Scientific collaboration is critical in high performance computational (HPC) environments. Computer security incidents, however, are a constant threat in today's interconnected computational environments. Many sites struggle with finding a balance between the needs of users and the threat from unauthorized usage or access. Understanding the constantly changing battlefield is critical for effective and optimal deployment of computer security resources.This tutorial will provide an underlying knowledge of the current state of computer security, its effects on HPC environments and mitigation strategies. Topics we will address include:1.HPC Security Fundamentals2.HPC Security Protection Fundamentals3.Intrusion Detection Using Bro4.The Changing Computer Protection Environment5.Cross-site Implications of Collaborative Environments6.Keeping One Step Ahead7.Risk Assessment, Mitigation and Compliance8.Components of a Good Protection ProgramWe will also show how described techniques are in use at SC06 to protect SCinet.