Fig. 2

Qualitative Modeling Framework applied on a simple BRN. a BRN of Pseudomonas aeruginosa [16] shown as weighted directed graph by using Definition 1. The nodes/vertices represent genes whereas edges represent activation(s) and inhibition(s). The network comprises of two entities: x represents ALGU and y represents its inhibitor. b Experimental observations encoded as CTL (Computation Tree Logic) formula by using Definition 5. The formula describes a behavior in which the system exhibits normal and pathogenic responses (over-expression of gene X) in a single model that encodes two wet-lab observations is used for finding model parameters. c-a combination of logical parameters that satisfy CTL observations. d The dynamic model of the BRN is shown as a State Graph (see Definition 4). The state graph shows two important behaviors i.e. oscillation (homeostasis) as a cycle and a stable state (2,1) that represents a pathogenic behavior