PNNL

Abstract

At the Pacific Northwest National Laboratory, the Visual Modeling Environment for Biology (VMEB) is being developed to allow biologists to construct visual representations of scientific concepts and theories. Unlike existing scientific visual modeling environments, VMEB captures and manages visual concepts and diagrams in a computational form that may be transferred across sessions, shared among collaborators, linked to external data sources, and searched against to identify relevant or matching information. VMEB captures not only generated graphical objects and their spatial relationships, but also the underlying biological meanings of those objects as defined by biologists. The biological meanings are translated into graphical rules that are saved to a rules base. With a set of rules, VMEB may then automatically identify and attach biological meaning to graphical objects and patterns as they are constructed if those objects and patterns match existing entries in the rules base. The collection of graphical rules constitutes an underlying visual language built upon emerging user-defined symbols and concepts. As such, the visual language dynamically evolves along with the biological theory under investigation.