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To study binary neutron star systems and to interpret observational data such as gravitational-wave and kilonova signals, one needs an accurate description of the processes that take place during the final stages of the coalescence, for example, through numerical-relativity simulations. In this work, we present an updated version of the numerical-relativity code BAM in order to incorporate nuclear-theory-based equations of state and a simple description of neutrino interactions through a neutrino leakage scheme. Different test simulations, for stars undergoing a neutrino-induced gravitational collapse and for binary neutron stars systems, validate our new implementation. For the binary neutron stars systems, we show that we can evolve stably and accurately distinct microphysical models employing the different equations of state: SFHo, DD2, and the hyperonic BHB Lambda phi. Overall, our test simulations have good agreement with those reported in the literature.