tellurium.analysis package

Submodules

tellurium.analysis.annotations module

tellurium.analysis.bifurcation module

Utility classes for computing bifurcations.

tellurium.analysis.bifurcation.bifurcation(model, parameter, lowerBound, upperBound, maxPoints=5000, scanPositive=True)

Plot a bifurcation diagram.

Parameters:

• model – A path to an SBML or Antimony file, or raw SBML or Antimony string.
• parameter – The principal continuation parameter.
• lowerBound – The lower bound of the continuation.
• upperBound – The upper bound of the continuation.
• maxPoints – The maximum number of points.
• scanPositive – Scan from lower to upper bound (direction is reversed if false).

tellurium.analysis.bifurcation.plotBifurcation(model, parameter, lowerBound, upperBound, maxPoints=5000, scanPositive=True)

Plot a bifurcation diagram.

Parameters:

• model – A path to an SBML or Antimony file, or raw SBML or Antimony string.
• parameter – The principal continuation parameter.
• lowerBound – The lower bound of the continuation.
• upperBound – The upper bound of the continuation.
• maxPoints – The maximum number of points.
• scanPositive – Scan from lower to upper bound (direction is reversed if false).

tellurium.analysis.parameterestimation module

Parameter estimation in tellurium.

class tellurium.analysis.parameterestimation.ParameterEstimation(stochastic_simulation_model, bounds, data=None)

Bases: object

Parameter Estimation

run(func=None)

Allows the user to set the data from a File This data is to be compared with the simulated data in the process of parameter estimation

Args:

func: An Optional Variable with default value (None) which by default run differential evolution

which is from scipy function. Users can provide reference to their defined function as argument.

Returns:

The Value of the parameter(s) which are estimated by the function provided.

setDataFromFile(FILENAME, delimiter=', ', headers=True)

Allows the user to set the data from a File This data is to be compared with the simulated data in the process of parameter estimation

Args:

FILENAME: A Complete/relative readable Filename with proper permissions delimiter: An Optional variable with comma (“,”) as default value.

A delimiter with which the File is delimited by. It can be Comma (“,”) , Tab (” “) or anyother thing

headers: Another optional variable, with Boolean True as default value

If headers are not available in the File, it can be set to False

Returns:

None but sets class Variable data with the data provided

tellurium.analysis.parameterscan module

Utility classes for parameter scans.

class tellurium.analysis.parameterscan.ParameterScan(rr, startTime=0, endTime=20, numberOfPoints=50, polyNumber=10, startValue=None, endValue=None, value=None, independent=None, selection=None, dependent=None, integrator='cvode', color=None, width=2.5, alpha=0.7, title=None, xlabel='toSet', ylabel='toSet', zlabel='toSet', colormap='seismic', colorbar=True, antialias=True, sameColor=False, legend=True)

Bases: object

collect_plotArray_result()

collect_plotGraduatedArray_result()

collect_plotPolyArray_result()

colorCycle()

Adjusts contents of self.color as needed for plotting methods.

createColorPoints()

Sets self.color to a set of values that allow plotPolyArray, plotArray, or plotGraduatedArray to take on colors from a colormap. The colormap can either be user-defined using createColormap or one of the standard colormaps.

classmethod createColormap(color1, color2)

Creates a color map for plotSurface using two colors as RGB tuplets, standard color names, e.g. ‘aqua’; or hex strings.

p.colormap = p.createColorMap([0,0,0], [1,1,1])

plotArray()

Plots result of simulation with options for linewdith and line color.

p.plotArray()

plotArrayFunction(result)

plotGraduatedArray()

Plots array with either default multiple colors or user sepcified colors using results from graduatedSim().

p.plotGraduatedArray()

plotGraduatedArrayFunction(result)

plotMultiArray(param1, param1Range, param2, param2Range)

Plots separate arrays for each possible combination of the contents of param1range and param2range as an array of subplots. The ranges are lists of values that determine the initial conditions of each simulation.

p.multiArrayPlot(‘S1’, [1, 2, 3], ‘S2’, [1, 2])

plotPolyArray()

Plots results as individual graphs parallel to each other in 3D space using results from graduatedSim().

p.plotPolyArray()

plotPolyArrayFunction(result)

plotSurface()

Plots results of simulation as a colored surface. Takes three variables, two independent and one dependent. Legal colormap names can be found at http://matplotlib.org/examples/color/colormaps_reference.html.

p.plotSurface()

class tellurium.analysis.parameterscan.SteadyStateScan(rr, startTime=0, endTime=20, numberOfPoints=50, polyNumber=10, startValue=None, endValue=None, value=None, independent=None, selection=None, color=None, width=2.5, alpha=0.7, title=None, xlabel=None, ylabel=None, zlabel=None, colormap='seismic', colorbar=True, antialias=True, sameColor=False, legend=None)

Bases: object

collect_plotArray_result()

plotArray()

steadyStateSim()

tellurium.analysis.parameterscan.plot2DParameterScan(r, p1, p1Range, p2, p2Range, start=0, end=100, points=101)

Create a 2D Parameter scan and plot the results.

Parameters:

• r – RoadRunner instance
• p1 – id of first parameter
• p1Range – range of first parameter
• p2 – id of second parameter
• p2Range – range of second parameter

tellurium.analysis.sensitivityanalysis module

class tellurium.analysis.sensitivityanalysis.SensitivityAnalysis(model=None, sbml=False, conservedMoietyAnalysis=True)

Bases: object

allowLog

args

bounds

conservedMoietyAnalysis

filename

model

sbml

simulation

tellurium.analysis.simulator module

class tellurium.analysis.simulator.Simulator

get_computed_values()

pre_simulation(model_roadrunner)

push(key, value)

simulate_sensitivity(model_roadrunner)

tellurium.analysis.stochasticmodel module

class tellurium.analysis.stochasticmodel.StochasticSimulationModel(model=None, integrator='gillespie', seed=1234, variable_step_size=False, from_time=0, to_time=40, step_points=50)

Bases: object

from_time

integrator

model

seed

step_points

to_time

variable_step_size

tellurium.analysis.test module

Working

Module contents