Quantitative modeling has become a major tool in biology, to help the understanding of complex systems by combining the biology experiment with the mathematical theory and models. In this talk, we will review some of our recent works in computational systems biology, from gene regulatory network to cellular and tissue systems. First, we start with finding the role of Nanog gene in stem cell regulatory network. Next, we present a phase field model for the cell polarity. Then we extend to the tissue level by showing the neuroblast delamination in Drosophila embryo. The joint work with Qing Nie (UC Irvine), Chao Tang (PKU), Feng Liu (PKU), Yan Yan (HKUST), Yuling Jiao (CAS).