The purpose of this dissertation is to describe and demonstrate a computer-aided design (CAD) framework for the field of synthetic biology. Synthetic biology is an emerging discipline with the ambition of engineering biological systems with the same efficiency by which mechanical machines or electrical circuits are engineered. The synthetic biology vision is to provide an efficient framework for engineering biological systems using established design principles, mathematical modeling, reliable databases, and standard (or automated) protocols for implementing and testing the engineered system inside living cells. CAD takes a central role in this vision because it integrates information from multiple sources and presents it to the researcher in a user-friendly manner. There are many challenges that need to be resolved before making CAD a reality, one being the lack of a software framework that can bridge sequence-level information and models as well as support engineering concepts such as modularity. The software application that is presented in this dissertation, TinkerCell, is intended to partly fulfill this requirement. TinkerCell uses a novel visual representation that combines biological mechanisms with mathematical models and sequence-level details. Further, TinkerCell is designed to promote collaboration in the synthetic biology community by allowing researchers to conveniently share computer programs with the community. TinkerCell is freely available at http://www.tinkercell com.