def spark_work(model_with_parameters):
import tellurium as te
if(antimony == "antimony"):
model_roadrunner = te.loada(model_with_parameters[0])
else:
model_roadrunner = te.loadSBMLModel(model_with_parameters[0])
parameter_scan_initilisation = te.ParameterScan(model_roadrunner,**model_with_parameters[1])
simulator = getattr(parameter_scan_initilisation, function_name)
return(simulator())
"""
Create a colormap.
"""
from __future__ import print_function, division
import tellurium as te
model = '''
$Xo -> S1; vo;
S1 -> S2; k1*S1 - k2*S2;
S2 -> $X1; k3*S2;
vo = 1
k1 = 2; k2 = 0; k3 = 3;
'''
# load model
rr = te.loada(model)
# perform parameter scan
colormap = te.ParameterScan.createColormap([.86, .08, .23], [.12, .56, 1])
p = te.ParameterScan(rr, endTime=3, colormap=colormap)
p.createColorPoints()
p.plotSurface()
"""
Plot array.
"""
from __future__ import print_function, division
import tellurium as te
model = '''
$Xo -> S1; vo;
S1 -> S2; k1*S1 - k2*S2;
S2 -> $X1; k3*S2;
vo = 1
k1 = 2; k2 = 0; k3 = 3;
'''
rr = te.loada(model)
p = te.ParameterScan(rr,
startTime=0,
endTime=20,
numberOfPoints=50,
width=2,
xlabel='Time',
ylabel='Concentration',
title='Cell')
p.plotArray()
as a surface plot.
"""
import tellurium as te
model = '''
$Xo -> S1; vo;
S1 -> S2; k1*S1 - k2*S2;
S2 -> $X1; k3*S2;
vo = 1
k1 = 2; k2 = 0; k3 = 3;
Xo = 0; S1 = 0; S2 = 0; X1 = 0;
'''
rr = te.loada(model)
p = te.ParameterScan(rr)
p.startTime = 0
p.endTime = 6
p.numberOfPoints = 50
p.startValue = 1
p.endValue = 5
p.independent = ["Time", "k1"]
p.dependent = "S1"
p.xlabel = "Time"
p.ylabel = r"$k_{1}$"
p.zlabel = r"$S_{1}$"
p.plotSurface()
k1 = 0.9;
k2 = 0.3;
k3 = 0.7;
x = 0;
''')
# parameter scan
p = te.ParameterScan(
r,
# settings
startTime=0,
endTime=15,
numberOfPoints=50,
polyNumber=10,
endValue=1.8,
alpha=0.8,
value="x",
selection="x",
color=[
'#0F0F3D', '#141452', '#1A1A66', '#1F1F7A', '#24248F', '#2929A3',
'#2E2EB8', '#3333CC', '#4747D1', '#5C5CD6'
])
# plot
p.plotPolyArray()
# In[2]:
r = te.loada('''
$Xo -> S1; vo;
S1 -> S2; k1*S1 - k2*S2;