Simulation and object-oriented programming: the development of SERB

Abstract

An object-oriented programming language (OOPL), Flavors, was used to implement a modeling language and ancillary simula tion tools designed specifically to meet the needs of research biologists. A biological system is typically considered as a set of interacting entities, an abstraction which closely matches the pro gramming paradigm of Flavors. Some of the important charac teristics of Flavor programming are presented. Then SERB (the Simulation Environment for Research Biologists) is described. SERB uses Flavor objects to represent biological entities, resulting in a high degree of transparency between model and simuland. The simulationist creates model components from a library of component types and defines a model as some interacting set of these components. These models can then be used in simula tions or by higher level functions, such as sensitivity analysis. Flavors was found to be an ideal language for implementing modeling and simulation software for this domain.