Geeneus (Fall 2012)
Geeneus is a smart, simple, NCBI API access tool in python. It makes no assumptions regarding the user’s knowledge of the underlying RESTful API NCBI provides, instead giving you a nice session manager instance, from which you can (seemingly) directly pull sequence, mutant, and annotation data from. Still a work in progress, and I may look to integrate with biopython at some point.
As of the 28th of October, Geeneus is available (in alpha) through pip. To try it out just run
sudo pip install Geeneus
For more information check out either the Python package index entry or the github page
 Stanford Machine Learning Coursenotes (Spring 2012)
Complete, stand alone coursenotes for Andrew Ng’s machine learning course. Gained some coverage on Hacker News and has generated some very positive feedback, which is always nice .
 AutoClasser (Winter 2011)
Tiny, scriptlike C++ project to automatically generate .h and .cpp files for writing software. Takes a config file and adds the content as an automatic header (including things like copyright, version details etc).
 Pufferfish (Winter 2011)
Pufferfish is a lightweight DNA compressor. At the moment the compression is just straight 4:1 compression, although I’m hoping to run Huffman encoding on top of that for added compression [Sept 2012 - still hoping...]. Works nicely at the moment, encoding is fast and lossless. I’ve got some ideas of things I want to add, but I’m pleased with the start.
 unpack (Fall 2011)
It’s 169 lines of pretty verbose Perl, but it’s also arguably the thing I’ve written I use most. Any kind of compressed archive, just
unpack file.tar.gz [or .zip, .rar etc)and it unpacks it into a new directory without having to remember a single command line option.
 SBMLIntegrator (Summer 2011)
Part of my Masters thesis project, allows you to integrate two SBML models together in a semi-automated way. For more information, have a look at my thesis (not the most riveting read, I'll confess).