In this paper, we discuss the possibility of using computer algebra tools in the process of modeling and qualitative analysis of mechanical systems and problems from theoretical physics. We describe some constructions-Courant algebroids and Dirac structures-from the so-called generalized geometry. They prove to be a convenient language for studying the internal structure of the differential equations of port-Hamiltonian and implicit Lagrangian systems, which describe dissipative or coupled mechanical systems and systems with constraints, respectively. For both classes of systems, we formulate some open problems that can be solved using computer algebra tools and methods. We also recall the definitions of graded manifolds and Q-structures from graded geometry. On particular examples, we explain how classical differential geometry is described in the framework of the graded formalism and what related computational questions can arise. This direction of research is apparently an almost unexplored branch of computer algebra.