Do you use Zotero? Do you wish that your folder collections showed all the items in their various subfolders? I do. And there is a hidden setting in Zotero to allow you to change the behavior.

Here’s the official explanation:

By default, each of your collections displays only the items you have placed there. When you place a collection inside another collection, the contents of the second collection are not added to the first. If you enable recursive collections, items from subcollections will appear in all higher-level collections.

To change this behavior, type the following into your Firefox URL bar:

about:config

Be careful when you are on this special page. Firefox stores all of its settings here, and you can really mess things up if you go poking around without knowing what you are doing.

In the “filter” bar at the top of the page type:

zotero.recursive

You should see a line pop up that says:

extensions.zotero.recursiveCollections

Set the “value” of this setting to “true,” which you can do by double-clicking the line.

Now your folders are recursive! You can find other “hidden” settings, and what they do, here.

Related posts:

1. Zotero 2.0 Launches (What a Pleasant Surprise!)
2. A Guide to Using Zotero in Biblical Studies: Collecting, Annotating and Citing Bibliographic Data
3. Zotero Updates Word Processor Plugins

I do a lot of teaching and preaching and writing, and often an idea will occur to me at an inconvenient time–that is, when I don’t have pen and paper handy. No problem, though, RTM makes a great idea-catcher! (Ideas can be anything, by the way, like “I need to do such and such of Friday”).

The best way to catch ideas is through your phone. I have a special drop with drop.io that I can call and leave myself a voice message. Any internet-based voice messenger will work, though. I call my voice-messaging service and leave myself a message with my idea. I have it set up so that anytime I get a voice message it sends me a little notification in my email.

So how does this get added to RTM? There are two very easy ways. I use Gmail filters and RTM’s awesome Gmail plugin. RTM lets you automatically create tasks from a Gmail Label, and Gmail in turn lets you automatically label incoming emails based on a set of preconditions. So I have Gmail set to automatically label all my voice-mail messages with the label “Task,” and I have RTM set to automatically create Tasks from any email with that Label. Presto: instant automatic idea catcher.

The second way you can set up independently of Gmail. Your RTM account also has an email address, so alternatively you could set up Gmail (or whatever email program you use) to auto-forward all emails of a certain type to that address, which would then get created as tasks.

Related posts:

1. Getting Things Done with Remember the Milk
2. Gmail Adds To-do Lists
3. Multitasking Mondays: New Features in Gmail

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

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

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

The full set of images and text from Codex Sinaiticus, the oldest complete copy of the entire NT, is now online. Check out their webpage. The interface is pretty slick, allowing you to change lighting options, zoom in and out, and bookmark and print pages. It also includes a transcription and translation. Anyone interested should definitely check this out.

Update: The always intriguing ReadWriteWeb has also posted a story on this, with a little analysis and some extra technical details. Read that here.

HT: NT Interpretation

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Good news! The lawsuit filed against the developers of Zotero (which I wrote about here) by the makers of EndNote has been dismissed. There are few details as yet–like whether or not the suit will be refiled–but hopefully this is a sign of things to come. From ArsTechnica:

Thomson Reuters, which makes EndNote, an academic reference management product, had filed suit against George Mason University, claiming that its support of the open source Zotero project, which imports EndNote files, was in contravention of the university’s license to EndNote. The suit, which requested an injunction against the distribution of Zotero, has now been dismissed. Depending on whether Thomson Reuters appeals or refiles the suit, this may leave Zotero in the clear.

Need a little more background?

Academic reference managers, which allow their users to keep track of the publications that they cite when writing up their own research, are a fairly specialized market. EndNote has a number of features that make it a compelling option, including a series of filters for online search queries and tight integration with document preparation software, notably Microsoft Word. It also offers one of the few cross-platform options on the market, and has a large library of reference styles to match the formats used by different journals. But there is also a degree of product lock-in, as many researchers have built up libraries of thousands of references over the years.

Zotero undoubtedly looks a bit threatening to Thomson Reuters, as it has a number of these features. It operates as a browser plug-in, which allows it to cross platforms easily and integrate well with online searches; it is also able to import EndNote reference databases. But the key feature that got it into legal trouble was the fact that it was able to import and use EndNote reference style files.

The full article is worth reading, especially since some reflection is offered by the authors regarding the merits of the lawsuit.

Related posts:

1. Zotero Lawsuit
2. Zotero Gets New Partners
3. Zotero 2.0 Launches (What a Pleasant Surprise!)

Copies of Westcott/Hort and Tischendorf have long been available online in digital form. Tragelles’s Greek New Testament predates both of these and is now available as a digital (Unicode!) text. Even better: the text is open licensed under the Creative Commons Attribution-Noncommercial-Share Alike license, which means you can use it, modify it, and distribute it to your heart’s content; just don’t try to make money off it!

You can download the digital text here. More information is available here and here.

Michael Hanel already has a Bibleworks version ready for download here. And this is a great candidate for an eBook, so I will begin working on that soon (hopefully).

Related posts:

1. Which Greek Text?
2. How to Type in Greek Part II: Setting Up the Microsoft Greek Polytonic Keyboard
3. Greek Flash Cards