lose them.

This led me on a quest to find a slightly better reference management system.

Endnote? Mendeley? Papers?

There’s actually no lack of citation managers out there. Endnote is a relatively long-standing program that is known for providing citation management to Word. Papers is an award-winning paper management program for Mac OS X. Mendeley is a free cross-platform solution that can scan PDF files and automatically fill in a citation with data online.

Collaboration with Mendeley

Mendeley Desktop Screenshot

Mendeley Desktop. Notice how OMGHUGE it is.

My choice for about the past year was Mendeley. It is a closed-source program that has an online web presence and a sync server, meaning that once you put your papers into the software, it can display them for you on the web, or sync them onto a new computer. You can also share groups of citations with others – great when you’re surveying literature.

However, the program is big, slow, and uses tons of screen space. I’ve also been experiencing issues with it recently of it not quite finding the right information based on a search of the title. When it was given the paper’s title, it was often filling in the journal with “Society” or something ridiculous like that. It was also not recognizing conference papers as such, often leaving them as the default “Article”.

I began to search for something more robust.

Enter Zotero

I had actually heard of Zotero about the same time I acquired Mendeley (thanks Neil!), but I hadn’t ever bothered to figure it out. Then, I heard that there was a plugin to Microsoft Word that helped you manage references.


Zotero Panel

Zotero, Firefox Extension

Zotero is a free Firefox add-on. It lives and dies with the web browser, and by default is a little panel at the bottom of your browser window. It, like Mendeley and BibDesk, has the three-panel layout that is “Citation groups”, “Citation list” and “Citation details”.

However, I never really figured out Zotero until I learned about this button that doesn’t exist in the “proper” Zotero panel:

Zotero Add to Library Button

The Zotero Add to Library Button

The “Automatically Capture Bibliographic Information From The Web” button (it doesn’t have a name in the Zotero documentation) appears on pages like ACM Digital Library, IEEE Xplore, and Amazon, where information about references is displayed. When you click this button, it creates an entry for you and populates it with the correct information. Suddenly, I realised that this is a tool that I’ve wanted for a while, because where do I get most of my scientific articles from? I get them from the Web. So, rather than having to copy and paste the BibTex entry into BibDesk (annoying but doable) or downloading the PDF and dragging and dropping it into Mendeley (and then having Mendeley get the information with a 70% chance of it succeeding), I can just skip the process and import it all directly.

Microsoft Word Integration

In addition to being able to import references from the web, Zotero integrates with Word. You need to follow the instructions for installing it which includes downloading Zotero, a Python plugin, and the Word add-on. If you’re using the latest-and-greatest version of Firefox, you might have to also download the Mozilla Add-on Compatibility Reporter to force the Word extension to load (it turns itself off because it’s not certified with the latest version of Firefox, but I force-loaded it and so far don’t have any problems).

Zotero in Microsoft Word

Zotero in Microsoft Word. There is a toolbar as well as a "Script" menu item in Mac OS X.

When you restart Word, you’ll get a little toolbar as well as a script menu. The script menu contains items that are relatively self-explanatory. You can add citations, add the bibliography, edit the citations and bibliography, refresh the document if you change the database from Zotero, and set your preferences (i.e. your citation format).

One reason why I like this tool is that it’s very lightweight. You can send this version of the document to someone without Zotero, and as long as they don’t try editing all of the fields, they will see the references just fine. This enables you to collaborate with them without having to worry about getting the references out of format (which was something that happened a lot in EndNote X2).

However, Zotero also has cloud-based sync and group-sharing features like Mendeley does, so you can use those features as well to keep your computers in order, and to share citations with your collaborators.

Right now I’m pretty sold on this tool. It is cross-platform (though unfortunately tied to Firefox, but I hear there are Chrome and Safari alphas), syncs documents, imports data automatically, keeps files organized (it saves them in your Mozilla Profile unless you tell it otherwise), and integrates with Word. And, it costs no money. It even imports and exports BibTeX, meaning that I don’t have to give up or even migrate from BibDesk.

If you’re struggling with reference management then I think Zotero is something you might want to try. Happy citing!


Simplifying Your Life With Password Management

Not too long ago, I was able to memorize passwords. Like many people, I used a common set of passwords and had “tiers”.

There came a point when I suddenly stopped being able to memorize passwords. While I wish I could blame aggressive password policies, the reality is that there simply started to be too many to remember. It coincided about the same time that I signed onto Twitter, because around then I also signed up for services like Dropbox, WordPress, and continued to post on forums at ArsTechnica. It started to become a mess – I was resetting my Facebook password every time I visited the site (which is probably about twice a week) and every time I wanted to post a comment on Ars Technica. It was rather ridiculous.

