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BMCBI
2011

Hierarchical graphs for rule-based modeling of biochemical systems

10 years 6 months ago
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...
Nathan W. Lemons, Bin Hu, William S. Hlavacek
Added 12 May 2011
Updated 12 May 2011
Type Journal
Year 2011
Where BMCBI
Authors Nathan W. Lemons, Bin Hu, William S. Hlavacek
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