I don’t use the software and so cannot comment on it personally, but Mike Aubrey has a thorough review of the new version of the always well-received Logos platform of bible study tools Check it out. I have been particularly interested in the sentence flow diagramming feature of the platform. Someday I will be able to try it out, but those who are already using Logos should comment on your experiences below!

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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.

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).

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.

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).

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.

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.

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.



4. 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.

Related posts:

1. Zotero Supports 1100 Bibliographic Styles
2. Zotero Updates Word Processor Plugins
3. Setting Up Zotero: Link by Link

If you are a blogger (and that includes Bibliobloggers!), and you haven’t already heard the news, be aware that new FCC guidelines may affect you. Here’s an explanation from the fine folks at CNET:

Independent bloggers who fail to disclose paid reviews or freebies can face up to $11,000 in fines from the Federal Trade Commission, according to revisions to the agency’s “Guides Concerning the Use of Endorsements and Testimonials in Advertising” published Monday.

So if you are reviewing a book, and you received that book for free, you now need to note that in your review. Silly, right? Well, I agree, and so does the Internet Advertising Bureau, but we’re stuck with it for now.

On a related note, I receive occasional gift certificates from the always wonderful wtsbooks.com on a click-by-click basis. If that bothers you, then I suggest you don’t click any links for books on this site.

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My dissertation advisor Dr. Dan McCartney has a new commentary out on the Epistle of James that I’m picking up today and looking forward to reading. You can get a copy too from the always wonderful Westminster Bookstore.

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OCR is the technology used to turn an image of text into plain (editable, search-able) text. If you’re like me (i.e., a nerd) you probably have a pile of scanned journal articles and books and such meticulously sorted on your hard drive (PDFs for example). You can read them and print them, but you can’t search them or edit them. Wouldn’t it be nice if you could?

Well, there are a number of free options on the web, but they all have their problems. Google has some of the best OCR technology out there–they recently acquired CAPTCHA to make it even better–and they have apparently been rolling this out into Google Docs. The Google Docs version is not as wonderful as you might like, but it works on high-res documents. Read about how to turn your images into text here.

Update: I was not able to get this to work with PDFs, surprisingly. The web-app only accepts PNG, JPEG, or GIF images right now. That is unfortunate, and I assume will be “corrected” in the future. Has anyone tried this on an image yet?

Related posts:

1. Send Web Documents Straight to Google Docs
2. Search your PDFs with OCR
3. Even More PDF Tools

If you are using the 2.0 Beta version of Zotero then I have good news. Zotero has recently updated their plugins for word processor integration. I have had a couple of problems with the OpenOffice plugin, so I am excited to see that work continues.

It appears that the update is fairly significant. One major change is that the both the Microsoft Word and the OpenOffice plugins are installed as browser components. Previously you had to add them as Word Processor macros, which can be messy and is difficult to upgrade when there are changes. By contrast, the new plugins are always up-to-date because Firefox does the checking for you, and all the messy installation is handled by the plugin itself, rather than the old manual process. In short: if you can install a Firefox plugin, you can install Zotero’s Word Processor integration.

There are a number of back-end changes to the plugins (ie., Java), with the result that everything seems to run a lot more smoothly. Two major problems I had with the previous plugins—errors in footnotes with multiple Zotero fields, and lack of support for adding citations within a table—are now fixed, which makes me an even happier camper than I was before.

How to get it

You will need the latest Beta of Zotero for the new plugins to work. To install the plugins follow the instructions on this page (be sure to install the 2.0 plugins, about half-way down, rather than 1.0 plugins). Once you restart your browser Zotero will do the rest.

If you are not already familiar with Zotero check out my description and guide.

Note for Linux users: if you haven’t already, you will need to install Sun’s version of Java (”sudo apt-get install sun-java6-plugin” in a terminal).

Related posts:

1. Zotero 1.5 and OpenOffice 3.0: Getting it all to Work
2. A Guide to Using Zotero in Biblical Studies: Collecting, Annotating and Citing Bibliographic Data
3. Zotero: An Introduction, now with SBL support

I often find it helpful to have a Bible Atlas near me when I’m reading through large chunks of the Bible. I have been unable to find a real good online version, but here is a pretty decent offering from the Access Foundation. It is listed on Scribd as licensed under the Creative Commons non-Commercial Attribution license.

