Rule-Based Modelling of Cellular Signalling

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Bio-PEPA: A framework for the modelling and analysis of biological systems (2009, background): “A few applications have been completed, as reported in [28].”
Quantitative and logic modelling of gene and molecular networks (2015, methodology): “Entity relationships are thus a perfect graphical representation for rule-based models (44,45).”
Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data (2009, positive): “However, thorough treatment of interactions among 13 ligands, 4 ErbB receptors and 8–12 adapters will require both conceptual and technical advances in modeling reaction networks (Hlavacek, 2003; Danos et al , 2007).”
Rule-based modeling of biochemical systems with BioNetGen. (2009, background): “A recent model of EGFR signaling by Danos et al. ( 27 ) provides an example.”
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim (2011, background): “Rule-based modeling offers a promising approach to combinatorial complexity and coarse-grained simulatio”