def GetModel(numberOfGenes,
modelName,
folderPath,
Probabilities,
rSeed=0,
ParamRange=[],
MAX_TRIES=100,
InducedGenes=[]):
if len(InducedGenes) > 0:
for i in range(len(InducedGenes)):
InducedGenes[i] -= 1
if rSeed != 0:
np.random.seed(rSeed)
# Percent /= 100
tries = 0
antStr = ''
while tries < MAX_TRIES:
try:
Regulations, antStr = RandomGRN(numberOfGenes, Probabilities,
ParamRange, InducedGenes)
# print "AntString = ", antStr
r = te.loadAntimonyModel(antStr)
r.steadyState()
print('Success! A random GRN was generated after ' +
str(tries + 1) + ' tries')
Output(modelName, folderPath, rSeed, r, antStr, Regulations)
break
except:
tries = tries + 1
print "Failed to find steady state, generating a new GRN"
return antStr
def test_latex_export2(self):
"""Test latex export. """
temp_dir = tempfile.mkdtemp()
# export is writing files which have to be handeled in temp_dir
try:
tmp_f = tempfile.NamedTemporaryFile()
import tellurium as te
newModel = '''
$Xo -> S1; k1*Xo;
S1 -> S2; k2*S1;
S2 -> $X1; k3*S2;
Xo = 50; X1=0.0; S1 = 0; S2 = 0;
k1 = 0.2; k2 = 0.4; k3 = 2;
'''
rr = te.loadAntimonyModel(newModel)
result = rr.simulate(0, 30)
p = te.LatexExport(rr,
color=['blue', 'green'],
legend=['S1', 'S2'],
xlabel='Time',
ylabel='Concentration',
exportComplete=True,
saveto=temp_dir,
fileName='Model')
p.saveToOneFile(result)
# test that file was written
self.assertTrue(os.path.isfile(os.path.join(temp_dir, 'Model.txt')))
finally:
shutil.rmtree(temp_dir)
def test_latex_export2(self):
"""Test latex export. """
temp_dir = tempfile.mkdtemp()
# export is writing files which have to be handeled in temp_dir
try:
tmp_f = tempfile.NamedTemporaryFile()
import tellurium as te
newModel = '''
$Xo -> S1; k1*Xo;
S1 -> S2; k2*S1;
S2 -> $X1; k3*S2;
Xo = 50; X1=0.0; S1 = 0; S2 = 0;
k1 = 0.2; k2 = 0.4; k3 = 2;
'''
rr = te.loadAntimonyModel(newModel)
result = rr.simulate(0, 30)
p = te.LatexExport(rr,
color=['blue', 'green'],
legend=['S1', 'S2'],
xlabel='Time',
ylabel='Concentration',
exportComplete=True,
saveto=temp_dir,
fileName='Model')
p.saveToOneFile(result)
# test that file was written
self.assertTrue(os.path.isfile(os.path.join(temp_dir,
'Model.txt')))
finally:
shutil.rmtree(temp_dir)
def GetModel(genes, Probabilities, InitVals, Name):
tries = 0
while tries < 10:
try:
antStr = RandomGRN(genes, Probabilities, InitVals, {'Tra1': [10]})
r = te.loadAntimonyModel(antStr)
print r.steadyState()
break
except:
tries = tries + 1
print "Failed to find steady state"
return ((r, antStr))
def spark_sensitivity_analysis(model_with_parameters):
import tellurium as te
sa_model = model_with_parameters[0]
parameters = model_with_parameters[1]
class_name = importlib.import_module(sa_model.filename)
user_defined_simulator = getattr(class_name, dir(class_name)[0])
sa_model.simulation = user_defined_simulator()
if (sa_model.sbml):
model_roadrunner = te.loadAntimonyModel(
te.sbmlToAntimony(sa_model.model))
else:
model_roadrunner = te.loadAntimonyModel(sa_model.model)
model_roadrunner.conservedMoietyAnalysis = sa_model.conservedMoietyAnalysis
#Running PreSimulation
model_roadrunner = sa_model.simulation.presimulator(model_roadrunner)
#Running Analysis
computations = {}
model_roadrunner = sa_model.simulation.simulator(
model_roadrunner, computations)
_analysis = [None, None]
#Setting the Parameter Variables
_analysis[0] = {}
for i_param, param_names in enumerate(sa_model.bounds.keys()):
_analysis[0][param_names] = parameters[i_param]
setattr(model_roadrunner, param_names, parameters[i_param])
_analysis[1] = computations
return _analysis
def __init__(self, n_times, real_time):
ContinuousSimulation.__init__(self, n_times=n_times,
u_tracks_from_knots=self.step_u_tracks,
real_time=real_time,
output_vars=['OCT4', 'SOX2', 'NANOG',
'OCT4_SOX2', 'Protein'],
u_type="step")
file_name = \
get_file_name('biomodels/oct4_reversible_0203_template.ant')
with open(file_name, 'r') as myfile:
data = myfile.read()
r = te.loadAntimonyModel(data)
self.model_str = r.getCurrentAntimony()
def spark_sensitivity_analysis(model_with_parameters):
import tellurium as te
sa_model = model_with_parameters[0]
parameters = model_with_parameters[1]
class_name = importlib.import_module(sa_model.filename)
user_defined_simulator = getattr(class_name, dir(class_name)[0])
sa_model.simulation = user_defined_simulator()
if(sa_model.sbml):
model_roadrunner = te.loadAntimonyModel(te.sbmlToAntimony(sa_model.model))
else:
model_roadrunner = te.loadAntimonyModel(sa_model.model)
model_roadrunner.conservedMoietyAnalysis = sa_model.conservedMoietyAnalysis
#Running PreSimulation
model_roadrunner = sa_model.simulation.presimulator(model_roadrunner)
#Running Analysis
computations = {}
model_roadrunner = sa_model.simulation.simulator(model_roadrunner,computations)
_analysis = [None,None]
#Setting the Parameter Variables
_analysis[0] = {}
for i_param,param_names in enumerate(sa_model.bounds.keys()):
_analysis[0][param_names] = parameters[i_param]
setattr(model_roadrunner, param_names, parameters[i_param])
_analysis[1] = computations
return _analysis
def GetModel(tries,numGenes,regProb, InitParams, Name):
print 'Model simulation tries = ' + str(tries)
#Set Lists and Empty Dictionaries
Interactions = ["SingleAct", "SingleRep", "and", "or", "Nand", "Nor", "Counter"]
GRN = {'Rate': [], 'mRNA':[], 'Prot': [],'PDeg':[],'mDeg': [],'Leak': [],'Vm':[], 'a_p':[], 'DualDissoc':[], 'Dissoc':[], 'HillCoeff': []}
GRNInt = {'TF':[],'TFs':[]}
#Perturbation = {'TRa1':[10]}
StringList=[]
modelCreationTries = 0
while modelCreationTries < 3:
try:
ModelInitNames(GRN)
print 'ModelInitNames done.'
AssignRegulation(numGenes,GRN,GRNInt,Interactions)
print 'AssignRegulation done.'
DetermineInteractors(GRN,GRNInt,regProb)
print 'DetermineInteractors done.'
ChooseProtein(GRNInt)
print 'ChooseProtein done.'
Rates = GetReactionRates(GRN,GRNInt)
print 'GetReactionRates done.'
GetReactions(GRN,StringList,Rates)
print 'GetReactions done.'
ValueGeneration(InitParams,StringList)
#GetEvents(Perturbation,StringList)
print 'ValueGeneration done.'
antStr = GetModelString(StringList)
print('Loading model into Antimony...\n')
#print StringList
except Exception as error:
print "Something went wrong when constructing Model (GetModel method)!"
ErrorPrinting(error)
return(0,0,0)
try:
model = te.loadAntimonyModel(antStr)
print('Success!')
break
except:
modelCreationTries = modelCreationTries + 1
print "Failed to load model code into Antimony."
if antStr == '':
return(0,StringList.join('This is a pre-loaded string into Antimony that failed.\n'),GRN)
return(0,antStr,GRNInt)
return (model, antStr,GRNInt)
# -*- coding: utf-8 -*-
"""
Created on Wed May 30 16:39:36 2018
@author: Joshua Ip - Work
"""
import tellurium as te
import numpy as np
import CIDmodelAdvanced as model
r = te.loadAntimonyModel(antimonyString);
r.integrator = 'gillespie';/
r.integrator.seed = 1234;
r.integrator.variable_step_size = False;
# selections specifies the output variables in a simulation
selections = ['time'] + r.getBoundarySpeciesIds() + r.getFloatingSpeciesIds()
numberOfOutputs = len(selections)
timesToSimulate = 10;
pointsToSimulate = 101;
sumOfSimulations = np.zeros(shape = [pointsToSimulate, numberOfOutputs])
for k in range(timesToSimulate):
r.resetToOrigin()
currentSim = r.simulate(0, 24, pointsToSimulate, selections)
# we record the sum of the simulations to calculate the average later
sumOfSimulations += currentSim
def run_model2(antStr,
noiseLevel,
species_type,
species_nums,
timepoints,
exportData=False,
input_conc=1,
perturbs=[],
perbParam=[.20, .50],
bioTap='',
save_path=os.getcwd(),
filename="results",
showTimePlots=False,
seed=0,
runAttempts=5):
"""Checks if Antimony models will reach steady-state, generates visualizations, and exports data.
Arguments
antStr = antimony string for the given model
noiseLevel = (float) level of noise as a decimal. Ex: 0.05 = 5%
species_type = 'P' for protein, or 'M' for mRNA
species_nums = The gene numbers for associated to the species you are interested in.
i.e. species_type = 'P' and species_nums =[1,2,3,4] will return the data for P1, P2, P3, and P4
timepoints = specifies length and resolution of simulation/experimental data -> [max time value, resolution (i.e. stepsize)]:
exportData = whether or not to include additional files in the output. These files include the antimony string and the SBML Model
NOTE: should probably stay at FALSE for student usage
input_conc = what the value INPUT should be set to before running model
perturbs = Perturbations to apply -> [(perturbation type, [target1, target2, ...]), (<next perturbation)>)]
i.e. perturbs =[ ("UP", [1, 2, ...]), ("DOWN", [4,5,6])]
perbParam = For Up/down regulation, this specifies the min/max amount you want to change regulation -> perbParm = (min percent change, max percent change)
i.e. perbParam = (0.20, 0.50) specifies that you want the up/down regulation to change transcription between 20 and 50 percent.
