The Josephson effect is a well known macroscopic quantum phenomenon which has been discovered in the context of superconductivity and has prompted multiple technological applications. In ultracold atomic setups novel Josephson effects were predicted 15 years ago and recently observed in bosonic systems trapped in double well geometries. The recent realization and control of interacting ultracold fermionic systems constitutes a new platform where the effects of quantum coherence can be tested on a wide range of interaction strengths, along the so-called BCS-BEC crossover. Our research focus on the theoretical investigation of the Josephson effects with ultracold Bose and strongly interacting Fermi gases in connection with experiments that are conducted at LENS.