For minimal installation of Ubuntu 9.10 download alternate version here
Start virtual box
enter name for new virtual machine ('nextrnai') and select 'Linux' as 'Operating System' and 'Ubuntu' as 'Version'
Adjust base memory size to 1024 MB
Leave 'Boot Hard Disk' (Primary Master) and 'Create new hard disk' checked
Select 'Dynamically expanding storage' as 'Storage Type'
In the 'Create New Virtual Disk' window type 'nextrnai' as location and leave 'Size' at 8.00 GB
'Finish' will create the new virtual machine 'nextrnai'
Select 'nextrnai' virtual machine and 'Start'
Select the Ubuntu iso image (e.g. 'ubuntu-9.10-alternate-i386.iso') as 'Media Source' ('Add' the location of the *.iso file in the 'Virtual Media Manager' window)
'Finish' will start the Ubuntu iso image
Installation of Ubuntu
Select the language (e.g. 'English')
In the Ubuntu startup screen press F4 and select 'Install a command-line system'
Then 'Install Ubuntu'
Choose language, location and keyboard layout (e.g. 'English', 'Germany' and 'USA')
Type 'nextrnai' as hostname
Use 'Manual' partition to initialize a primary partition with ext4 format and root ('/') mount point and a logical 'swap area' partition
'Finish and write partitions to disk' to start installation of the system
Type 'NEXT-RNAi', as full user name; 'nextrnai' as username and password, do not use encryption for the home directory
Further configurations: do not specify any proxy, use UTC time, unmount CD and finally allow restart
login as 'nextrnai' with password 'nextrnai'
to update the system, run the following commands (sudo password is 'nextrnai'):
sudo apt-get update
sudo apt-get upgrade
to get a small graphical user interface running run the following commands:
sudo apt-get install xorg
sudo apt-get install xfce4
type 'startx' to start XServer with xfce4
install unzip program with 'sudo apt-get install unzip'
install Firefox webbrowser via X terminal with 'sudo apt-get install firefox'
install emacs editor via X terminal with 'sudo apt-get install emacs'
generate autologin file (e.g. using emacs editor) that runs 'startx' command during system restart and paste the following content
sudo emacs /etc/init/X.conf
# X - start X
description "Start X"
author "Thomas Horn"
start on (filesystem and started hal)
stop on runlevel 
su - nextrnai -c startx
Installation of VirtualBox support for Linux
To improve graphics support etc. of VirtualBox with the Linux system run 'Install Guest Additions' in the VirtualBox 'Devices' option, allow to 'autorun' the installation in the virtual machine (use again sudo password 'nextrnai' when asked)
Unmount the virtual box guest addition drive (on the desktop) and restart the system
Installation of NEXT-RNAi (including dependencies)
Download ViennaRNA package, e.g. ViennaRNA-1.8.4.tar.gz and unpack (e.g. in X terminal with 'tar xvzf ViennaRNA-1.8.4.tar.gz')
Change to ViennaRNA-1.8.4 and run './configure', 'make' and 'sudo make install' (during 'make' and 'sudo make install' error messages for the 'RNAforester' program are reported, they do not influence NEXT-RNAi that only requires the 'RNAfold.pl' script in the 'ViennaRNA-1.8.4/Perl' folder)