def generateODEScript(modelfile,
mtype='ASM',
solver='RK4',
timestep=1,
endtime=21600,
lowerbound='0;0',
upperbound='1e-3;1e-3',
odefile='odescript.py'):
'''!
Function to generate Python ODE script from a given model
specification file.
Usage:
python astools.py genODE --modelfile=models/asm/glycolysis.modelspec --mtype=ASM --solver=RK4 --timestep=1 --endtime=21600 --lowerbound=0;0 --upperbound=1e-3;1e-3 --odefile=glycolysis.py
@param modelfile String: Name of model specification file in
models folder. This assumes that the model file is not in models
folder.
@param mtype String: Type of model specification file. Allowable
types are 'ASM' (AdvanceSyn Model Specification). Default = 'ASM'.
@param solver String: Type of solver to use. Allowable types
are 'Euler', 'Heun' (Runge-Kutta 2nd method or Trapezoidal),
'RK3' (third order Runge-Kutta), 'RK4' (fourth order
Runge-Kutta), 'RK38' (fourth order Runge-Kutta method, 3/8 rule),
'CK4' (fourth order Cash-Karp), 'CK5' (fifth order Cash-Karp),
'RKF4' (fourth order Runge-Kutta-Fehlberg), 'RKF5' (fifth
order Runge-Kutta-Fehlberg), 'DP4' (fourth order Dormand-Prince),
and 'DP5' (fifth order Dormand-Prince). Default = 'RK4'.
@param timestep Float: Time step interval for simulation.
Default = 1.0.
@param endtime Float: Time to end simulation - the simulation
will run from 0 to end time. Default = 21600.
@param lowerbound String: Define lower boundary of objects. For
example, "1;2" means that when the value of the object hits 1,
it will be bounced back to 2. Default = 0;0; that is, when the
value of the object goes to negative, it will be bounced back
to zero.
@param upperbound String: Define upper boundary of objects. For
example, "10;9" means that when the value of the object hits 1,
it will be pushed down to 9. Default = 1e-3;1e-3; that is, when
the value of the object above 1e-3, it will be pushed back to
1e-3.
@param odefile String: Python ODE script file to write out. This
file will be written into odescript folder. Default = odescript.py.
@return: A list containing the Python ODE script (one element =
one line).
'''
modelfile = os.path.abspath(modelfile)
(spec, modelobj) = modelReader(modelfile, mtype, 'extended')
datalist = ASModeller.generate_ODE(spec, modelobj, solver, timestep,
endtime, lowerbound, upperbound)
filepath = fileWriter(datalist, 'odescript', odefile)
return datalist
def generateODEScript(modelfile,
mtype='ASM',
solver='RK4',
timestep=1,
endtime=21600,
odefile='odescript.py'):
'''!
Function to generate Python ODE script from a given model
specification file.
Usage:
python astools.py genODE --modelfile=asm/glycolysis.modelspec --mtype=ASM --solver=RK4 --timestep=1 --endtime=21600 --odefile=glycolysis.py
@param modelfile String: Name of model specification file in
models folder. This assumes that the model file is in models
folder.
@param mtype String: Type of model specification file. Allowable
types are 'ASM' (AdvanceSyn Model Specification). Default = 'ASM'.
@param solver String: Type of solver to use. Allowable types
are 'Euler', 'Heun' (Runge-Kutta 2nd method or Trapezoidal),
'RK3' (third order Runge-Kutta), 'RK4' (fourth order
Runge-Kutta), 'RK38' (fourth order Runge-Kutta method, 3/8 rule),
'CK4' (fourth order Cash-Karp), 'CK5' (fifth order Cash-Karp),
'RKF4' (fourth order Runge-Kutta-Fehlberg), 'RKF5' (fifth
order Runge-Kutta-Fehlberg), 'DP4' (fourth order Dormand-Prince),
and 'DP5' (fifth order Dormand-Prince). Default = 'RK4'.
@param timestep Float: Time step interval for simulation.
Default = 1.0.
@param endtime Float: Time to end simulation - the simulation
will run from 0 to end time. Default = 21600.
@param odefile String: Python ODE script file to write out. This
file will be written into odescript folder. Default = odescript.py.
