A Design for Framework-Independent Model Components of Biophysical Systems

Abstract: Most efforts in the design of software frameworks for biophysical systems simulation have focused on the compromise between domain specificity and use flexibility. Models in such frameworks fall in two main categories: either framework-specific, or “legacy ” code. In the former case, models implemented as software components can take full advantage of the framework services, but they depend on the framework. In the latter case, components are seen as discrete units of software, in general of coarse granularity in modelling terms, and the dependency on the framework is minimal, but the potential for composition and reuse is limited. Thus, modellers who want to use a modelling framework are faced with two choices: if the framework is extensible, implement a framework specific component (i.e. not reusable outside the specific framework); else, the alternative is to provide a component as a black-box, taking little or no advantage of the framework itself. We argue that component design choices, rather than being driven by the specific framework architecture, should rather promote re-usability by including design traits tha