title: Modeling for (physical) biologists: an introduction to the rule-based approach.
abstract: Models that capture the chemical kinetics of cellular regulatory networks can be specified in terms of rules for biomolecular interactions. A rule defines a generalized reaction, meaning a reaction that permits multiple reactants, each capable of participating in a characteristic transformation and each possessing certain, specified properties, which may be local, such as the state of a particular site or domain of a protein. In other words, a rule defines a transformation and the properties that reactants must possess to participate in the transformation. A rule also provides a rate law. A rule-based approach to modeling enables consideration of mechanistic details at the level of functional sites of biomolecules and provides a facile and visual means for constructing computational models, which can be analyzed to study how system-level behaviors emerge from component interactions.
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA. Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Lily A
authors.initials: LA
authors.lastname: Chylek
authors.forename: Leonard A
authors.initials: LA
authors.lastname: Harris
authors.forename: James R
authors.initials: JR
authors.lastname: Faeder
authors.forename: William S
authors.initials: WS
authors.lastname: Hlavacek
mesh_terms: D019295:Computational Biology; D008954:Models, Biological; D008956:Models, Chemical; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins