:Computer modeling of biological systems, a process of building new sets of conceptualizations, theories, and implementations is cov-ered in depth. The emphasis is on how computer modeling encom-passes three distinct areas of science (computer science, biology, and medicine) for building a framework for investigating the behavior of a complex biological system. Simulation and modeling are dis-cussed because these two factors provide the methodology for the design, development, experimentation, analysis, and evaluation of a experiment under study. Because of their high degree of modular-ity and collective complexity, computer systems such as analog, digital, or hybrid are reviewed. This presentation of computer mod-eling of biological systems delves into the study of data represen-tation (or data structures) and their transformation into an empirical model via a software program.