NOTE: percents are chosen uniformally between the min and max
bioTap: (str) If this is not empty, a csv file to use for BioTapestry will be exported.
save_path = directory to save output folder to
filename = file to save the experimental data to
showTimePlots: whether or not to output timeplots of the data (as png) in the output file
seed: random number generator seed
runAttempts: number of attempts to load/run model before exiting and suggesting to rebuild the model
Outputs:
model: roadrunner model for the full working GRN
result: experimental data without noise
resultNoisy: experimental data with noise
"""
# Attempt to execute run_model up to runAttempts times with different generated models.
for retry in range(runAttempts):
# Load the Antimony string as a model
try:
model = te.loadAntimonyModel(antStr)
print('Successfully loaded in Antimony string as a model.')
except Exception as error:
ErrorPrinting(error)
raise RuntimeError(
"Failed to load antimony string due to parsing error. Check that your antStr is correct."
)
# Check that the model reaches steady-state. If the model has any issues running, it will raise an Exception. The user should run get_model again.
plt.close('all')
model.resetToOrigin()
tStep = int(math.ceil(timepoints[0] / timepoints[1]))
try:
model.steadyState()
except Exception:
try:
model.conservedMoietyAnalysis = True
model.steadyState()
except Exception as error:
print(
"Failed to reach steady-state or there is an Integrator error. Check your model or run get_model again."
)
ErrorPrinting(error)
raise error
model.resetToOrigin()
#Specify input
model.INPUT = input_conc
# set seed
if seed != 0:
np.random.seed(seed)
if len(perturbs) > 0:
#specify perturbations
for next_type, targets in perturbs:
for gene in targets:
currVm = eval("model.Vm" + str(gene))
if next_type == 'UP':
newVm = currVm + np.random.uniform(
perbParam[0] * currVm, perbParam[1] * currVm)
exec("model.Vm" + str(gene) + " = " + str(newVm))
elif next_type == 'DOWN':
newVm = currVm - np.random.uniform(
perbParam[0] * currVm, perbParam[1] * currVm)
exec("model.Vm" + str(gene) + " = " + str(newVm))
elif next_type == 'KO':
exec("model.L" + str(gene) + " = 0")
exec('model.Vm' + str(gene) + ' = 0')
exec('model.d_mRNA' + str(gene) + ' = 0')
exec('model.d_protein' + str(gene) + ' = 0')
exec('model.mRNA' + str(gene) + ' = 1E-9')
exec('model.P' + str(gene) + ' = 1E-9')
#change initVals to 1E-9 instead of 0 to prevent possible solver hanging bug
else:
raise ValueError(
"Perturbation type is not recognized; expected UP, DOWN, or KO"
)
# Run a simulation for time-course data
if species_type == 'P':
selections = ["P" + str(i) for i in species_nums]
elif species_type == 'M':
selections = ["mRNA" + str(i) for i in species_nums]
else:
raise ValueError(
"Output data type not recognized (must be P or M)")
selections = ['time'] + selections
result = model.simulate(0,
timepoints[0],
tStep + 1,
selections=selections)
model_name = model.getInfo().split("'modelName' : ")[1].split("\n")[0]
# Specify (and make if necessary) a folder to save outputs to
filesPath = save_path + "/experimental_data_" + model_name + '/'
if os.path.exists(filesPath) == False:
os.mkdir(filesPath)
print('\nFolder created: ' + filesPath)
# Create results with artificial noise
noise = np.random.normal(1, noiseLevel, size=result.shape)
noise[:, 0] = 1 # we dont want there to be noise in the time
resultNoisy = np.multiply(result, noise)
# Create graphs
if showTimePlots == True:
data = {
next_name: resultNoisy[:, i]
for i, next_name in enumerate(selections)
}
df = pd.DataFrame.from_dict(data)
df.set_index('time', inplace=True)
df.plot()
plt.title("Noisy Data")
plt.xlabel("time")
plt.savefig(filesPath + 'Simulation_Noisy_Plot2.png', dpi=400)
# do not want to give students the clean data
#data = {next_name:result[:,i] for i,next_name in enumerate(selections)}
#df = pd.DataFrame.from_dict(data)
#df.set_index('time', inplace=True)
#df.plot()
#plt.title("Normal Data")
#plt.xlabel("time")
#plt.savefig(filesPath + 'Simulation_Clean_Plot2.png', dpi=400)
plt.show()
# Export datasets
Output(exportData, model, seed, result, noiseLevel, resultNoisy,
filesPath, antStr, bioTap, selections, filename)
#returns the model, and result and/or resultNoisy arrays
return (model, result, resultNoisy)
raise RuntimeError('Could not create a working model for ' +
str(runAttempts) + ' tries.')
