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pyLM
v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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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... | |
def pySTDLM.StandardReactionSystems.addLacTwoStateSystem | ( | sim, | |
inducerType = 'TMG' |
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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.
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 |
def pySTDLM.StandardReactionSystems.addMinDESystem | ( | sim | ) |
Adds the MinDE system in Ecoli as a standard reaction network.
Reference:
sim | A RDMESimulation object with the "cytoplasm" and "membrane" regions defined |
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.
sim | A RDMESimulation object with the "cytoplasm", "default" and "membrane" regions defined |