pySTDLM.StandardReactionSystems Namespace Reference

Functions
	addMinDESystem (sim)
	addLacTwoStateSystem (sim, inducerType='TMG')
	addPTSPathway (sim)

Function Documentation

addLacTwoStateSystem()

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

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.

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

Returns:
    A pointer to the simulation object that was passed in

addMinDESystem()

pySTDLM.StandardReactionSystems.addMinDESystem

(

sim

)

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

Args:
    sim:
        A RDMESimulation object with the "cytoplasm" and "membrane" regions defined
Returns:
    A pointer to the simulation object that was passed in

addPTSPathway()

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.

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

Returns:
    A pointer to the simulation object that was passed in