def RunModel(numberOfGenes, modelName, filePath, rSeed, NLevel, tMax, Steps, DataExport, ModelString ='', ExternalModel = ''):
if ModelString =='' and os.path.isfile(ExternalModel):
AntImport = open(ExternalModel, 'r')
ModelString = AntImport.read()
if rSeed != 0:
np.random.seed (rSeed)
NLevel /= 100
# Values = {'M':[InitVals[0]], 'P':[InitVals[1]],'Dp':[InitVals[2]],'Dm':[InitVals[3]],'L':[InitVals[4]],'TRa':[InitVals[5]], 'TRb':[InitVals[6]],'Kd':[InitVals[7]], 'K':[InitVals[8]], 'H': [InitVals[9]]}
# InitParams = [0,0,0.5,0.9,0.8,30,30,0.2,0.5,1]
r = te.loadAntimonyModel(ModelString)
# Regulations,r,antStr = Syn.GetModel(numberOfGenes, InitProb, InitParams)
tries = 0
while tries < 10:
try:
plt.close('all')
r.reset()
result = r.simulate(0,tMax, Steps)
NoisyResult = np.zeros([len(result[:,0]), len(result[0,:])])
if numberOfGenes<11:
vars = {'P':[],'M':[]}
for e in vars.keys():
plt.figure(1)
for k in np.arange(1,numberOfGenes+1):
vars[e].append(e + str(k))
tStep = int(math.ceil(tMax)/20)
if tMax < 20:
tStep = int(math.ceil(tMax)/(tMax/2))
tRange = np.arange(0,(int(math.ceil(tMax)))+ tStep,tStep)
if e=='P':
plt.subplot(2,1,1)
plt.title('Protein Vs. Time', fontsize=8)
plt.grid(color='k', linestyle='-', linewidth=.4)
plt.ylabel('count',fontsize=6)
plt.yticks(fontsize=6)
if tMax > 999:
plt.loglog(result[:,0],result[:,(k-1)+1], label = vars[e][k-1])
plt.xticks(fontsize=6)
else:
plt.semilogy(result[:,0],result[:,(k-1)+1], label = vars[e][k-1])
plt.xticks(tRange, fontsize=6)
plt.xlim(0,tMax)
plt.legend(loc='upper right', bbox_to_anchor=(1.13, 1.035), fontsize=6)
else:
plt.subplot(2,1,2)
plt.title('mRNA Vs. Time', fontsize=8)
plt.grid(color='k', linestyle='-', linewidth=.4)
plt.xlabel('time(s)',fontsize=6)
plt.ylabel('count',fontsize=6)
plt.yticks(fontsize=6)
if tMax > 999:
plt.loglog(result[:,0],result[:,(k-1)+numberOfGenes+1], label = vars[e][k-1])
plt.xticks(fontsize=6)
else:
plt.semilogy(result[:,0],result[:,(k-1)+numberOfGenes+1], label = vars[e][k-1])
plt.xticks(tRange, fontsize=6)
plt.xlim(0,tMax)
plt.legend(vars[e],loc='upper right', bbox_to_anchor=(1.13, 1.035), fontsize=6)
manager = plt.get_current_fig_manager()
manager.window.showMaximized()
plt.savefig(filePath + modelName + ' Simulation Plot.png', dpi=400)
plt.close('all')
if NLevel != 0:
for k in range(len(result[:,0])):
for i in range(len(result[0])):
if i == 0:
NoisyResult[k,i] = result[k,i]
else:
CurrVal = -1
while CurrVal < 0:
CurrVal = result[k,i] + np.random.normal(0,NLevel*result[k,i])
NoisyResult[k,i] = CurrVal
if numberOfGenes<11:
for e in vars.keys():
plt.figure(2)
for k in np.arange(1,numberOfGenes+1):
vars[e].append(e + str(k))
if e=='P':
plt.subplot(2,1,1)
plt.title('Protein Vs. Time (Noisy)', fontsize=8)
plt.grid(color='k', linestyle='-', linewidth=.4)
plt.ylabel('count',fontsize=6)
plt.yticks(fontsize=6)
plt.legend(vars[e])
if tMax > 999:
plt.loglog(NoisyResult[:,0],NoisyResult[:,(k-1)+1], label = vars[e][k-1])
plt.xticks(fontsize=6)
else:
plt.semilogy(NoisyResult[:,0],NoisyResult[:,(k-1)+1], label = vars[e][k-1])
plt.xticks(tRange, fontsize=6)
plt.xlim(0,tMax)
plt.legend(loc='upper right', bbox_to_anchor=(1.13, 1.035), fontsize=6)
else:
plt.subplot(2,1,2)
plt.title('mRNA Vs. Time (Noisy)', fontsize=8)
plt.grid(color='k', linestyle='-', linewidth=.4)
plt.yticks(fontsize=6)
plt.xlabel('time(s)',fontsize=6)
plt.ylabel('count',fontsize=6)
plt.legend(vars[e])
if tMax > 999:
plt.loglog(NoisyResult[:,0],NoisyResult[:,(k-1)+numberOfGenes+1], label = vars[e][k-1])
plt.xticks(fontsize=6)
else:
plt.semilogy(NoisyResult[:,0],NoisyResult[:,(k-1)+numberOfGenes+1], label = vars[e][k-1])
plt.xticks(tRange, fontsize=6)
plt.xlim(0,tMax)
plt.legend(loc='upper right', bbox_to_anchor=(1.13, 1.035), fontsize=6)
manager = plt.get_current_fig_manager()
manager.window.showMaximized()
plt.savefig(filePath + modelName + ' Noisy Simulation Plot.png', dpi=400)
plt.close('all')
break
except:
tries = tries + 1
print "Failed to simulate your model, generating a new GRN."
if tries ==10:
print('Sorry you network was not able to be simulated, please try again, or read the documentation')
Output(DataExport, modelName, r, result, NLevel, NoisyResult, filePath)
timePoints = [
1.0, 2.0, 3.0
] #zu welchen Zeitpunkten soll die Konfiguration gespeichert werden?
tStart = 0 #Start- und Endzeit der Simulation
tEnd = 3.01
doplot = True #plotten?
plotlegend = True #Legende plotten?
verbose = 2 #Verbose level: 0 = garnicht, 1 = Statistik 1x je outerLoop, 2 = Statistik nach jedem N, 3 = +Schleifenzaehler (Haengt sich die Simulation auf?)
