The dynamics of complex biological systems is often driven by multiscale,rare but important events.In this talk,I will introduce the numerical methods for computing transition states,and then give two examples in distinct biological systems: one is a multiscale stochastic model to investigate a novel noise attenuation mechanism that relies on more noises in different cellular processes to coordinate cellular decisions during embryonic development; the other is a phase field model to study the neuroblast delamination in Drosophila.