Implementing generic, object-oriented models in biology

This paper describes object-oriented programming (OOP) in terms relevant to the modeling of biological systems. Object-oriented programming is not a new technique but remains mostly unexploited in biosystems modeling. For biological scientists, the ideas of object-oriented design, based on the notions of taxonomy, discrete structures, behavior, and scale, make the approach intrinsically familiar and thus inherently compelling. We present a new OOP framework that may serve as a generic foundation for the production of plant models. This OOP framework represents a first step towards the development of generic model architectures and provides modularity, mechanistic richness, and advantages in process evaluation previously unavailable.