BNMPy.booleanNetwork

class BNMPy.booleanNetwork.BooleanNetwork(numberOfNodes, linkages, functions, initialNodeValues=None, outputFilePath='', nodeDict=None, equations=None)[source]

Boolean network object…

Methods

buildK()

This rebuilds the K array.

knockout(key, value)

Sets a specific node to be permanently fixed to a given value.

setInitialValue(key, value)

Sets a particular node to a given initial value, where the key is indexed in nodeDict.

setInitialValues(initialNodeValues)

Sets the initial values of the boolean network.

undoKnockouts()

Undoes all knockouts.

updateUntilAttractorIsReached(giveUpIterations)

update_noise(p[, iterations])

update_one()

Asynchronous update: Update one random non-constant node for one step.

getBias

getMaxConnectivity

getMeanConnectivity

getRealization

getTrajectory

initializeOutput

stateToWrite

toGraph

update

writeNetworkHistory
buildK()[source]

This rebuilds the K array.

getBias()[source]
getMaxConnectivity()[source]
getMeanConnectivity()[source]
getRealization()[source]
getTrajectory()[source]
initializeOutput()[source]
knockout(key, value)[source]

Sets a specific node to be permanently fixed to a given value.

setInitialValue(key, value)[source]

Sets a particular node to a given initial value, where the key is indexed in nodeDict.

setInitialValues(initialNodeValues)[source]

Sets the initial values of the boolean network.

stateToWrite()[source]
toGraph()[source]
undoKnockouts()[source]

Undoes all knockouts. Does not change initial values, however.

update(iterations=1)[source]
updateUntilAttractorIsReached(giveUpIterations)[source]
update_noise(p, iterations=1)[source]
update_one()[source]

Asynchronous update: Update one random non-constant node for one step.

This method randomly selects one non-constant node and updates only that node based on its Boolean function, while keeping all other nodes unchanged. This simulates asynchronous dynamics where nodes update at different times.

writeNetworkHistory()[source]
BNMPy.booleanNetwork.getDataFromFile(filepath, startIndex=0, invert=False)[source]
BNMPy.booleanNetwork.getParametersFromFile(numberOfNodes, linkagesFilePath, functionsFilePath, initialNodesFilePath)[source]
BNMPy.booleanNetwork.getRandomInitialNodeValues(numberOfNodes)[source]
BNMPy.booleanNetwork.getRandomParameters(numberOfNodes, connectivity, isConstantConnectivity=True, bias=0.5)[source]