The Stanford Center for Systems Biology was established in the fall of 2013 under a grant from the National Institute of General Medical Science and the National Centers for Systems BIology. The overarching aim of the Stanford Center for Systems Biology is to gain a systems-level understanding of cellular decision-making during proliferation, migration, and differentiation. These processes are critically controlled by signaling and mechanical interactions between neighboring cells. We will draw upon progress in understanding how these processes are regulated in individual cells and will now move towards the challenge to understand how cells make decisions collectively. Our model systems include Xenopus laevis embryos, epithelial cells and endothelial cells as well as human induced pluripotent stem (iPS) cells, granule neuron precursors (GNP), adipocytes, and drosophila wing epithelial cells. Our biological projects are supported by modeling and technology efforts to advance the quantitative analysis of our experimental studies and to support the development of better imaging and image analysis methods. We are also developing courses and will train people in the use of computational, imaging, and perturbation methods to investigate cell decision processes.