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.