Programming
I have been programming it seems all my life. Our first computer was an Apple IIe which I could operate from a very young age. Around 12 years old I learned Basic, then taught myself C and C++ and soon after learned Assembly x86. In high school I took a beginning course in C at a local college which I finished early by completing all the assignments in a couple of weeks. I originally enrolled in college as a computer science major, and later added mathematics as a second major. Whether I am doing theoretical research or applying current methods in novel ways, my research is always in close proximity to computers.
When it comes to computers, I am a "learner". I love to pick up all sorts of computer knowledge, be it a new computer language, new unix commands, productivity tools, or anything! As such I have experience with C/C++, Assembly, Unix shell scripting, autotools, Perl, R, Matlab, Maple, Mathematica, Microsoft Office, Google Docs, Dropbox, SVN, git, latex, etc.
Below you will find some details on software I have developed.
Github
I have recently started using git and I love it. I try to host all of my software on github. On my github page you will find small and large software packages. It seems I write small programs and scripts all the time, and I think they are pretty useful. I have even been using git locally to track latex manuscripts that I email between colleagues.
MOCHA
MOCHA stands for Matroid Optimization: Combinatorial Heuristics and Algorithms. It is a software package developed in conjunction with my paper "Computation in Multicriteria Matroid Optimization", submitted to the Journal of Experimental Algorithmics, 2009. The software, along with documentation and supplementary data can be found on the COIN-OR repository.LattE
LattE is software for enumerating lattice points in polytopes. I was part of the LattE team as an undergraduate at UC Davis. LattE has progressed significantly since I last worked on it. It is fantastic software and is widely used. Go check it out!
GeneOut
Gene Outlier is a software packaged developed for the paper “A support vector machine based test for incongruence between sets of trees in tree space”. It takes as input two sets of phylogenetic trees and uses support vector machines to test the null hypothesis that the two set of trees came from the same distribution.