Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
Figure 1
Basic workflow of the HPP simulation method.
Given a rule-based model and a user-specified set of population-mapping rules (which define the population species), partial network expansion (PNE) is performed to generate a hybrid version of the original model. The hybrid model is then passed to a population-adapted network-free simulator (e.g., NFsim 1.11), which generates the time-evolution trajectories for all observable quantities specified in the original model.