In the last quarter century, biologists have made great strides towards understanding biology at the molecular scale. The human genome has been sequenced and the structures of many proteins, the molecular machines responsible for the function and structure of cells, have been solved. Single-molecule techniques and advances in microscopy have significantly changed the way in which biologists ask and answer questions. As biological measurements and techniques have become increasingly quantitative, they have allowed biologists to ask ever more quantitative questions: How do the molecular machines, which comprise the cell, function microscopically? Can we understand the design principles that govern the structure and function of biological systems on a microscopic scale? What role does the chaotic microscopic environment play in cellular function? One outcome of this new generation of quantitative biological questions is the need to greet quantitative experiments with models at a higher level of abstraction than the traditional cartoons of molecular biology. Our work centers on the interface between mathematical models of biological systems and this new generation of quantitative biological experiments.