We consider hydrodynamic limits of interacting particles systems with open boundaries, where the exterior parameters change in a time scale slower than the typical relaxation time scale. The limit deterministic profiles evolve quasi-statically. These limits define rigorously the thermodynamic quasi static transformations also for transition between non-equilibrium stationary states. We study first the case of the symmetric simple exclusion, where duality can be used, and then we use relative entropy methods to extend to other models like zero range systems. Finally we consider a chain of anharmonic oscillators in contact with a thermal Langevin bath with a temperature gradient and a slowly varying tension applied to one end.