AEGeAn Toolkit

I am the primary developer of the AEGeAn Toolkit, an integrated toolkit for anlaysis and evaluation of genome annotations. AEGeAn includes a collection of programs and scripts—most notably ParsEval and LocusPocus—as well as a C library whose API provides access to all of AEGeAn's core functions and data structures.


GenHub is a companion to the AEGeAn Toolkit and the LocusPocus program, which implements iLocus parsing functionality. GenHub's Fidibus program provides a more comprehensive pipeline around LocusPocus for data retrieval, pre-processing, post-processing, and computing statistics on iLoci.

GenomeTools Library

I am an avid user of and contributor to the GenomeTools library, a collection of excellent genome informatics tools. Most of my contributions come in the form of small patches, bug reports, and feature requests, although I have implemented one core data structure.

In many ways GenomeTools served as a model for my development of the AEGeAn Toolkit. The GenomeTools development community is small but active, and were very accomodating when I first starting using their API, and then later when I began patching and extending it. I can thank these kind folks for most of what I know about software engineering!

khmer Library

I am a frequent user of the khmer library, and contributed several new features during the khmer code sprint at Pycon 2015 in Montreal. The khmer library is also an excellent model of research software development, in terms of both process and community engagement.