Bible Atlas

Related posts:

1. Greek Summer Reading
2. How to Type in Greek Part I: An Introduction to Unicode
3. Free Media Players and Media Tools

There is a new Unicode Polytonic Greek font available for all you font collectors out there. Rod Decker has the details and download instructions. His post is so complete, there is not much need for me to add to it.

The basic idea: this font supports a very wide range of characters—Hebrew glyphs, for example–but is not as professional looking as (my still-standing recommendation) Gentium (or GentiumAlt).

If you are clueless regarding this discussion, but want to better understand fonts and right way to type in Greek, start with this post by yours truly.

Related posts:

1. Type in Polytonic Greek in Linux
2. New Unicode Greek Font with Text-Critical Glyphs
3. SBL’s Unicode Greek Font Finally Released!

Everyone who’s anyone is familiar with Facebook, and most people probably know about other social networks like LinkedIn and Twitter. Well if your in the academy you can add yet another social network to your list: Academia.edu.

Similar to LinkedIn, Academia.edu allows users to establish networks of contacts specializing in their field. You can fill in your credentials, upload papers, add information about the rest of your department (which might be problematic…), and a whole host of other thinks.

The site looks pretty slick, though I noticed a good deal of sluggishness and some less-than-attractive interface problems (text going off-screen, etc). There also seemed to be some privacy bugs to work through. For example, the front page of the site shows you a structural tree of a variety of Universities. It appears that you can add your name anywhere you like, provided you have an email address from that University. That could be problematic as the information included is now not only about you, but also about the University in question. How does the site verify the information entered? Or is that the responsibility of the University? That’s not so much of a problem for LinkedIn–your lies stay on your page–but for something like this fact-checking seems to be more necessary. Since I could not find answers to those questions on the site, I thought it best to refrain from taking part. Perhaps more information will be released soon, or perhaps Nerdlets readers who have taken the plunge can provide some info in the comments.

In short, while this might be promising, but I’m holding off for now.

Related posts:

1. Dropbox: Part Sync, Part Backup, All Good

We’ve commented on this before at Nerdlets, but now there is a definitive reason for doing so. It’s not really a surprise, but Google is about to tie all its seemingly disparate services together. Introducing the Google Operating System. Why a new operating system? Well, we use our computers differently now. We use them to access the web. Your browser, by and large, is your OS (at least according to Google), which is why Google has recently invested so much time into their entry into the browser wars: Google Chrome.

And the Google OS is actually the Google Chrome OS. According to Google, it is little more than a (Linux!) wrapper around Google’s browser. There is therefore no need to download, install, or develop applications. According to the official Google Blog post:

For application developers, the web is the platform. All web-based applications will automatically work and new applications can be written using your favorite web technologies. And of course, these apps will run not only on Google Chrome OS, but on any standards-based browser on Windows, Mac and Linux thereby giving developers the largest user base of any platform.

There are advantages to this approach. Developers can spend their time programming applications that work on any Computer, and because users do not have to install, update, tweak, or otherwise fuss with their applications, developers can pump out updates quickly and efficiently. Furthermore, provided your browser is secure, you need not worry too much about viruses and malware, or at least not yet. And, of course, since all your data is on the web, you can access your files anywhere! Finally, since Google promises that it’s vision will remain Open Source focused, you (presumably) will not need to worry about Google hijacking your data. If Google does something you don’t like, you can just switch.

There are serious disadvantages as well. Your data is on a server somewhere, and not on your computer. There is also a certain amount of loss of control.

Windows, Linux, and OSX take a hybrid approach to the OS and browser relationship, and I prefer that personally. With the mainstream operating systems your data resides primarily on your computer, but is synced to the web at your request. This is what I practice, since I don’t always have an Internet connection.

So what do you fine folks think? Is the future of computing web-based services running in your browser, or is it something more like what we’re doing now? Your comments are welcome!

Update: Some excellent analysis by Louis Gray.

Related posts:

1. Send Web Documents Straight to Google Docs
2. Google enters the Browser Wars with “Chrome”
3. On to Something