The FALCON pipeline does not accept certain logical gate combinations

Currently, there is certain limitation on the assignment of logical gates in the FALCON framework. Namely, the assignment of logical gate(s) only accepts the same type of interaction. The assignment of combined activating and inhibiting interactions into a single logical gate e.g. “activating Input1 AND/OR inhibiting Input2” will lead to an error during the model building phase (FalconMakeModel).

Nevertheless, such arguments can be converted into the logical gate “Input1 AND/OR NOT Input2”. In the first case with the AND gate, the argument actually fits to the description of the master equation in the FALCON framework and users can simply assign the two interactions separately without specifying the AND logical gate. In the second case with the OR gate, users can transform the argument “Input1 OR NOT Input2” into “NOT (NOT Input1 AND Input2)”. The clause in the parenthesis can be assigned separately like the first case but the types of the interaction had to be reversed. Then, the users are required to assign an intermediate node e.g. “Temp” and assign it to the target node as an inhibitory interaction to reflect the NOT gate in the clause outside the parenthesis. These solutions are demonstrated in the figure below.