@return: A list containing the Python ODE script (one element =
one line).
'''
modelfile = 'models\\' + modelfile
(spec, modelobj) = modelReader(modelfile, mtype, 'extended')
datalist = ASModeller.generate_ODE(spec, modelobj, solver, timestep,
endtime)
filepath = fileWriter(datalist, 'odescript', odefile)
return datalist
def localSensitivity(modelfile, multiple=100, prefix='',
mtype='ASM', solver='RK4', timestep=1,
endtime=21600, cleanup=True,
outfmt='reduced', sampling=100,
resultfile='sensitivity_analysis.csv'):
'''!
Function to perform local sensitivity analysis using OFAT/OAT
(one factor at a time) method where the last data time (end
time) simulation results are recorded into results file.
Usage:
python astools.py LSA --modelfile=models/asm/glycolysis.modelspec --prefix=sen01 --mtype=ASM --multiple=100 --solver=RK4 --timestep=1 --endtime=21600 --cleanup=True --outfmt=reduced --resultfile=sensitivity_analysis.csv
@param modelfile String: Name of model specification file in
models folder. This assumes that the model file is not in models
folder.
@param multiple Integer: Multiples to change each variable value.
Default = 100 (which will multiple the original parameter value
by 100).
@param prefix String: A prefixing string for the set of new model
specification for identification purposes. Default = ''.
@param mtype String: Type of model specification file. Allowable
types are 'ASM' (AdvanceSyn Model Specification). Default = 'ASM'.
@param solver String: Type of solver to use. Allowable types
are 'Euler', 'Heun' (Runge-Kutta 2nd method or Trapezoidal),
'RK3' (third order Runge-Kutta), 'RK4' (fourth order
Runge-Kutta), 'RK38' (fourth order Runge-Kutta method, 3/8 rule),
'CK4' (fourth order Cash-Karp), 'CK5' (fifth order Cash-Karp),
'RKF4' (fourth order Runge-Kutta-Fehlberg), 'RKF5' (fifth
order Runge-Kutta-Fehlberg), 'DP4' (fourth order Dormand-Prince),
and 'DP5' (fifth order Dormand-Prince). Default = 'RK4'.
@param timestep Float: Time step interval for simulation.
Default = 1.0.
@param endtime Float: Time to end simulation - the simulation
will run from 0 to end time. Default = 21600.
@param cleanup String: Flag to determine whether to remove all
generated temporary models and ODE code files. Default = True.
@param outfmt String: Output format. Allowable types are 'reduced'
(only the final result will be saved into resultfile) and 'full'
(all data, depending on sampling, will be saved into resultfile).
@param sampling Integer: Sampling frequency. If 100, means only
every 100th simulation result will be written out. The first
(start) and last (end) result will always be written out.
Default = 100.
@param resultfile String: Relative or absolute file path to
write out sensitivity results. Default = 'sensitivity_analysis.csv'
'''
MSF = sensitivityGenerator(modelfile, multiple, prefix, mtype)
outfmt = str(outfmt).lower()
sampling = int(sampling)
resultfile = os.path.abspath(resultfile)
resultfile = open(resultfile, 'w')
header = False
msf_count = len(MSF)
model_count = 0
for param in MSF:
model_count = model_count + 1
# Generate ODE codes from model
(spec, modelobj) = modelReader(MSF[param]['ASM'],
mtype, 'extended')
print('Processing model %s of %s: %s' % \
(model_count, msf_count, MSF[param]['ASM']))
ODECode = ASModeller.generate_ODE(spec, modelobj, solver,
timestep, endtime)
odefile = re.sub('\.', '_', param)
filepath = fileWriter(ODECode, 'models/temp', odefile + '.py')
MSF[param]['ODE'] = filepath
# Simulate ODE codes
m = importlib.import_module('models.temp.'+ odefile)
if header == False:
labels = ['Parameter', 'Change'] + m.labels
resultfile.write(','.join(labels) + '\n')
header = True
simData = []
data_row_count = 0
for data in m.model:
if outfmt == "reduced":
simData = [str(x) for x in data]
elif outfmt == "full":
if (data_row_count % sampling) == 0:
simData.append([str(x) for x in data])
data_row_count = data_row_count + 1
MSF[param]['Data'] = simData
# Write out sensitivity results to resultfile
if outfmt == "reduced":
data = [param, MSF[param]['Change']] + MSF[param]['Data']
data = [str(x) for x in data]
resultfile.write(','.join(data) + '\n')
elif outfmt == "full":
for datarow in MSF[param]['Data']:
data = [param, MSF[param]['Change']] + datarow
data = [str(x) for x in data]
resultfile.write(','.join(data) + '\n')
resultfile.close()
if str(cleanup).upper() == 'TRUE':
for param in MSF:
ASMfile = MSF[param]['ASM']
ODEfile = MSF[param]['ODE']
os.remove(ASMfile)
os.remove(ODEfile)
def localSensitivity(modelfile,
multiple=100,
prefix='',
mtype='ASM',
solver='RK4',
timestep=1,
endtime=21600,
cleanup=True,
resultfile='sensitivity_analysis.csv'):
'''!
