pySTDLM.StandardReactionSystems#

Functions

addLacTwoStateSystem(sim[, inducerType])

Lac switch reaction with two states of the DNA.

addMinDESystem(sim)

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

addPTSPathway(sim)

Adds the Phosphoenolpyruvate-depenedent phosphotransferase reaction system.

getReactionString(rct, prd, rate)

setLMLogConsole([level])

Set the logger to write to the console as the code is working

setLMLogFile(filename[, level])

Set up file handler to print log to file

setLMLoggerLevel(level)

Set the level of the logger for the application

visualizeRDMEInitialConditions(sim)

Visualize the RDME simulation volume inside Jupyter.

writeTable(columnNames, rows)

Classes

CMESimulation([volume, name])

A constructor for the CMESimulation

IntRDMESimulation(dimensions, spacing[, ...])

RDMERegion(name)

A class that represents a type region of an RDME simulation.

RDMESimulation(dimensions, spacing[, name, ...])

A class that contains all regions, reactions, diffusions and rules for a RDME simulation

tqdm(*_, **__)

Decorate an iterable object, returning an iterator which acts exactly like the original iterable, but prints a dynamically updating progressbar every time a value is requested.
pySTDLM.StandardReactionSystems.addLacTwoStateSystem(sim, inducerType='TMG')[source]#

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

  • inducerType – The type of inducer used for the switch, either TMG or IPTG

Returns:

A pointer to the simulation object that was passed in

pySTDLM.StandardReactionSystems.addMinDESystem(sim)[source]#

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

Parameters:

sim – A RDMESimulation object with the “cytoplasm” and “membrane” regions defined

Returns:

A pointer to the simulation object that was passed in

pySTDLM.StandardReactionSystems.addPTSPathway(sim)[source]#

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