In this paper, the early design of our self-organized agent-based simulation model for ex- ploration of synaptic connections that faithfully generates what is observed in natural situation is given. While we take inspiration from neu- roscience, our intent is not to create a veridical model of processes in neurodevelopmental biol- ogy, nor to represent a real biological system. In- stead, our goal is to design a simulation model that learns acting in the same way of human ner- vous system by using findings on human subjects using reflex methodologies in order to estimate unknown connections.