Wednesday, November 5, 2008

Growth of phylogenetics, or at least phylogen*

I'm working on slides for a job talk. I made one that might be of interest to readers of this blog, a plot of number of references with "phylogen*" in any field in Scopus through time (line on the figure, also the position of the blue circles). I also found the number of references with "evolution" or "ecolog*" as well as all combinations of these three terms to make Venn diagrams of the overlap of the terms (using Google Charts). It's interesting to see how the three areas overlap and change in size through time: "phylogen*" is now much more common (up to 38% of the frequency of "evolution") and now overlaps more with references with "ecolog*" than with references with "evolution". I'm sure there are all sort of artifacts and biases, but interesting to look at nonetheless. It does suggest that I should start thinking more about ecologists using TreeTapper.

Monday, November 3, 2008

Viewing missing methods/software, part VII: PHP+GD

I was getting dissatisfied with Processing for visualizing missing methods. It was nice to have animation of the diagrams, but it was just too brittle: it would only work in certain browsers, it stopped working sometimes when you moved between tabs or windows, it was hard to update and keep working. This is probably more due to my lack of experience in the language and the odd way I was using it (read a variable stored in Javascript on a page to talk to a PHP script to talk to a Postgres database and display the results in real time) than any inherent flaws in it. I had thought about going to Flash, but that also involved learning a new programming language. I had recently started using PHP with GD to visualize progress of my jobs on Duke's computing cluster and found it easy to use (though I'm having issues with transparency). I decided to try this with the method visualization (I wanted to get TreeTapper cleaned up a bit more before a job interview next week). I wrote a script that reads information stored in GET variables and saves an image and image map. In front of this I wrote a controller script that only calls the drawing script when an entry in the database is newer than the saved image and image map (using ideas from my Google Summer of Code student Paul McMillan, who put sophisticated caching in his DBGraphNav). The image and image map are displayed in an iframe in the calling page. There's a Javascript function that calls the controller script as a user chooses which options to display. There's also a Javascript function that uses a Panel object from YUI to display a lot of information about each node on the diagram on mouseover in a floating panel. This is a lot more flexible than the Processing implementation. For example, you can now go to a summary page for each node or click on an entry in the floating panel to go to an info page on just that item (such as a program).  Caching the images makes display a lot faster, though only a subset of possible combinations can be cached. The cache of images also provides some nice pictures for screen savers or talks.

You can try out the new interface here.

Here's a picture of the new display:

And some of the cached images: