Updates

• sudo apt-get update

Installing software

Languages 

• C++
• sudo apt-get install build-essential
• Fortran
• sudo aptitude install g77
• java
• sudo apt-get install sun-java5-jdk
• Python
• sudo apt-get install python 

Packages 

• Python packages
• Lapack support 
• sudo apt-get install python-numarray
• to use linear algebra module type
• from numarray.linear_algebra import * 
• Biopython
• m4 (sudo apt-get install m4)
• download and unpack flex
•  ./configure
• make
• make check (some tests failed)
• sudo make install
• sudo apt-get install python-egenix-mxtexttools
• sudo apt-get install python-numeric
• sudo apt-get install python-dev
• sudo apt-get install build-essential
• download ant unpack biopython
• sudo python setup.py install
• to use (from Bio import *)  

Desktop 

• KDE (desktop environment alternative to GNOME)
• sudo apt-get install kubuntu-desktop
• Beryl (3D desktop)
• sudo apt-get install beryl 

Server 

• Apache2 
• PHP
• mySQL
• Wikimedia
• Trac 
• Subversion
• sudo apt-get install subversion 

Misc

• Real player
• sudo apt-get install realplay