Function to perform local sensitivity analysis using OFAT/OAT
(one factor at a time) method where the last data time (end
time) simulation results are recorded into results file.
Usage:
python astools.py LSA --modelfile=asm/glycolysis.modelspec --prefix=sen01 --mtype=ASM --multiple=100 --solver=RK4 --timestep=1 --endtime=21600 --cleanup=True --resultfile=sensitivity_analysis.csv
@param modelfile String: Name of model specification file in
models folder.
@param multiple Integer: Multiples to change each variable value.
Default = 100 (which will multiple the original parameter value
by 100).
@param prefix String: A prefixing string for the set of new model
specification for identification purposes. Default = ''.
@param mtype String: Type of model specification file. Allowable
types are 'ASM' (AdvanceSyn Model Specification). Default = 'ASM'.
@param solver String: Type of solver to use. Allowable types
are 'Euler', 'Heun' (Runge-Kutta 2nd method or Trapezoidal),
'RK3' (third order Runge-Kutta), 'RK4' (fourth order
Runge-Kutta), 'RK38' (fourth order Runge-Kutta method, 3/8 rule),
'CK4' (fourth order Cash-Karp), 'CK5' (fifth order Cash-Karp),
'RKF4' (fourth order Runge-Kutta-Fehlberg), 'RKF5' (fifth
order Runge-Kutta-Fehlberg), 'DP4' (fourth order Dormand-Prince),
and 'DP5' (fifth order Dormand-Prince). Default = 'RK4'.
@param timestep Float: Time step interval for simulation.
Default = 1.0.
@param endtime Float: Time to end simulation - the simulation
will run from 0 to end time. Default = 21600.
@param cleanup String: Flag to determine whether to remove all
generated temporary models and ODE code files. Default = True.
@param resultfile String: Relative or absolute file path to
write out sensitivity results. Default = 'sensitivity_analysis.csv'
'''
MSF = sensitivityGenerator(modelfile, multiple, prefix, mtype)
for param in MSF:
# Generate ODE codes from model
(spec, modelobj) = modelReader(MSF[param]['ASM'], mtype, 'extended')
print('Processing model: %s' % MSF[param]['ASM'])
ODECode = ASModeller.generate_ODE(spec, modelobj, solver, timestep,
endtime)
odefile = re.sub('\.', '_', param)
filepath = fileWriter(ODECode, 'models/temp', odefile + '.py')
MSF[param]['ODE'] = filepath
# Simulate ODE codes
m = importlib.import_module('models.temp.' + odefile)
labels = [param, 'Change'] + m.labels
for data in m.model:
simData = [str(x) for x in data]
MSF[param]['Data'] = simData
resultfile = os.path.abspath(resultfile)
resultfile = open(resultfile, 'w')
resultfile.write(','.join(labels) + '\n')
for param in MSF:
data = [param, MSF[param]['Change']] + MSF[param]['Data']
data = [str(x) for x in data]
resultfile.write(','.join(data) + '\n')
resultfile.close()
if str(cleanup).upper() == 'TRUE':
for param in MSF:
ASMfile = MSF[param]['ASM']
ODEfile = MSF[param]['ODE']
os.remove(ASMfile)
os.remove(ODEfile)