The convergence of cloud, communication and IoT structure and the trend towards virtual applications bring about new challenges for application developers and infrastructure providers. The resulting systems are complex with dynamic resources that could possibly hide issues. This creates a demand for flexible monitoring and optimisation methods. The Flex4Apps Itea project, set up by German and Belgian organisations including Sirris and various companies, tackles the challenges of monitoring and optimising large distributed cyber-physical systems. The project objective is to create a solution to manage large volumes of data and to control the complexity of system monitoring with minimal disruption of the target system.