cSimulator: C-implementation of simulatorT1.

Description

This is the simulator, inspired from BoolSimEngMKM in the Matlab CellNOpt, to be used on one time point simulations. Use the R interface provided by simulatorT1.

Usage

cSimulator(CNOlist, model, simList, indexList, mode=1)

Arguments

CNOlist

a CNOlist

model

a model that only contains the reactions to be evaluated

simList

a simList as created by prep4sim, that has also already been cut to contain only the reactions to be evaluated

indexList

an indexList as created by indexFinder

mode

switch to use the cSimualor for time 0 or 1

Value

This function outputs a single matrix of format similar to valueSignals in the CNOlist but that contains an output for each species in the model. This matrix is the simulated equivalent of valueSignals at time 1, if you consider only the columns given by indexSignals.

Details

Differences from the BoolSimEngMKM simulator include: the valueInhibitors has not been previously flipped; the function outputs the values across all conditions for all species in the model, instead of only for the signal species. This is because then the output of this function can be used as initial values for the version of the simulator that works on time point 2 (not implemented in this version).

If you would like to compute the output of a model that contains some of the gates in the model but not all, we suggest that you use the function SimulateT1 and specify in the bStringT1 argument which gates you want to be included. Indeed, SimulateT1 is a wrapper around simulatorT1 that takes care of cutting the model for you before simulating it.

References