Nscale = 100
#Produkt der naechsten 3 Variablen ist die Anzahl der insg. simulierten Pfade
outerLoop = 1 #Anzahl Wiederholungen festlegen (multipliziert sich mit AnzahlPfade zur Anzahl der simulierten Pfade je N)
Nrange = range(
3
) #Bereich von N festlegen. range(5) == 0,1,2,3,4. Daher Multiplikator N = (N+1)*Nscale
AnzahlPfade = 40 #Anzahl Wiederholungen festlegen (multipliziert sich mit outerLoop). Fuer schoene Plots hier Wert 40-100. Fuer grosse N: doplot=False, hier 1, dafuer bei outerLoop gewuenschte Werte eintragen.
r = te.loadAntimonyModel(
antStr) #Modell laden, kann auch URL sein z.B. von www.biomodels.net
r.setIntegrator(
'gillespie') #Integrator auswaehlen. Andere unterstuetzen z.B. ODEs
r.getIntegrator().setValue(
'variable_step_size', True
) #Parameter fuer Integrator setzen, anderer Integrator unterstuetzt andere Parameter
Config.setValue(Config.MAX_OUTPUT_ROWS, pow(
10, 7)) #bei 64-bit pow(10,11) oder weniger bei wenig Arbeitsspeicher
#----------------------------
Reactions = 0
start_time = time.time()
selectToSave = ['N'] + selectToPlot
form = (1, len(selectToSave))
r.selections = selectToSave
simuliertePfade = 0
PfadeGesamt = outerLoop * AnzahlPfade * len(Nrange)
def test_loadAntimonyModel_file(self):
r = te.loadAntimonyModel(self.ant_file)
self.assertIsNotNone(r)
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 11 15:06:33 2014
@author: mgaldzic
"""
import tellurium as te
from roadrunner import Config
Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, True)
model = '''
model pathway()
$Xo -> S1; k1*Xo - k2*S1
S1 -> S2; k3*S2
S2 -> $X1; k4*S2
Xo = 1; X1 = 0
S1 = 0; S2 = 0
k1 = 0.1; k2 = 0.56
k3 = 1.2; k4 = 0.9
end
'''
r = te.loadAntimonyModel(model)
# Compute the steady state
r.getSteadyStateValues()
Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, False)
print "S1 =", r.S1, ", S2 =", r.S2
""" Created on Thu Feb 27 18:56:59 2014 @author: mgaldzic """ import tellurium as te import roadrunner import libantimony antStr = ''' model feedback() // Reactions: J0: $X0 -> S1; (VM1 * (X0 - S1/Keq1))/(1 + X0 + S1 + S4^h); J1: S1 -> S2; (10 * S1 - 2 * S2) / (1 + S1 + S2); J2: S2 -> S3; (10 * S2 - 2 * S3) / (1 + S2 + S3); J3: S3 -> S4; (10 * S3 - 2 * S4) / (1 + S3 + S4); J4: S4 -> $X1; (V4 * S4) / (KS4 + S4); // Species initializations: S1 = 0; S2 = 0; S3 = 0; S4 = 0; X0 = 10; X1 = 0; // Variable initialization: VM1 = 10; Keq1 = 10; h = 10; V4 = 2.5; KS4 = 0.5; end''' rr = te.loadAntimonyModel(antStr) result = rr.simulate(0, 40, 500) rr.plot(rr, result)
def test_loadAntimonyModel_str(self):
r = te.loadAntimonyModel(self.ant_str)
self.assertIsNotNone(r)
# -*- coding: utf-8 -*-
"""
Setting boundary species in a model
"""
from __future__ import print_function
import tellurium as te
model = '''
model cell()
# The $ character is used to indicate that a particular species is FIXED
$S1 -> S2; k1*S1
S2 -> S3; k2*S2 - k3*S3
S3 -> $S4; Vm*S3/(Km + S3)
# Initialize values
S1 = 1.0; S2 = 0; S3 = 0; S4 = 0.0
k1 = 0.2; k2 = 0.67; k3 = 0.04
Vm = 5.6; Km = 0.5
end
'''
r = te.loadAntimonyModel(model)
result = r.simulate(0, 50, 201)
r.plot(result)
eV=0.00018; ////////////////// Initial Conditions ///////////////////// E = 5.0*10^5; // Uninfected epithelial cells Ev = 10.0; // Virus-infected epithelial cells V = 1000.0; // Da = 0.0; // Infected-activated dendtritic cells in Tissue Dm = 0.0; // Migrated dendritic cells in Lymph Tc = 1.0; // Effector cytotoxic T-cells in Lymph Tct = 0.0; // Effector cytotoxic T-cells in Tissue Th1 = 1.0; // Type I helper T-cells Th2 = 1.0; // Type II helper T-cells B = 1.0; // Activated B-cells pSs = 0.0; // SP-RBD-specific Short-living plasma cells pLs = 0.0; // SP-RBD-specific Long-living plasma cells pSn = 0.0; // NP-specific Short-living plasma cells pLn = 0.0; // NP-specific Long-living plasma cells sIgM = 0.0; // SP-RBD-specific IgM sIgG = 0.0; // SP-RBD-specific IgG nIgM = 0.0; // NP-specific IgM nIgG = 0.0; // NP-specific IgG ''' rr = te.loadAntimonyModel(model_string) n = rr.simulate(0, 30, 10000, ['time', 'Tc', 'Tct', 'Da', 'Dm']) rr.plot()
r.k_off_anchor_binder = r.K_d_dimerization_binder * r.k_on_dimerization_binder
arrayOfRates = r.simulate(0, secondsToSimulate, secondsToSimulate / 30 + timeshiftToStopWeirdODEIntegratorErrors)
measuredReporter = np.amax(column(arrayOfRates, 16))
if debug:
print(" Molecule added: " + str(r.MoleculeAdded))
print(" Measured reporter of: " + str(measuredReporter))
r.plot(show = False)
#input("Press Enter to continue...")
