Graduate Projects

A listing of some of my work that I thought was interesting, either serious efforts to solve a problem, or just amusing. Many don't have web pages so for those that are truly curious you can contact me for more information.

VirtualPlant
VirtualPlant is a site designed to help biologists store and analyze biological data, where I was one of the primary developers for some time. The idea behind the site is that with the increasing abundance of biological data it is necessary to not only have a repository for all the data but also a collection of tools by which to analyze the data.
SSA Project
Comparison of several programs that use secondary structure predictions against primary structure programs to see which gave better multiple sequence alignments for several non-coding RNA families.
CytoDiff
A visualization tool to identify changing gene expression via statistical analysis. Genes are represented as nodes and are colored based on their change in expression level between different microarrays. Written as a Cytoscape plugin.
Invadens Unite
A collaboritve effort of Melissa Conrad, Haig Alexander, Trishank Karthik, and I to assemble and annotate a newly seqenced species, Entamoeba invadens. Several assemblies were constructed using various assembler programs and then annotated by comparing the results to the Entamoeba histolytica genome. Different techniques were used in the annotation and included reverse blast, glimmer hmm, and motif similarity.
SEER Analysis
A machine learning project to identify which cancer treatments would be most effective for a patient. The type of treatment was based off statistics that used patient demographic information and cancer conditions from the Surveillance Epidemiology and End Results(SEER) data set.
Graph Clustering in Cytoscape
Finding related subnetworks within a biological network using Antipole Clustering. Related subnetworks are shown separately in a visual list and are highlighted within the network.
SwissBot
A framework for easily programming single player puzzle games.
Attendance List Protocol in C
The attendance list protocol for maintaining consistent group membership within a network of computers. This is up here in larger part because I got to use sockets and program in C, which it seems I never get to do anymore. While I love doing things high level, python thank you, sometimes it just feels good to dig down.
Django(The Virtual Marionette)
A collaborative effort by Chris Harrison, Andrew Chizhik, and I to bring the world a virtual marionetted, named Django. Django was an OpenGL bird whose body,head,and feet were controlled by a marionette controller( 2 wooden rods in an x formation with strings attached). Django would also jump and flap his wings by watching your movements on a webcam.
Visions
A video application for modifying and mixing multiple video streams. Streams can come in the form of video files or from captured sources like a webcam. Video streams can be changed using dials and sliders or by using physical devices such as touch pads.