is an interactive tool for visualizing protein-protein interaction networks. I did quite a bit of research into protein interaction networks in graduate school, and one thing that I found surprising was the lack of a good, web-based network visualization tool. There were good desktop tools like Gephi and Cytoscape, but the appeal of having it just run in your browser is that it becomes accessible to everyone. After I completed my PhD, I found myself with some spare time on my hands -- and I had been interested in learning a web-based graphing tool, such as sigma.js -- so I built The back-end of the site is PHP (which I set up in a "hand-rolled" MVC pattern, something I was pretty fired up about for a while), supported by a MySQL database, but the real heavy lifting here is all JavaScript, using the fantastic sigma.js library.
GeoNIS, a web mapping service to store, process, and display geospatial data collected by ecological researchers, might be the most technically interesting web development project I've done. This June, someone from the U.S. Forest Service contacted me, and said they needed a programmer to write Python scripts for an ArcGIS-based service. ArcGIS is a very fancy piece of mapping software that I've wanted to learn for years, so of course I jumped at this opportunity. The catch was that this project had very tight deadlines, but I was excited to learn ArcGIS, so I signed up, and we were off to the races -- I spent 70+ hours on this project just about every week this summer. It was hectic, but I ended up completing the web service, and I'm proud to say that I'm now competent with ArcGIS, in addition to its JavaScript and Python bindings.
I spent about 9 months doing biophysics research with the Laufer Center, a gleaming new research institute on the Stony Brook University campus. It seemed like the perfect gig -- good people, a fancy new building, plus a decent salary to do whatever research struck my fancy. About the only thing it didn't have was the possibility of becoming filthy, stinking rich -- and so, in what turned out to be one of my poorer decisions, I jumped ship to join a little startup in NYC. Not too many months later, I found myself jobless and living out of the back of my truck as I slowly made my way west. While I was wandering, I got an email asking if I'd like to help rebuild the Laufer Center's website -- and I had good feelings about the people and the research there, and of course I needed the money, so I dove right on in. This was a joint effort between myself, Sarina Bromberg, and Geoff Rollins, and I think we made a great team -- I like the way the site turned out.
dataRonin is a fun little project I've been tinkering with over the past 6 months or so. My wife, Fox, had expressed interest in setting up a personal/research site, and I convinced her to let me do it. We brainstormed about what else might be cool to put on the site, and one thing we realized is that there is a real lack of good, easy-to-use plotting/statistical tools for large ecological data sets -- of course, you can always use Matlab or R, but that requires you to know Matlab or R. What if you're not a programmer and don't want to be, but you have a giant data set and you just want to have a look at it? So, Fox started outlining to me what might be useful, and I started tinkering with it. The plotting program we came up with -- which I dubbed FoxPlot -- is actually still in development, but I think it's quite promising!

For the code behind these — and many other — projects, check out my Github page.