Biological primitives

In developing the graphics computer system BIOMOD, we were concerned primarily with the user-system interface. Rather than developing a formal higher-level language specific to modeling in biology, it appeared more fruitful to examine empirically the activities of the modeling process, and to attempt to design so that these activities would be simple to perform.

Unfortunately, however, it still functioned easily only for chemists, mathematicians, and programmers; a biologist would still not write FORTRAN or differential equations to describe the basic functions—for example, a neuron—of his problem. We would like, therefore, to describe a set of basic biological functions, or primitives, which can have unambiguous definitions and can be parameterized as required in a straightforward, clear way so that they can be called from the library and used in a new problem context. An extension of this concept is to prepare programmed modules, such as a capillary resistance bed, or models, such as a model of the four-chambered heart as a pump, which could be used as required. However, these latter modeling units are not easily parameterized and are usually too individually stylized to carry over from model to model. Instead, we have been concerned with more basic units which can be standardized, as will be described in subsequent sections of this paper. We first briefly describe the BIOMOD system itself.