Software list

ryan — Wed, 05 Dec 2007 16:35:01 +0000

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

The Software List

ryan — Sat, 03 Nov 2007 18:20:53 +0000

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