This chapter primarily describes a system-level approach to modeling the brain, focusing on the interactions between different brain areas and the overall neural activity trends of entire regions rather than individual areas or single neurons. The emphasis is on the dynamics of neural activity across networks of areas. In particular, the chapter covers the following topics. The first part introduces critical theoretical concepts necessary to understand the role of system-level models in simulating some brain functions. It explores the potential of using computational models to create ‘digital twins’ of subjects, simulating the effects of therapies before testing on actual subjects, and reducing future reliance on animal models. The second part details the method proposed in this book for constructing system-level models using Python and ODEs and includes several code examples.