Software: Managing references

You read a paper three days ago and now you want to dig up the citation for an argument, or for that footnote you forgot to include. Can you find the paper again? If you've been managing your references well, you might be able to! Luckily now you have software options.

The tool I've used longest is Zotero, a Firefox add-on. Zotero keeps a "library" and lets you create infinitely nested "collections" within the library. That means you could have a collection for each class, for each subject, for each body system, whatever. When you come across a paper you like on PubMed or dozens of other databases and libraries, you click a button and Zotero adds that paper (or book or article or record) to your Zotero library. It recognizes authors, titles, keywords, etc, and you can add your own tags and notes. You can also grab a snapshot of the page for off-line reading, or even PDFs. Since I beta tested Zotero, I've gone back and forth with Zotero developers a few times trying to work out issues, and they're very cool and very responsive.

Favorite features:

• integration with Microsoft Word or Open Office -- add a citation in the format of your choice with 3 clicks
  
• highlight text and right click to add a note to your library, which conveniently also carries all the information about the original page, so you know what you were looking at at the time
  
• Saved Searches in the Collections window, like the Smart Folders in OS X. I have Smart Searches defined to show me only those articles with "emedicine" or "mdconsult" in their URL, since those are sites I use often in my current classes

Recently I started using Connotea, which works on similar principles (in terms of recognizing that something is a title or author), but it lives online instead of on your computer. It's like del.icio.us for researchers, clinicians and scientists, complete with tags, user groups, and being able to see who else is interested in the papers you're interested in (if you designate the listing as public). Connotea is a little further behind Zotero on features -- they're still working on an export to a simple MLA/APA/Chicago manual format, but you can already export to other citation managers or BibTex. But if you're looking for an easy-to-access, easy-to-share reference manager, Connotea might be the tool you're looking for.

Favorite features:

• links to other users who cited the same paper
  
• user groups, so you can easily share references with friends
  
• can handle info: links

How do y'all organize all the papers you read?

Software: Play back lectures faster

Joe S passes along this for those of you who record lectures, or who download the lecture mp3s from the library e-reserves:

I have been using Express Scribe Transcription Playback Software to speed up audio lectures to 140%+ without pitch change/distortion: http://nch.com.au/scribe/index.html

It’s free & available for Windows, Mac & Linux as well. I find it invaluable to listen to lectures at a faster pace with no pitch distortion. It saves me time and I hope it helps you as well.

OS X: Flow charts and schemas

In Clinical Diagnosis we started off having to make a bunch of clinical diagnosis decision-making schema. People used Powerpoint, Word, OmniGraffle, and other disasters-fests; the situation was dire! Thankfully someone in my group had Visio, so it was up to him to produce our Glucose-6-Phosphate Dehydrogenase Deficiency schema.

Hands down, the best flow chart / schema software is yEd Java Graph Editor. It's available for just about every OS, so there's finally something useful in this blog for Windows users.

The image in this post is the giant master schema I made for one of our exams -- don't copy it because there are mistakes in it that I've caught since then, and it's not logically sound, but admire its vastness! -- there are nice PNG (image) and PDF exports (so you can share it with people who don't have the software and print it anywhere), it can print across multiple pages (very handy for giant messes like that one), it has snap-to grids, you can set the default node properties (including size, shape, background and text color), and you can have it do all sorts of fancy graph analysis and redistribution. The arrows are flexible, the labels are flexible, and it's absolutely the best tool I've found.

There are some user interface quirks that are frustrating, especially for novice users. Clicking once creates a new node, but clicking an existing node isn't enough to edit it -- you have to hit F2 to edit the label, whether that's the node label (the text inside) or the arrow label (the text accompanying the label). If you have a Mac laptop and your F2 is truly a function key (like screen brightness), you either have to hit Function-F2 to get the F2 yEd is expecting, or you have to override the setup in the keyboard preferences in the System Preferences (Keyboard & Mouse :: Use the F1-F12 keys to control software features). Overall, you can be very productive with yEd after 5-10 minutes of basic acclimation, and it's well worth the time investment.

The other tool I found was Gliffy, but that was mostly because they have cool room layout modes where you can drag couches and bookcases around, and as someone who's tried everything from construction paper to Photoshop to mock up a room, that's very cool.

Have you been using yEd? Any tips for readers? Is there some other software you've found productive? Please comment!

OS X: Flash cards and quizzing

Once a software engineer, always a software engineer. And once stubborn -- well, still stubborn. I tend to have an idea, code it poorly, work on it for a long time, then look around and find someone else has done it already, and way better than I ever would.

As is the case with flash cards / quizzing applications. A few years ago I wrote a PHP/MySQL web site for flash cards and shared it with my Anatomy & Physiology class. It was clumsy, web-based, I was the only one who could add cards, but it worked for me. It wasn't the solution I needed for med school though, so I finally looked around for OS X software to do the job.

I found two:

iFlash is $12 and has some excellent features -- your cards can have multiple "sides" (which is handy given that there's more than one thing we need to know for each herb, for example), and they can have embedded sounds, which means that I just made a deck of cards incorporated the lung sounds I downloaded from somewhere. There's a free 30-day trial, which I'm still working from. [iFlash review and iFlash download]

Genius is free and has a cool quizzing algorithm. One of the features I liked about the tool I wrote was that you had to get questions right more than once in order to have them deemed "known," and the more you got them wrong, the more you had to get them right to get back in the black. Genius has a similar idea going and seems like an excellent tool. [Download Genius]

What's your impression? Are flash cards helpful for you in learning? Do you find added value from computer-based flash cards instead of that huge deck of 3x5s fraying in your back pack?