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()))
#------------------------------------------------------------------------------- # 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()))
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)
#------------------------------------------------------------------------------- # 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()))