return measuredReporter;
except:
if debug:
print("Threw CVODE error! Attempting timeshift of " + str(timeshiftToStopWeirdODEIntegratorErrors + 1))
continue;
raise RuntimeError('Unable to resolve ODE integrator errors despite timeshift of 20 steps')
r = te.loadAntimonyModel(model.antimonyString);
# This is the range of anchor and dimerization binder binding affinities we will scan through
ancArray = np.arange(-12.0, -5.0, 1.00)
dimArray = np.arange(-9.0, -3.0, 1.00)
# These parameters inform how the simulation is run each time
SECONDS_TO_SIMULATE = 14 * 60 * 60 # 14 hours
PERCENT_CHANGE_PER_STEP = 0.03
INITIAL_MOLECULE_ADDED = 0.0001
# If DEBUG is True, the script outputs some debug information to the console. A lot of debug information.
# It also plots the curve, but that's not really working right. One thing to fix.
DEBUG = True
def test_loadAntimonyModel_str(self):
r = te.loadAntimonyModel(self.ant_str)
self.assertIsNotNone(r)
import tellurium as te
newModel = """
$Xo -> S1; k1*Xo;
S1 -> S2; k2*S1;
S2 -> $X1; k3*S2;
Xo = 50; S1 = 0; S2 = 0;
k1 = 0.2; k2 = 0.4; k3 = 2;
"""
rr = te.loadAntimonyModel(newModel)
result = rr.simulate(0, 30)
p = te.Export.export(rr)
p.color = ["blue", "green"]
p.legend = ["S1", "S2"]
p.xlabel = "Time"
p.ylabel = "Concentration"
p.exportComplete = True
p.location = "./"
p.filename = "newModel"
p.saveToFile(result)
p.getString()
import tellurium as te
# convert to eliminate rate rules
model = te.loadAntimonyModel(te.sbmlToAntimony('huang-ferrell-96.xml'))
model.conservedMoietyAnalysis = True
print(model.steadyStateNamedArray())
# need to pre-simulate to converge in COPASI's solution
model.simulate(0,1000,5000)
# the output variable is PP_K (which represents doubly phosphorylated MAPK)
# parameter 2: r1b_k2 (original: MAPKKK activation.k1)
fig1a_local = model.getCC('PP_K', 'r1b_k2')
print('Figure 1A: local value = {}'.format(fig1a_local))
# parameter 5: r8a_a8 (original: binding MAPK—Pase and P-MAPK.k1)
fig1b_local = model.getCC('PP_K', 'r8a_a8')
print('Figure 1B: local value = {}'.format(fig1b_local))
# parameter 7: r10a_a10 (original: binding MAPK—Pase and PP—MAPK.k1)
fig1c_local = model.getCC('PP_K', 'r10a_a10')
print('Figure 1C: local value = {}'.format(fig1c_local))
k2 = 0.018
k3 = 1.6
A = 5.
AE = 0.
E = 3.
B = 0.
"""
"""
# Create exact results
result = opt.model.simulate(0,15,300)
result = np.asarray([[y for y in x] for x in result])
entities = [x.replace('[','').replace(']','') for x in opt.model.selections]
opt.model.plot()
print('{}\t{}\t{}\t{}\t'.format(*entities))
for i in range(len(result)):
print('{}\t{}\t{}\t{}\t'.format(*result[i]))
"""
opt = Optimization(model=te.loadAntimonyModel(soe))
opt.LoadMeasurements('data2.txt')
opt.CreateParameterMap()
#opt.FixParameter('k1')
#m = opt.CreateRandomMember()
opt.Run()
print('\n')
for k in opt.parameter_map:
print('{}={}'.format(k,opt.model.__getattr__(k)))
def run_model(antStr,noiseLevel,inputData=None,genesToExport=None,perturb=None,exportData=None,bioTap='',
savePath='results',fileName = '',showTimePlots=False,seed=0,drawModel=None):
"""
Checks if Antimony models will reach steady-state, generates visualizations, and exports data.
Arguments:
antStr (str) :
- The Antimony model.
noiseLevel (float):
- level of noise as a decimal. Ex: `0.05` = 5%
inputData (list: [inputVal,maxTime,resolution]) :
- **inputVal** (float) : The initial concentration of the input species (name in model: INPUT). Default: 1
- **maxTime** (int) : Duration of minutes to simulate model. Default: 100
- **resolution** (int) : The resolution of datapoints. Eg: If resolution = 5, the data will include data every 5 minutes. Default: 1
perturb (list: [pertSpecies, pertType, mean, stdev]) :
- **pertSpecies** (int list) : Which species to perturb, if perturbation is necessary. Default: 0
- The following are parameters needed for perturbation of species. They are **optional** inputs.
You can just supply pertSpecies, or pertSpecies and pertType, and the rest will use default parameters.
