Here’s a list of the software I use frequently. Best part: everything is completely free.
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
I use gvim as a text editor for writing scripts and IPython as an interactive shell.
A few notes on why I like Python (and why not some other potential choices);
- I can code quickly in it — it seems to fit my brain
- Everything I like about Perl (text processing, quickly write code, free) without the annoying syntax ($, @, %, $_, ; )
- Everything I like about Matlab (plotting, fast math, interactive interpreter) without the cost ($100′s with toolboxes)
- Object oriented programming is easy, which makes writing larger programs a cinch
- syntax that reads like pseudocode
- interactive interpreter (IPython)
- interactive debugger (pdb)
- code is readable several months later (as opposed to Perl), which means it is easily reusable
- modules for interfacing with all kinds of other useful programs
Tiddlywiki for notes.
MySQL for database stuff.
Ubuntu for an operating system.
Thunderbird and Firefox for email and browser
Inkscape for vector graphics
pstoedit and ImageMagick for converting images from vector to raster or between vector formats
WordPress for this blog
Scribus for posters
Blender for 3D graphics and animations
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