Fast emerging mobile edge computing, mobile clouds, Internet of Things (IoT) and cyber physical systems require many novel realistic real time multi-layer algorithms for a wide range of domains, such as intelligent content provision and processing, smart transport, smart manufacturing systems and mobile end user applications. This paper proposes a low cost open source platform, MODiToNeS, which uses commodity hardware to support prototyping and testing of fully distributed multi-layer complex algorithms over real world (or pseudo real) traces. MODiToNeS platform is generic and comprises multiple interfaces that allow real time topology and mobility control, deployment and analysis of different self-organised and self-adaptive routing algorithms, real time content processing, and real time environment sensing with predictive analytics. Our platform also allows rich interactivity with the user. We show deployment and analysis of two vastly different complex networking systems: fault and disconnection aware smart manufacturing sensor network and cognitive privacy for personal clouds. We show that our platform design can integrate both contexts transparently and organically and allows a wide range of analysis.