- **pertType** (str) : either `UP` or `DOWN` or `KO` used as a flag for upregulation, repression, or knockout, respectively. Default: 'UP'
- **mean** (int list) [mean,accuracy]: The mean value used in `np.random.normal` to generate a random perturbation, along with an accuracy value (in ##%) Default: [35,15]
- **stdev** (float) : The stdev value used in `np.random.normal` to generate a random pertrubation. Default: 4
genesToExport (list: [genesToExport,speciesType]) :
- **genesToExport** (int list): Which genes you want to export. Pass in [0] to export all proteins or mRNA. Default: [0]
- **speciesType** (str) : `P`rotein or `M`rNA. Default: 'P'
exportData (list: [sbml, antimony]) :
- **antimony** (bool) : This is a flag for the export of the Antimony model as a txt. Default:True
- **sbml** (bool) : This is a flag for the export of the model in SBML format (version based on Tellurium). Default:False
bioTap (str):
- If this is not empty, a csv file to use for BioTapestry will be exported. Default: ''
savePath (str):
- All output files will be saved to `current_working_directory\savePath\modelName\` . Default: 'results'
fileName (str):
- A name that will prefix all filenames generated by the script. Default: Name of model taken from antStr
showTimePlots (bool):
- Flag for if you want plots to be generated and saved. Default: False
seed (int):
- Seed for reproducibility purposes when generating random data. Default: 0
drawModel (bool):
- Generates a graph with PyGraphViz. Requires pygraphviz and graphviz installed Default: False
Outputs:
- model (model object): Roadrunner instance of the model.
- result (np.array): Numpy matrix of the result data
- resultNoisy (np.array): Numpy matrix of the result data (Noisy)
"""
# Creating default lists
if inputData is None:
inputData = [1,100,1]
if exportData is None:
exportData = [True,False]
if drawModel is None:
drawModel = [False,'fdp']
if genesToExport is None:
genesToExport = [[0],'P']
if perturb is None:
perturb = [0]
if len(perturb) == 1:
perturb = [perturb,'UP',[0,0],0]
if len(perturb) == 2:
perturb = [perturb, [35,15], 4]
#error catching
if genesToExport[1] not in ['P','M']:
raise ValueError("Output data type not recognized (must be P or M)")
# Load the Antimony string as a model
try:
model = te.loadAntimonyModel(antStr)
print('Successfully loaded in Antimony string as a model.')
except Exception as error:
ErrorPrinting(error)
raise RuntimeError("Failed to load antimony string due to parsing error. Check that your antStr is correct.")
# Check that the model reaches steady-state. If the model has any issues running, it will raise an Exception.
# If an exception is reached, the user should run get_model again.
plt.close('all')
model.resetToOrigin()
tStep = int(math.ceil(inputData[1]/inputData[2]))
try:
model.steadyState()
except Exception:
try:
model.conservedMoietyAnalysis = True
model.steadyState()
except Exception as error:
print ("Failed to reach steady-state or there is an Integrator error. Check your model or run get_model again.")
ErrorPrinting(error)
raise error
# reset model
model.resetToOrigin()
# specify input
model.INPUT = inputData[0];
# specify perturbations
if perturb != 0 and not 0 in perturb[0]: #i.e. not wild-type
pertSpecies = perturb[0]
pertType = perturb[1]
mean = perturb[2]
stdev = perturb[3]
for species in pertSpecies:
if pertType == 'KO':
exec('model.Vm' + str(species) + ' = 0') in locals(), globals()
exec('model.d_mRNA' + str(species) + ' = 0') in locals(), globals()
exec('model.d_protein' + str(species) + ' = 0') in locals(), globals()
exec('model.mRNA' + str(species) + ' = 1E-9') in locals(), globals()
exec('model.P' + str(species) + ' = 1E-9') in locals(), globals()
exec('model.L' + str(species) + ' = 0') in locals(), globals()
#change initVals to 1E-9 instead of 0 to prevent possible solver hanging bug
else:
currVm = eval('model.Vm' + str(species))
randPert = mean[0]
if mean[1]!=0:
randPert = np.random.normal(mean[0],stdev)
while mean[0] - mean[1] > randPert or randPert > mean[0] + mean[1]:
randPert = np.random.normal(mean[0],stdev)
while randPert >= 0:
randPert = np.random.normal(mean[0],stdev)
randPert /= 100.0
if pertType == 'UP':
newVal = currVm * (1 + randPert)
exec('model.Vm' + str(species) + ' = ' + str(newVal)) in locals(), globals()
if pertType == 'DOWN':
newVal = currVm * (1 - randPert)
exec('model.Vm' + str(species) + ' = ' + str(newVal)) in locals(), globals()
# Construct the selection arguments for simulation
exportSpecies = genesToExport[0]
species_type = genesToExport[1]
if exportSpecies==0:
allGenes = int((model.getNumFloatingSpecies() - 1)/2)
if species_type == 'P':
selections = ["P" + str(i+1) for i in range(allGenes)]
elif species_type == 'M':
selections = ["mRNA" + str(i+1) for i in range(allGenes)]
else:
if species_type == 'P':
selections = ["P" + str(i) for i in exportSpecies]
elif species_type == 'M':
selections = ["mRNA" + str(i) for i in exportSpecies]
selections = ['time'] + selections
# Run a simulation for time-course data
result = model.simulate(0,inputData[1],tStep+1,selections=selections)
# Retrieve model name
if fileName == '':
fileName = model.getInfo().split("'modelName' : ")[1].split("\n")[0]
# Specify (and make if necessary) a folder to save outputs to
folderPath = Path(os.getcwd()) / savePath
if not os.path.exists(folderPath):
os.mkdir(folderPath)
print('\nFolder created: ' + folderPath.name)
#fileName = fileName + '_'
# Create results with artificial noise
if noiseLevel != '0':
resultNoisy = np.zeros([len(result[:,0]), len(result[0,:])])
for k in range(len(result[:,0])):
for i in range(len(result[0])):
if i == 0:
resultNoisy[k,i] = result[k,i]
else:
CurrVal = -1
while CurrVal < 0:
CurrVal = result[k,i] + np.random.normal(0,noiseLevel*result[k,i])
resultNoisy[k,i] = CurrVal
# Export datasets
Output(exportData,model,seed,selections,result,noiseLevel,resultNoisy, folderPath, fileName, antStr,bioTap)
# Create graphs
if showTimePlots:
data = {next_name:resultNoisy[:,i] for i,next_name in enumerate(selections)}
df = pd.DataFrame.from_dict(data)
df.set_index('time', inplace=True)
df.plot()
plt.title("Noisy Data")
plt.xlabel("time")
plt.savefig(folderPath / (fileName +'_Simulation_Noisy_Plot.png'), dpi=400)
data = {next_name:result[:,i] for i,next_name in enumerate(selections)}
df = pd.DataFrame.from_dict(data)
df.set_index('time', inplace=True)
df.plot()
plt.title("Clean Data")
plt.xlabel("time")
plt.savefig(folderPath / (fileName +'_Simulation_Plot.png'), dpi=400)
# Draw the model (requires pygraphviz module)
if drawModel[0]:
try:
imp.find_module('pygraphviz')
model.draw(layout=str(drawModel[1]))
except ImportError:
print('pygraphviz is not installed!')
