Programming Languages
Python
Java
C++
C
C#
SQL
Ruby
$\LaTeX$
JavaScript
XHTML/CSS

Frameworks
Biopython
Django
Rails
.NET
CUDA

Software Libraries
GNU Scientific Library
POSIX Threads
GDB
NumPy
SciPy
Python Imaging Library (PIL)

Computational Bio Tools
NCBI Cn3D
NCBI CDTree
NCBI BLAST Programs
NCBI Entrez
Ensembl
BioMart
T-Coffee
ClustalW
PHYLIP

Computational Mathematics Systems
SAGE
R
Matlab
Mathematica
Minitab

Server Administration
Apache
lighttpd

Source Control
P4
Git
Subversion