In addition to managing passwords, I had to know them – I had an iPad (and now an iPhone) and if I need to check some online cloud-based service using one of them, I have to be able to access my passwords. I think the final straw was when I forgot my Mastercard Secure Code, had to reset it twice (I forgot the password as soon as I hung up the phone with the bank) and consequently ended up accidentally ordering four rice cookers from NewEgg. Fortunately they were willing to RMA them without a restocking fee, but it was a large hassle to even have to deal with that.

Buying into Password Manager Software

I eventually caved and bought into the Password Manager tools. I had heard about these here and there for a few years but had never really tried them. I caved and tried 1Password (they’re a Canadian company, actually).

I must say that the simplification that using a Password Manager affords is immense and is extremely reassuring. I now get to keep one main password in my head and I can make it as complicated as I want. In the meantime, the other ones are kept secured (and encrypted). I sync the accounts across Dropbox, and I can use both my iPad and iPhone to access them.

For those of you who don’t want to spend the money of 1Password (it’s about $50 but there are occasional promotions – I got an educational discount as well as an iSlayer coupon code; the iOS version is  $20) I’ve heard of free, open-source alternatives like KeePass. Though I haven’t used it myself, it works across multiple platforms including Windows, Linux, Mac OS X, iOS, and Android. It’s not really the specific software that counts, but the mere idea of using software to manage your hundreds of logins that reduces your cognitive load significantly.

Less Security? Maybe More?

One concern that you might have is that keeping one password instead of many is less secure than memorizing a few. This might be the case until you forget them. The problem with having to frequently recover passwords is then you’re simply using your email client as a very inefficient password manager – you’re asking the site to send you a password and then you’re using the email account’s password to keep track of things for you.

Just skip the middle man!

The alternative situation is that if you don’t know your online banking or credit card passwords, you have to call them and verify your information. This is inconvenient and time consuming, and can actually be a security risk for yourself because if you happen to be on the phone in a public place, someone might listen in on your call and catch a little too much information about you.

Manage Data, Not Just Passwords

In addition to managing passwords, 1Password also keeps data secure and encrypted too, which is a nice little benefit. I have started to put receipts and other data there, not because they’re so valuable that they need encryption, but because it’s a convenient place to look when you think, “Ah hah, I need to recover this important document.”

Browser Integration

One of the benefits of using a Password Manager is that it integrates with the major browsers through the use of Add-ons. Firefox, Chrome, Safari, and Internet Explorer have compatible extensions for 1Password. The system recognizes if you’re logging in or registering for web sites and automatically adds an entry for that web site.

Do you need to create a new password? The system has a password generation tool that you can use to create a password without the effort of having to come up with something.

While there are some limitations with the page login (it doesn’t automatically work on many financial web site logins because they are multi-stage), you can still check the passwords manually if you can’t remember them. Overall, the convenience outweighs the few situations where it does not work exactly as intended.


The 1Password tool also synchronizes using DropBox. Quite simply, it means that I can keep the same database across multiple computers and even on my mobile phone

Overall, I recommend the shift to Password Management Software. The simplicity that switching has afforded me has reduced my overall stress level immensely.

Using Technology To Simplify Your Life In Spite of Technology

Hi everyone!

For those of you who haven’t heard, I’ve graduated from the University of Victoria with a Ph.D and have moved on to Oregon State University doing a postdoctoral research position. I am currently working with Margaret Burnett. Her group is mostly a Human-Computer Interaction group with flavours of Software Engineering. She is especially focused on end-user programming, in which ordinary end users have to solve programming problems, like when they use Excel; as well as human interactions with machine learning systems.

There are many interesting things going on at OSU. I think it’s partly because it’s a new place, but also because as a postdoc, I have a number of additional commitments I didn’t have as a student. I’ve participated in grant proposal writing, paper writing, and similar duties, and as the postdoc in the group, I am involved across a larger number of projects than as a Ph.D student. This means that I have more things to keep track of, more meetings to go to, and more people to interact with.

While in the United States, I took the plunge and bought an iPhone 4S. This adds another level of complexity: a smartphone requires data for it to be useful, and now I have yet another device in which I have to manage data on. The iPhone is useful as a way to check my calendars, my To-Do lists, and to read papers on, but it requires a new level of organization to ensure that it can serve these purposes.

As a result of this rather increased level of complication in my life I am going to write about Using Technology To Simplify Your Life In Spite of Technology. Why the funny title? Well, technology has the ability to help you, especially through automation, but at the same time it requires time. You need to commit to keeping the devices updated and working, and you need to ensure that they’re going to be serving you.

I’m hoping that these upcoming articles will help some people gain ideas about how they can synchronize, share, and acquire knowledge, and maybe stay organized in the process. I’m sure that many of you readers are familiar with many of the tools and techniques I’ll discuss (since, after all, you might have told me about some of this stuff in the first place) but I hope that hearing about how these services are integrated together might help others out there.