In this chapter a model of the molecular networks, created by using a network of communicating automata, is described as a dynamic structure, discrete event system, and interesting theoretical results are provided. This formal model provides a detailed approach of the biological system, and its implementation is able to handle large amounts of data. This model is applied to T cell signalling networks. T cell shows a hierarchical organization depending on various factors. Some mechanisms are still unresolved, including contribution of each signalling pathway to each response type. The software tool produced is used to simulate and analyze the T cell behaviour. The simulation reflects, quite faithfully, the process of T cell activation and T cell responses. This increases the confidence in using this model and its implementation both as descriptive and prescriptive tools. The interactions that govern the T cell behaviour are simulated and analyzed, providing statistical correlations according to software experiments, together with new insights on signalling networks that trigger immunological responses. The software tool allows users to systematically perturb and monitor the components of a T cell molecular network, capturing biological information relevant to immunology.