Hierarchical graphs for rule-based modeling of biochemical systems

Background: In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Results: For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how h...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Nathan W. Lemons, Bin Hu, William S. Hlavacek
• Keywords: Artificial Intelligence, BMCBI 2011, Hierarchical Graphs, Regular Graphs, Vertex Attribute