Roles of Diagrams in Computational Modeling of Mechanisms

As tools in science, diagrams not only serve as vehicles for communication but also facilitate and constrain scientific rea-soning. We identify roles that diagrams play when computa-tional models and synthesized organisms are used to recom-pose mechanisms proposed to explain biological phenomena. Diagrams not only serve as locality aids for constructing computational models but also help in identifying ways to manipulate these models and interpret the results. Moreover, they serve as blueprints for constructing synthetic organisms and then guide the interpretation of discrepancies between these organisms and computational models