GINsim provides the functionality context (if not empty) of each circuit.
The functionality context of the positive auto-regulatory circuit is defined by ERK = 0.
The functionality context of the negative circuit corresponds to IKK = 1 (which is the case when TNFα is 1).
Similarly, the simulation of ERK ectopic expression, disrupting the functionality context of ph auto-regulation, leads to the loss of the multi-stability when EGF = 0.
The functionality context of each feedback loop in the logical model was identified on the basis of the logical model with the JAVA tool GINsim 2.4 alpha[ 84].
The (sole) positive circuit of the network encompasses CDK2CycE, RB1 and E2F and has a functionality context in which the system cannot be maintained.
The functionality context of a feedback loop is defined as a set of constraints on the values of the external regulators of that loop [ 83].
Noteworthy, if p16INK4a is maintained at a positive level (1 or 2), this functionality context is stable when DSB=SSB = 0 and indeed, there is multi-stability under this stress condition, with two stable states differing by their values of the circuit members.
Lastly, as genes can be associated with GO terms reflecting different functionalities which indicates their participation in several functional contexts, we suggest Individual Coverage (IC) as a quantity which measures how well the functionalities of the individual genes are covered.
Overheads can include node discovery, context aware functionalities (context gathering, maintenance and distribution), cluster functionalities (cluster formation, cluster maintenance, etc).