#returns the model, and result and/or resultNoisy arrays
return(model,result,resultNoisy)
from __future__ import print_function
import tellurium as te
# Load an antimony model
ant_model = '''
S1 -> S2; k1*S1;
S2 -> S3; k2*S2;
k1= 0.1; k2 = 0.2;
S1 = 10; S2 = 0; S3 = 0;
'''
# At the most basic level one can load the SBML model directly using libRoadRunner
print('--- load roadrunner ---')
import roadrunner
# convert to SBML model
sbml_model = te.antimonyToSBML(ant_model)
r = roadrunner.RoadRunner(sbml_model)
result = r.simulate(0, 10, 100)
r.plot(result)
# The method loada is simply a shortcut to loadAntimonyModel
print('--- load tellurium ---')
r = te.loada(ant_model)
result = r.simulate(0, 10, 100)
r.plot(result)
# same like
r = te.loadAntimonyModel(ant_model)
# In[2]:
import seaborn as sns
sns.set_style("ticks")
import matplotlib.gridspec as gridspec
import FigureTools as FT
def apply_param_dict_to_model(model, param_dict):
for param in param_dict.keys():
if param_dict[
param] is not None: # do not change parameters marked with value==None.
#print param_dict[param]
model[param] = param_dict[param]
return model
volume_and_hog_model = te.loadAntimonyModel("volume_and_hog.txt")
volume_model = te.loadAntimonyModel("volume_reference_radius.txt")
volume_and_hog_model.integrator.relative_tolerance = 1e-10
volume_model.integrator.relative_tolerance = 1e-10
volume_and_hog_model_species = [
'time', 'vol_V_tot_fl', '[hog_Glyc_in]', '[vol_c_i]', 'hog_Glyc_in',
'vol_c_i', 'hog_totalHog1PP', 'hog_n_totalHog1', 'hog_Hog1PPn',
'hog_Hog1PPc', 'hog_Hog1n', 'hog_Hog1c', '[hog_Hog1PPn]', '[hog_Hog1PPc]',
'[hog_Hog1n]', '[hog_Hog1c]', 'vol_pi_t', 'vol_pi_i'
]
volume_model_species = [
'time', 'V_tot_fl', 'V_ref', 'r_os', 'r_b', '[c_e]', '[c_i]', 'c_i',
'pi_t', 'pi_i'
]
def test_loadAntimonyModel_file(self):
r = te.loadAntimonyModel(self.ant_file)
self.assertIsNotNone(r)
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 05 12:28:35 2018
@author: Yoshi
"""
import os
import tellurium as te
import matplotlib.pyplot as plt
import numpy as np
np.set_printoptions(linewidth=160)
#%% Visualize the models used in DREAM7
r = te.loadAntimonyModel(
'C:\Users\Yoshi\Documents\GitHub\DREAM-work\model1_0\model_without_parameters\model1_antimony.txt'
)
r.draw()
import tellurium as te
cell = '''
$Xo -> S1; vo;
S1 -> S2; k1*S1 - k2*S2;
S2 -> $X1; k3*S2;
vo = 1
k1 = 2; k2 = 0; k3 = 3;
'''
rr = te.loadAntimonyModel(cell)
p = te.ParameterScan.ParameterScan(rr)
p.endTime = 3
p.colormap = p.createColormap([.86,.08,.23], [.12,.56,1])
p.createColorPoints()
p.plotSurface()
ant_model = '''
S1 -> S2; k1*S1;
S2 -> S3; k2*S2;
k1= 0.1; k2 = 0.2;
S1 = 10; S2 = 0; S3 = 0;
'''
# At the most basic level one can load the SBML model directly using libRoadRunner
print('--- load roadrunner ---')
import roadrunner
# convert to SBML model
sbml_model = te.antimonyToSBML(ant_model)
r = roadrunner.RoadRunner(sbml_model)
result = r.simulate(0, 10, 100)
r.plot(result)
# The method loada is simply a shortcut to loadAntimonyModel
print('--- load tellurium ---')
r = te.loada(ant_model)
result = r.simulate (0, 10, 100)
r.plot(result)
# same like
r = te.loadAntimonyModel(ant_model)
# In[2]:
