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Zotero is free bibliographic software that allows you to easily collect, annotate, and cite bibliographic data. It runs as a plugin for the excellent Firefox browser, which means that you have the web at your fingertips as kyou manage information, and also that it can run on any operating system that Firefox can run on (that is, all of them). It is also open-source, which means that anyone can improve it and develop for it. It is a great alternative to more expensive software, and also has a number of advantages over its more wealthy brethren.

This is a guide to using Zotero effectively in biblical studies, though using Zotero effectively in biblical studies is usually similar to using Zotero effectively in other fields. I will add a couple of remarks along the way, however, especially for those of us in theological fields.

Step 1: Installing Zotero

Your first step in using Zotero is getting everything installed. If you are not already running Firefox (an excellent open-source web-browser), then shame on you. Install that by following the easy steps here.

Installing Zotero

Open up Firefox and browse to the Zotero site (here). Click on “try out 2.0 beta.” It might seem at first that 1.0 is the better option, but there are SO many new features with 2.0 that it’s really the way to go. I use Zotero daily and have had no major issues with 2.0. The rest of the guide will assume that you are running that version.

Once you click, Firefox will do the rest—download, install, and ask you to restart. Restart Firfox and you are ready to go.

The Zotero website is also a great place for guides and videos, so browse around a bit.

Step 2: Move Your Zotero Directory

The VERY FIRST thing you need to do with your new Zotero setup is change the location where it stores all its data. By default Zotero puts all the information you want it to remember in the same place where all your Firefox settings are stored. This is terrible. It’s like storing your valuables in something that looks exactly like a trash can—someone will eventually forget it’s not a trashcan and throw it away. You’ll either upgrade Firefox, or Windows, or something, and then it will be gone (and backup software may not know to back up this directory). So let’s move it. (Note: if you already have data in your Zotero directory, back it up first using Zotero’s export command. When you move your directory in Zotero it will seem like your data is gone, but it isn’t. It’s still in the old directory. Either move it manually or import the data you just exported).

Create a New Folder. Open up your file browser and go to a directory where you keep important data. Something like “My Documents” in Windows—you know, where you save documents. Hopefully it is also a directory that gets backed-up by your backup software. In that directory create a new (empty) directory called “Zotero.” (For an always-on backup solution that super-secures your data, you may want to put Zotero in a Dropbox directory; see “Securing Zotero” below).

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data directory

Tell Zotero what to do. Now in Firefox you will now notice an icon in the bottom right corner that says “Zotero” (labeled “1″ in the picture to the right). Click on that to get your Zotero window up. Then look for a gear icon (“2″ in the picture), which you should click, and select “Preferences.” We’re going straight to the “advanced” tab (“1″ in the second picture), then clicking the “Custom” option (2), and then clicking “choose” (3). Select the directory you created and click ”

Step 3: Get Some Data

Alrighty, now that we know our data isn’t going anywhere, let’s get some actual data. You can add books and articles and what not manually, but that is SO 2008. One of the great things about Zotero is that it sits in your web browser, so you can use the web to get data for you. A number of popular sites (Amazon, Google books, etc) support Zotero data. Chances are your school library does as well. Let’s start with Amazon, though. Go here. Now look at the address bar. There should be a little folder icon there. If you click on that, it will bring up all the books on the current page, from which you can select which to add to Zotero. Now go here. Just one book this time, and the Zotero icon in the address bar is now a book. Click on it and it will add the bibliographic data to your database.

A lot of blogs also support Zotero, including this one. See the icon in the address bar when you go to nerdlets.org? That means you can add blog entries straight into your Zotero database.

zotero bar

Play around for a bit. Try Google books. Or the library of congress. Or your favorite library site. Also notice the various icons in the middle section of your Zotero interface. These all allow you to add a variety of things to Zotero, from webpage snapshots, to manual data for books that are not on your preferred website, to files on your computer.

Step 4: Using Zotero with your Word Processor

Install Word Processor Plugins. Now that you have some data you probably want to use it. Zotero has a number of plugins that integrate with your favorite word processor. You can find out more about those here, and the install page is here. Make sure you scroll down for the 2.0 plugins; the 1.0 plugins will not work. The plugins install just like Zotero itself, as browser add-ins. The plugins update automatically, and automatically install all the needed files into your word-processor. Easy. There is one for Microsoft Word (here) and for OpenOffice (here).

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Format your citations in the correct style. Now Zotero will work with your word processor, adding data into footnotes as needed, and all in the proper format. Speaking of proper format, you may want to add bibliographic styles not included by default. For theology or church history you’ll probably want to use what Zotero calls “Chicago Manual of Style (Full Note with Bibliography),” which is included by default. For biblical studies you’ll probably want the SBL style, which is not installed by default, but fear not! Because Zotero is open source anyone can create their own style, and a number of users have done just that. Most likely your preferred style is out there somewhere. Let’s install the SBL Style as an example. Go to Zotero preferences and click on the “Styles” tab. Then click on “Get additional styles…” This will take you to a webpage with a whole list of styles; just click “install” to add it to Zotero. The SBL style guide is in that list, or you can install that by clicking here.

Back in the preferences dialog click on the “Export” tab. Select the style you prefer in the “Default Output Format” box.

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Cite, my friend, cite! Now open up your favorite word processor. I’m using OpenOffice, but the process is the same for Word. You should notice a new toolbar. If you don’t see it, go to “View” and “Toolbars” and look for one that says Zotero. Once you find it, hover over each button to see what they do.

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Let’s assume you want to add a citation that is SBL compliant. Create a footnote. Now add a citation (“1″ in the picture). If this is the first Zotero citation you have added a window will pop up asking about how you want to format this document. Make sure SBL is selected and click OK. You will notice that a field has been added to your footnote (2), and a new dialog window has popped up (3). Now search for a citation you want to add, either by browsing through folders or by using the search dialog (4). Select your citation (5), and add page numbers (6). You can also choose “Multiple Citations” if necessary (7). When you’re done click OK (8).

Once you are done with your document you can automatically generate a bibliography (3rd button). You can edit citations with the second button. Have fun!

Step 5: Helpful Hints and Best Practices

Zotero is pretty powerful software, but you have probably already encountered some problems. Here are a few tips on how to use Zotero effectively.

  1. Use folders sparingly, use tags generously. Folders are a great way of organizing information, provided you don’t have too many and the hierarchy doesn’t go too deep. I create folders for each major topic that I am studying. Every paper I write or class I teach gets a folder. This allows me to have a kind of record of research. But if you get to specific this can get unwieldy. Instead, use tags for the specifics. Tags are search-able and non-hierarchical. You can add as many as you want and it won’t junk up your database.
  2. Every paper your write gets its own folder. Again, this allows you to retain a record of research. Anything you cite in a paper goes in that folder.
  3. Stick to a standardized naming scheme for authors and publishers. One of the major problems with Zotero is that it does not store author and publisher names in a hierarchy. So if you add Calvin’s Institutes under “Calvin, J.” and then later one of his commentaries under “Calvin, John,” Zotero will think it is two different authors, which will mess up your bibliography. Rather than making lots of piddly changes down the road, stick to a standardized naming scheme now. Make it work with whatever bibliographic style you are using. For authors I stick to last name and 1-2 initials. For publishers I always exclude the words “Publishing” or “Press” unless its a university (“Oxford University Press”). If the book contains a number of articles, I always have a separate entry for the book as a whole, then “copies” of that entry for various articles. Find a system that works for you and stick with it.
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  5. Always type out quotes you want to use in Zotero first, then copy and paste into your article. I like to do research “on the fly”; that is, I like to research as I write, and write as I research. This means that my papers are always in process. It also could mean that my research is less easily reusable. In order to find that quote I need to find that paper in which I typed it out. To avoid this, type out all quotes as notes in Zotero. Right click on the book from which the quote is taken and select “Add note.” On the top line type two or so words that identify the topic of the quotes (think: “how will I search for this in two years”) and the page number. Then type out the quote (Zotero has a handy “quote” style), then any comments you might have. Notes like this will always be associated with their respective books, no matter where you drag and drop that book, and notes can be tagged like anything else.

Step 7: Syncing Zotero

The latest version of Zotero allows you to sync multiple databases, and also sync online. To set that up, follow the directions here. That will allow you to sync your data. To sync files—like all those PDFs you have saved—things get more complicated, but all is explained in the aforementioned link.

Please remember, though, that SYNC does not mean BACKUP. Sync means that everything you do is synced between multiple computers. If you do something idiotic, your idiocy will then be replicated 10 fold. A mirror doesn’t make your face any less dirty. You still need a backup, so keep reading.

Step 8: Securing your Life’s Work

I now use Zotero as my bibliographic database, as a document library for all my PDFs, as a web bookmarking database, a recipe book, an interview manager, and a job-search tool. If it fails, I’m sunk. You need to back up your Zotero database. How do you do that?

Zotero is just a collection of files. Place your Zotero directory somewhere that gets backed up every day, like your My Documents folder (see above for how to do this). Better yet, use Dropbox. Dropbox is an application that you can install that creates a folder, and then automatically backs-up and syncs any data you put into it. Dropbox is free, works on any OS, and provides you with 2gb of storage. You can install it by going here. Once you have your dropbox folder up and running, move your Zotero folder into it.

You should also have a local backup. That is, every night your computer should back up all important data onto a separate hard disk. By an external harddrive (newegg.com) and backup your data to it daily (using something like the free version of syncback.

Conclusion

When your research is searchable, re-usable, and secure, life is good.

 

Funambol Logo

It’s amazing how much your productivity increases when you have all the information for all your contacts on all your devices.

There is literally only one service that provides this functionality. And its free.

Try funambol.

There’s an iPhone app. Which syncs with Outlook. Or your smartphone. Or your Blackberry. And with some modern mobile phones.

And, of course, with Thunderbird.

No guide here; your on your own (Sorry—time constraints, but Google is your friend). I just wanted everyone to know that this is out there, and that chances are, it will help.

 

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The best kind of multitasking system is the one available to you anytime and anywhere. In today’s electronic world, that often requires having access to your files. What articles do you need to read? Or maybe you have some sermons or lectures you’d like to listen to? Regardless of your specific needs, if for whatever reason you want access to certain files (documents, music, etc.) on the go, there are several options available to iPhone owners.

Drop.io

The excellent and free web service drop.io is frequently mentioned on this blog. It is an easy way to securely share larger files with friends and colleges. But it can also be an excellent capture tool for storing ideas and tasks (read my guide to that here).

Either way, drop.io is now available on the iPhone, which means its usefulness has dramatically increased (for those lucky enough to have an iPhone, which I am not). You can find the app on the iTunes store here.

ZumoDrive

ZumoDrive allows you to access on online storage drive just like you would a hard-drive on your computer. It’s fast and it doesn’t take up any space on your computer or on your iPhone, which means you can keep a whole lot of information there without worrying about filling up your iPhone’s hard-drive. ZumoDrive gives you 1gb for free, and charges $2.99/month for 10gb. For a full review, check out this article.

Soonr

Another web-based storage service, Soonr, allows you to view and edit your documents online. Check out the details here.

Conclusion

All in all there are a lot of options available to those who need access to important files on-the-go. Of course, the options listed here are only available to those with an iPhone. In the interest of full disclosure, I don’t have one, and so cannot comment on these based on personal experience. Perhaps the fabled Google Drive will bring mobile cloud storage to the rest of us, and there is always Dropbox (any OS) or Microsoft for (Windows only) if you usually have a notebook or netbook on your person. Regardless, this is the future of multitask computing, so if there is an option available to you, consider setting it up now! You won’t regret it!

 

Well, I’m back after the holidays. Quess what happened on my New Years?

For reasons that boggle the mind, I decided to type in the Linux equivalent of “format c:/”. Seriously. The result? My entire Windows partition is irrevocably gone.

Not a problem. I back up my data. Everything iimportant is safe, and all my dissertation research is secure, largely because of an excellent backup utility called Dropbox. I put all my important files into my dropbox and they are automatically synced accross multiple computers, and online. So after a little drag-and-drop, I’m back to work.

Back up Zotero

As many of you know I am a big advocate of Zotero for research and bibliographic management. It is worth noting that by default Zotero puts all required files in your Firefox folder, which is generally not backed up by most software. You can always add it to your Dropbox, but a better idea is to change your settings. Go into Zotero’s Preferences dialog and the Advanced Settings to set a new location for Zotero files. Put it in your My Documents folder under a subfolder called “Zotero.” Almost all backup software will backup you My Documents folder by default, so this is the safest place.

One Dropbox Limitation

One thing to be noted: Dropbox is not true backup software. True backup software archives your files on a periodic basis. Dropbox does something a little different; it mirrors you files. Any changes you make on your computer are automatically changed in your dropbox. If you overwrite or delete a file, it will be overwritten or deleted in dropbox.

This might be a problem, except Dropbox saves all revisions, so if you do something stupid, and then your stupidity is mirrored by Dropbox, you can “undo” your changes by going to the Web interface and clicking “Restore my files.” That’s what I had to do, and it worked flawlessly and quickly.

Thanks Dropbox!

Make a New Year’s Resolution

I have two suggestions for nerdy New Year’s resolutions: (1) Backup your data, (2) Use Super-User priveledges responsibly.

 

Ok, so here is a list of Microsoft provided online storage/sync solutions, all of which are free. Windows Live Mesh offers an alternative to Dropbox if you need more than 5 gb of storage space and don’t need Mac/Linux support. These are all good options.

 

It’s a good idea to have an online backup of your important files, provided the service that provides the online space is reliable and secure. There are many such services (I have previously recommended Dropbox and Mozy). Those who need lots of space (for pictures, for example, or to have your music available anywhere you go) might be interested in Livedrive, which unlike all other services allows you an unlimited amount of space. Check out Lifehacker’s take on the subject here.

The only problem at this point is lack of information. I have not been able to determine how my files are secured and protected, among other things, and I would also be interested to know how the service plans to make money (particularly since you have to give them your address and phone number to sign up). But still, unlimited space is pretty awesome, so if you have some large files that you want to store or share online, Livedrive might be worth a try. Just don’t rely on it as your only backup (at least not yet) or use it to store private information.

Update: After further poking and prodding it appears that Livedrive will not be free past the initial Beta period. I guess this proves the old addage: if it sounds to good to be true… Sorry for the hasty post, I should have done more research before publishing this.

 

One of the real difficulties with Windows (at least versions prior to Vista) is the reinstall problem. After about 2 years or so your computer starts getting too slugish to be productive, and no amount of tweaking, defragmenting, or otherwise coaxing your computer to behave normally seems to help. Or perhaps something else has gone wrong. The bottom line: you need/want to start afresh, but are worried that you might loose something important in the process.

A Great Guide

Well, you’re right to be worried. Installing Windows is not a problem-free procedure. But there are steps you can take to make things easier and safer. Follow this guide for maximum security and minimum headache.

How to Backup your files (which you should be doing anyway)

One thing the guide does not mention (because it assumes you know to do this) is backing up your documents. You should already have a backup of your important files (Pictures, Music, Movies, regular documents, and program files such as your emails or Zotero database, etc.), so hopefully this step is pretty easy—just make sure that this backup is in a location that is not about to be erased when you reinstall Windows (the reinstallation will wipe your c:/ drive).

If you don’t already have a backup of these files, shame on you. You should. Really you should have 2 backup sets: one on an external hard drive, and one remote (that is, in an encrypted server somewhere far far away). As far as the remote backup set is concerned, Mozy Home and Carbonite are both great unlimited-space automated-backup solutions ($5 /month). Windows SkyDrive gives you 25 gb of free space (though you have to manage your files manually). And Dropbox provides 2 gb of free space and has a lot of great features like syncing across multiple computers.

 

The following is a set of links that will be useful for those trying to set up Zotero on their computers. (Not sure what Zotero is or why you would want it? Check out their site, and don’t miss the demo video).

Initial Setup

  1. Firefox Web Browser. Zotero runs as a plugin within this excellent browser.
  2. The Zotero Plugin. There are two options here. Pick one of the following:
    • Zotero 2.0 Beta (recommended). This is the latest release. It is Beta software, which means you may experience bugs. But I have been using this release for sometime and have not experienced any problems. There are several advantages of this release: online syncing (though see below), rich-text editor, more functionality. Create an account online to store your Zotero database here.
    • Zotero Version 1.0. This is the “safe” option, but you loose some functionality, and I have not had any problems with the “cutting-edge” version above. This version will be upgraded soon, so whichever option you pick will be fine in the long term.

Learning Zotero

  1. Demo Video
  2. Tour of Features
  3. Quick Start Guide
  4. Dan Cohen’s Blog often has good Zotero-related news
  5. As does my blog.

Extending Zotero

  1. Plugins for Microsoft Word or OpenOffice
    • If you chose the Beta version, go here and follow the instructions.
    • This now runs as a browser plugin, which installs the Word Processor integration utility automatically. Smooth and easy.

    • If you downloaded the regular 1.0 version, go here and follow the instructions.
  2. Customized Bibliography Styles. Zotero comes with a wide variety of default styles, including Chicago. But if there is a specific style that you need, check out this link to see if it is available. Researchers in Biblical Studies might be particularly interested in the SBL Style. Just click and Zotero will install everything for you.

Securing Zotero

  1. Use the Sync Preview release (above). It will securely back up and sync all your information and notes online, which can be accessed here. It does not backup stored files or PDFs, however; only text.
  2. If you are computer savvy, you can set up a WebDAV server to store and sync your entire Zotero database. This is like option (1) but also stores PDFs and other files. Check out this forum for suggestions.
  3. Use Dropbox. This is the best possible solution. Install Dropbox and then open your Zotero preferences dialog. Go to the Advanced tab, then place your Zotero database in a custom location: your “My Dropbox” folder. Now anytime a change is made the Dropbox software will upload it in real-time. You can also use this to sync your Zotero database accross multiple computers, and it includes all your files (movies, PDFs, images, etc). Your data is encrypted on Dropbox’s servers, so you don’t have to worry about security concerns.
  • Update: I should mention one issue I have had with the Dropbox solution. Dropbox cannot save open files, which means it will not upload or download your Zotero database until you close Firefox. If you are syncing your Zotero database across two computers, be aware of this limitation. Make sure you close Firefox on both computers, and that Dropbox has finished syncing all the data, before you switch workstations. Dropbox does save conflicting copies of files, so your data should ultimately be safe, but it may be a lot of work to recover it.

Update: This post was modified from the original on Sept. 17 2009 to bring it in line with the current status of the Zotero project.

 

Tiny application ShutdownGuard puts Windows automatic restarts back into your control.

I run an automated backup program on my Home computer (Vista) every night at 1am. Well, almost every night. Well, about every other night. The problem is that I have Windows set to download and install all those security updates, and it often decides to restart my computer as a result. When this happens my scheduled programs don’t run, and the only way to fix this is to turn off automatic updating.

I know many of you have had similar experiences. May I therefore suggest ShutdownGuard, a small and low-profile application that prevents Windows from its default “we know better than you” behavior.

 

Here is a great deal for those of you who NEED to find a better backup solution. You know who you are. Free

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