how to detect malicious activity from my server

view story

http://serverfault.com – I'm using a linode virtual server. My machine is Ubuntu 10.04. I got a ticket from Linode that they detected malicous activity coming from my server. "We have detected your system with an IP of, , scanning a client we monitor. This was not a short attack but a prolonged scan and/or probe that was designed to find and intrude into the target network." Now I'm hosting on linode to test an application, I have no idea how to manage and secure a server. Please can someone give me some lead on how i should investigate the issue and how to solve it. Thank you (HowTos)