pySTDLM.StandardReactionSystems Namespace Reference

Functions
def	addMinDESystem
	Adds the MinDE system in Ecoli as a standard reaction network. More...
def	addLacTwoStateSystem
	Adds the Lac switch reaction with two states of the DNA. More...
def	addPTSPathway
	Adds the Phosphoenolpyruvate-depenedent phosphotransferase reaction system. More...

Function Documentation

def pySTDLM.StandardReactionSystems.addLacTwoStateSystem	(		sim,
			inducerType = 'TMG'
	)

Adds the Lac switch reaction with two states of the DNA.

Reference: E. Roberts, A. Magis, J.O. Ortiz, W. Baumeister, Z. Luthey-Schulten. Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study. PLoS Comput. Bio. 7(3): 2011, e1002010.

Parameters

sim	A CMESimulation or RDMESimulation object with the "cytoplasm" region defined
sim	inducerType The type of inducer used for the switch, either TMG or IPTG

Returns

A pointer to the simulation object that was passed in

def pySTDLM.StandardReactionSystems.addMinDESystem

(

sim

)

Adds the MinDE system in Ecoli as a standard reaction network.

Reference:

Parameters

sim	A RDMESimulation object with the "cytoplasm" and "membrane" regions defined

Returns

A pointer to the simulation object that was passed in

def pySTDLM.StandardReactionSystems.addPTSPathway

(

sim

)

Adds the Phosphoenolpyruvate-depenedent phosphotransferase reaction system.

Reference: J.V. Rodriguez, J.A. Kaandorp, M. Dobrzynski, J.G. Blom Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinform. 22:15 (2006), pp. 1895-1901.

Parameters

sim	A RDMESimulation object with the "cytoplasm", "default" and "membrane" regions defined

Returns

A pointer to the simulation object that was passed in