GlycoDomain Viewer
Further refinement of the GATOR tool, incorporating conserved domain information, as well as information about post-translational modifications. The tool is integrated with online spreadsheets, allowing for easy overlay of your own data.
GATOR
Advanced web-app to present simply a wide variety of data from proteomic data sources. Designed to work on a wide variety of browsers, and be easy to use.
Sugar viewer/builder
Simple app/widget for drawing structures. Entirely vector-based, using SVG to generate the images. This application currently is dependent on a server-side component to run, but there's a long-running project where it will be eventually moved across to running in pure javascript on either the server or browser.
Sugarcore
Core classes written to manipulate carbohydrate structural data. Primarily written to assist me in doing analysis during my PhD, it was later enhanced to add the ability to generate composite structures, which can be seen in the Sugar viewer/builder. While this code largely works, it's not in a great state for anyone to simply use.
GlycoSuite
Perl web-app actively maintained from 2001-2003. Unfortunately, the source code for the application is not publicly available, but it is still alive, and can be found hosted at Expasy.
MASCP-jstools
A toolkit for performing bioinformatic analysis on proteomic data for Arabidopsis thaliana. Developed while at JBEI the software aggregates data from multiple data sources and presents it all in an easy to use interface. Even better, these same libraries can be taken from the web browser and run from the command line, or on the server with little to no modification of your code.
Phosphorylation / nsSNP
An analysis of the relationship between post-translational modifications and the rates of non-synonymous phosphorylation. In press.
Orthology map
Intricate map of how many proteins are shared between the golgi proteomes of multiple species.
