simulatorT1: Simulation of a boolean model
In CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description Usage Arguments Details Value Author(s) References See Also Examples

This is the simulator, inspired from BoolSimEngMKM in the Matlab CellNOpt, to be used on one time point simulations

1	simulatorT1(CNOlist, model, simList, indexList, mode=1)

`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

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.

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.

C. Terfve

J. Saez-Rodriguez, L. G. Alexopoulos, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger. Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction, Molecular Systems Biology, 5:331, 2009.
M. K. Morris, J. Saez-Rodriguez, D. Clarke, P. K. Sorger, D. A. Lauffenburger. Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli, PLoS Comp. Biol., 7(3): e1001099, 2011.

simulateTN, cutAndPlotResultsT1

#This computes the output of the full model, which is normally not done on a stand alone basis, but if you have a model and would like to visualise its output compared to your data, then this is what you should do

data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")

indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE)
ToyFields4Sim<-prep4sim(ToyModel)

Sim<-simulatorT1(
	CNOlist=CNOlistToy,
	model=ToyModel,
	simList=ToyFields4Sim,
	indexList=indicesToy)

Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: hash
hash-3.0.1 provided by Decision Patterns

Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

[1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun"
[1] "The following species are stimulated: EGF, TNFa"
[1] "The following species are inhibited: Raf, PI3K"