Computer science and biology have inspired each other by drawing analogies. Biological molecules are even used directly as new material building blocks for creating next generation computer hard- and software. Recently, biology is moving to larger scales, generating datasets of high complexity and size. This allows moving from studies of individual biological entities such as proteins to their complex networks of interactions. Since cells are able to respond to perturbations over time, it is becoming an important variable in these studies. This is analogous to systems of systems engineering to operate in dynamic environments, requiring the efficient monitoring of external variables and intelligent choice of adequate responses. Here, we survey previous successes in exploiting analogies between biology and computer science and propose novel avenues and potential for cross-fertilization of research in dynamic systems modeling in biology and systems-of-systems engineering.