A modeling tool for biomedical systems

This paper describes the tool Pansym for biomedical system modeling which has been designed primarily for representation of kinetics, transport and metabolism of biological substances. New modeling tools are needed in this research field because available simulation environments are often limited when applied to multidisciplinary studies in biomedicine. The aim of the new software is to allow a flexible specification of system structures using concurrently different formalisms that are conventionally used in different modeling domains. Starting from an intuitive model specification, mathematical system equations are first derived in symbolic form and subsequently coded as source code for different target applications. This multidomain modeling environment was built using bond graphs as common basis for automated analysis of system structures and symbolic derivation of system equations. Preliminary experience with the software showed that the adopted design strategy comes up to expectations, especially as regards the definition of complex hierarchical models that exhibit interactions between heterogeneous subsystems, e.g. cardiovascular and metabolic functions. Moreover, the specification of model structures is close to graphical object representation which helps defining a model of a system more in terms of its structure rather than its equations.