Software
Active and/or stable projects [primary language(s) in parentheses]:
- BioSRC: A Ports-like system for easily installing bioinformatics software [Make]
- Grotesque: A library manager for interactive fiction [Python]
- guile-file-names: A file-name abstraction module for Guile [Scheme]
- Idioma: A bare-bones language training application [Python]
- Librekontrol: A fully programmable controller editor [C, Scheme]
- m4-bloggery: A static website generator [Make, M4]
- molnet-recon: A suite of tools for reconstructing molecular networks from quantitative data [C]
- pacnanny: A wrapper for Arch Linux’s pacman package manager that enforces good discipline [Bash]
- paperq: A tool for managing a reading queue of academic/scientific papers [Bash, C]
- pyifbabel: A Python implementation of the Treaty of Babel for interactive fiction [Python]
- seqmi: A tool to quickly calculate mutual information between columns in a sequence alignment [C]
- tp-helix-orientation-lock: A small daemon program to support screen-orientation locking on the Lenovo ThinkPad Helix 2nd Gen 2-in-1 laptop/tablet in GNOME [C]
- zeptodb: Tiny tools for manipulating DBM (flat, non-relational) databases [C]
Other projects to which I’ve contributed:
- Biopython [Python]
- Bio.Phylo.PAML: a Python API to the PAML package of programs
- Bio.Phylo.BaseTree.py:
I provided a faster algorithm for the
root_at_midpoint()function - Bio.AlignIO.PhylipIO: I added support for sequential Phylip files
- GNU Source Release Collection: A BSD Ports-like system for easily installing GNU software from source [Make]
- GNU pyconfigure: Templates for easily implementing the standard GNU configure/install process for Python projects [Autoconf]
- nwm: I have added quite a few new features. [C, Scheme]
- st: I contributed patches to implement double-buffering via the XDBE extension (which was eventually removed) and to support mouse scrolling [C]
These are old or uninteresting and are therefore no longer maintained:
- gedit-bio: Handy biology plugins for Gnome Gedit
- GeneNetWalk: A user interface for randomly generating point mutations in a biological sequence for experimental design