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Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

Figure 8

HPP performance analysis for the EGFR signaling model.

(A) peak memory usage (left: absolute, right: relative to NFsim); (B) CPU run time (left: absolute, right: relative to NFsim); (C) number of reaction events fired during a simulation (); (D) timecourses (means and 5–95% frequency envelopes; ) for activated Sos (top) and nuclear phosphorylated ERK (bottom). The slight deviation from linearity for ‘NF’ in (A) is an artifact of how memory is allocated in NFsim. Due to high computational expense, SSA statistics were not collected in (C) and (D).

doi: https://doi.org/10.1371/journal.pcbi.1003544.g008