Michael Blinov 

University of Connecticut Health Center

Title: Bringing rule-based modeling to VCell users
 
Abstract: We are implementing the rule-based approach into the VCell
modeling and simulation framework. By combining a reaction network
specified in the VCell editor (explicitly specifying individual species
and reactions) with multi-component species and rules of interactions, a
user is able to use rule-based specifications within the familiar “look
and feel” environment of the VCell reaction editor. The new VCell
interface includes dual views for a reaction network: a set of tables
describing all model elements, and a bipartite graph with species and
reaction nodes. Both views are extended to support rule-based features.