January 13, 2010
I often find myself getting lost in Wikipedia. There are so many amazing things in this world. More recently, I've started keeping track of some of the more interesting / outlandish articles I come across. You can find the list here.
October 12, 2009
I wrote a program called PACT (Posterior Analysis of Coalescent Trees) this spring to properly analyze the genealogical trees produced by Migrate. I finally put in the extra effort to write documentation and make it easy for other people to use the software. It's now available for download.
I had originally wanted to estimate the relative contribution of various geographic regions to the evolution of the influenza virus. Trees produced by Migrate contain an explicit description of which geographic region branches reside in. It was just a matter a extracting, displaying and summarizing this information. The program can do a variety of things beyond this, and hopefully should prove a useful accessory to any sort of coalescent inference.
September 23, 2009
I've written a small Processing app to visualize the genealogical process. I've seen a lot of evolutionary trees drawn quite nicely. However, this is the first example that I've seen that presents trees in a dynamic fashion, showing how they evolve over time. It also allows for interactivity. For instance, you can see how adding more individuals to an evolving population causes their evolutionary tree to deepen.
Probably the best part about writing this in Processing is how nicely objected-orientated things are. Each individual in the simulation follows a simple physics simulation, repelling away from other individuals. This takes care of layout without having to worry about high-level control.
I'm planning on writing more apps in this vein. I think it might be a very useful framework for data analysis, rather than just simulation.
September 17, 2009
Welcome. I created this site to host my work, both large and small. Large projects have a natural home as articles in scientific journals. However, I'll often spend an afternoon following up on some small thing that's of passing interest to me. I would like to keep a journal of these small creations. Not planning a blog, but something involving a bit more novelty. We'll see what happens...