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
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