Exemple #1
0
def bifurcation(model,
                parameter,
                lowerBound,
                upperBound,
                maxPoints=5000,
                scanPositive=True):
    '''Plot a bifurcation diagram.

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

    if isinstance(model, RoadRunner):
        sbml = model.getSBML()
    elif os.path.exists(model) and os.path.isfile(model):
        # it's a file path
        if os.path.splitext(model)[1] == '.sb':
            # it's an Antimony file
            with open(model) as f:
                sbml = antimonyConverter.antimonyToSBML(f.read())
        elif os.path.splitext(model)[1] == '.txt':
            raise RuntimeError(
                'File ending in ".txt" is ambiguous - pass an SBML file (.xml) or an Antimony file (.sb).'
            )
        else:
            with open(model) as f:
                sbml = f.read()
    else:
        # check if it's Antimony source
        try:
            sbml = antimonyConverter.antimonyToSBML(model)
        except:
            # it better be SBML
            import tesbml as libsbml
            # this will throw if it's not SBML
            libsbml.readSBML(model)

    auto = Plugin('tel_auto2000')

    # Set SBML source
    auto.setProperty('SBML', sbml)

    # Set parameters
    auto.setProperty('ScanDirection',
                     'Positive' if scanPositive else 'Negative')
    auto.setProperty('PrincipalContinuationParameter', parameter)
    auto.setProperty('PCPLowerBound', lowerBound)
    auto.setProperty('PCPUpperBound', upperBound)

    # Set maximum numberof points
    auto.setProperty('NMX', maxPoints)

    # execute the plugin
    auto.execute()

    # plot Bifurcation diagram
    pts = auto.BifurcationPoints
    lbls = auto.BifurcationLabels
    biData = auto.BifurcationData
    return pts, lbls, biData
#-------------------------------------------------------------------------------
# Purpose: Example demonstrating how to setup and use the TestModel plugin
# This example also shows how to plot data and how to view a plugins
# embedded manual
#
# Authors: Totte Karlsson ([email protected]), J Kyle Medley
#-------------------------------------------------------------------------------
from rrplugins import Plugin

modelPlugin = Plugin("tel_test_model")

#Test model plugin depends on the add_noise plugin
noisePlugin = Plugin("tel_add_noise")

#Generate internal test data
modelPlugin.execute()
test_data = modelPlugin.TestData
test_data_with_noise = modelPlugin.TestDataWithNoise

test_data.plot()
test_data_with_noise.plot()

#modelPlugin.viewManual()
print('Plugin version: {}'.format(modelPlugin.getVersion()))
Exemple #3
0
#-------------------------------------------------------------------------------
# Purpose: Example demonstrating how to setup the add noise pluging and
# add noise to simulated data
#
# Authors: Totte Karlsson ([email protected]), J Kyle Medley
#-------------------------------------------------------------------------------
from rrplugins import Plugin

modelPlugin = Plugin("tel_test_model")        
noisePlugin = Plugin("tel_add_noise")

#Generate internal test data
modelPlugin.execute()
test_data = modelPlugin.TestData
    
test_data.plot()
# Assign the dataseries to the plugin inputdata
noisePlugin.InputData = test_data

# Set parameter for the 'size' of the noise
noisePlugin.Sigma = 8.e-6

# Add the noise
noisePlugin.execute()

# Get the data to plot
noisePlugin.InputData.plot()            

#noisePlugin.viewManual()
print('Plugin version: {}'.format(noisePlugin.getVersion()))
Exemple #4
0
def run_auto(pars, r, direction='Positive'):

    if pars:
        for k in pars:
            r[k] = pars[k]

    auto = Plugin("tel_auto2000")
    # Setup properties
    auto.setProperty("SBML", r.getCurrentSBML())
    auto.setProperty("ScanDirection", direction)
    auto.setProperty("PrincipalContinuationParameter", "mu")
    auto.setProperty("PreSimulation", "True")
    auto.setProperty("PreSimulationDuration", 30)
    auto.setProperty("RL0", 0)
    auto.setProperty("RL1", 2.5)
    auto.setProperty("NMX", 10000)
    #auto.setProperty("NDIM", 15)
    auto.setProperty("NPR", 2)
    auto.setProperty("KeepTempFiles", True)
    auto.setProperty("DS", 0.001)
    auto.setProperty("DSMIN", 0.0001)
    auto.setProperty("DSMAX", 0.1)

    auto.execute()
    pts1 = auto.BifurcationPoints

    if 1:
        lbl1 = auto.BifurcationLabels
        biData1 = auto.BifurcationData
        biData1.plotBifurcationDiagram(pts1, lbl1)
Exemple #5
0
#-------------------------------------------------------------------------------
# Purpose: Example demonstrating how to setup and use the TestModel plugin
# This example also shows how to plot data and how to view a plugins 
# embedded manual 
#
# Authors: Totte Karlsson ([email protected]), J Kyle Medley
#-------------------------------------------------------------------------------
from rrplugins import Plugin

modelPlugin = Plugin("tel_test_model")            

#Test model plugin depends on the add_noise plugin
noisePlugin = Plugin("tel_add_noise")

#Generate internal test data
modelPlugin.execute()
test_data = modelPlugin.TestData
test_data_with_noise = modelPlugin.TestDataWithNoise
    
test_data.plot()
test_data_with_noise.plot()
    
#modelPlugin.viewManual()   
print('Plugin version: {}'.format(modelPlugin.getVersion()))