Permeabilization of the mitochondrial outer membrane involves interactions among various members of the Bcl-2 family of proteins. These interactions lend themselves to analysis using techniques from systems biology. We consider the reactions we believe to be taking place between the proteins present. Together these form a model of the experimental system. By fitting observed data to the model we can estimate reaction rates and evaluate whether our model is satisfactory. We illustrate the techniques using borrowed data froman experimental model which incorporates Bax and Bid.