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I use a lot of open source software every day. Here’s what I use the majority of the time:
Python 2.5, with with the modules

• matplotlib for plotting and Matlab-like functionality
• NumPy for fast math
• RPyfor using R’s extremely powerful statistics functions from within Python scripts
• BioPython for manipulation of genomic data and running alignments, BLAST, and NCBI searches from within Python scripts
• MySQLdb for interfacing with MySQL databases

gvim as a text editor for writing scripts
IPython as an interactive shell.

Personal reasons why I like Python

• Makes good use of my time — I can code quickly in it with a surprisingly small number of bugs
• Interactive debugger for squashing those bugs (pdb)
• Python has everything I like about Perl (text processing, quickly write code, free) without the syntax overhead ($, @, %, {}, $_, ; )
• Python has everything I like about Matlab (plotting, fast math, interactive interpreter) without the cost ($100’s with toolboxes)
• Quick enough for small scripts but deep enough for larger programs, GUI and all
• Syntax that reads like pseudocode
• IPython

• Tiddlywiki for notes.
• MySQL for database stuff.
• Ubuntu for an operating system.
• Thunderbird for email
• Firefox for browser
• Inkscape for vector graphics
• pstoedit for converting SVG, EPS, and PDF files
• ImageMagick for converting all other images quickly
• WordPress for this blog
• Scribus for posters
• Blender for 3D graphics and animations

Here’s a list of the software I use frequently. Best part: everything is completely free. (more…)