예제 #1
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파일: datatools.py 프로젝트: LoLab-VU/anrm 
    def conditions_list(self, data_list):
        condnames = {}
        for d in data_list:
            condnames[d.con_name] = d.initials

        conditions = {k: ct.initial_conditions(v.keys(), v.values(), self.ic_params)
                for k, v in condnames.items()}
        return condnames, conditions
예제 #2
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from anrm.irvin_anrm_bid_experiment_3 import model

#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0,10000,100) #24hrs converted to seconds (1000 timepoints)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-4
sims.atol = 1e-8

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params  = model.parameters_initial_conditions()
conditions = ct.initial_conditions([], [], ic_params)
ysim = solve.simulate(position = None, observables=True, initial_conc = conditions)

yout = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL'])

PARP_MLKL_signals   = yout
td_PARP = ct.calculate_time_delay(PARP_MLKL_signals[:,0], sims.tspan)
td_MLKL = ct.calculate_time_delay(PARP_MLKL_signals[:,1], sims.tspan)
print td_PARP, td_MLKL

p.ion()
p.plot(sims.tspan, yout[:,0], label = 'Cleaved Parp')
p.plot(sims.tspan, yout[:,1], label = 'MLKL')

p.xlabel('time [sec]')
p.ylabel('PARP and MLKL concentration [molecules per cell]')
예제 #3
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import calibratortools as ct
import simulator_1_0 as sim

from pysb.integrate  import odesolve
from anrm.irvin_anrm_bid_experiment_0 import model 

#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0,86400,1000) #24hrs converted to seconds (1000 timepoints)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-3
sims.atol = 1e-6

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params  = model.parameters_initial_conditions()
conditions = ct.initial_conditions(['Bak_0', 'Bax_0', 'Bid_0'], [0, 0, 0], ic_params)
ysim = solve.simulate(position = None, observables=True, initial_conc = conditions)

yout = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL'])

p.ion()
p.plot(sims.tspan, yout[:,0], label = 'Cleaved Parp')
p.plot(sims.tspan, yout[:,1], label = 'MLKL')

p.xlabel('time [sec]')
p.ylabel('PARP and MLKL concentration [molecules per cell]')
p.legend()
예제 #4
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from pysb.integrate  import odesolve

#-----------Calibrated Parameters-----------------------
position = pickle.load(open('CompII_Hypthesis_123_addeddata_4run_v41_Position.pkl'))

#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0,20000,1000)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-3
sims.atol = 1e-6

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params  = model.parameters_initial_conditions()
conditions = ct.initial_conditions(['Bak_0', 'Bax_0', 'Bid_0', 'zVad_0'], [0.2e5, 40165, 0, 0], ic_params)
#20uM zVad == 9.6e6 zVad per cell for a cell volume of 8e-13m3
ysim = solve.simulate(position, observables=True, initial_conc = conditions)

yout = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL','Obs_TNFa','Obs_NFkB', 'ComplexI','ComplexI_ub', 'ComplexI_TRAF', 'TRADD_RIP1', 'TRADD_RIP1_2','Obs_FADD_Sole', 'ComplexII','Bid_Trunc', 'Bid_PO4','Obs_RIP1', 'RIP1_Trunc', 'RIP3_Trunc', 'Necrosome','Obs_proC8', 'Obs_C8', 'Obs_C3ub', 'Obs_C3', 'Obs_pC3', 'RIP1_FADD','Obs_cPARP', 'Obs_PARP', 'Obs_MLKL','Obs_CytoC'])

p.ion()
p.plot(sims.tspan, yout[:,0], label = 'Cleaved Parp')
p.plot(sims.tspan, yout[:,1], label = 'MLKL')

p.xlabel('time [sec]')
p.ylabel('PARP and MLKL concentration [molecules per cell]')
p.legend()
예제 #5
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#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0, 10000,
                         100)  #24hrs converted to seconds (1000 timepoints)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-4
sims.atol = 1e-8

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params = model.parameters_initial_conditions()
conditions = ct.initial_conditions([], [], ic_params)
ysim = solve.simulate(position=None, observables=True, initial_conc=conditions)

yout = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL'])

PARP_MLKL_signals = yout
td_PARP = ct.calculate_time_delay(PARP_MLKL_signals[:, 0], sims.tspan)
td_MLKL = ct.calculate_time_delay(PARP_MLKL_signals[:, 1], sims.tspan)
print td_PARP, td_MLKL

p.ion()
p.plot(sims.tspan, yout[:, 0], label='Cleaved Parp')
p.plot(sims.tspan, yout[:, 1], label='MLKL')

p.xlabel('time [sec]')
p.ylabel('PARP and MLKL concentration [molecules per cell]')
예제 #6
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    open('CompII_Hypthesis_123_addeddata_4run_v23_Position.pkl'))

#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0, 20000, 1000)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-3
sims.atol = 1e-6

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params = model.parameters_initial_conditions()
conditions = ct.initial_conditions(['Bak_0', 'Bax_0', 'Bid_0', 'zVad_0'],
                                   [0.2e5, 40165, 12044, 9.6e6], ic_params)
#20uM zVad == 9.6e6 zVad per cell for a cell volume of 8e-13m3
ysim = solve.simulate(position, observables=True, initial_conc=conditions)

yout = ct.extract_records(ysim, [
    'Obs_cPARP', 'Obs_MLKL', 'Obs_TNFa', 'Obs_NFkB', 'ComplexI', 'ComplexI_ub',
    'ComplexI_TRAF', 'TRADD_RIP1', 'TRADD_RIP1_2', 'Obs_FADD_Sole',
    'ComplexII', 'Bid_Trunc', 'Bid_PO4', 'Obs_RIP1', 'RIP1_Trunc',
    'RIP3_Trunc', 'Necrosome', 'Obs_proC8', 'Obs_C8', 'Obs_C3ub', 'Obs_C3',
    'Obs_pC3', 'RIP1_FADD', 'Obs_cPARP', 'Obs_PARP', 'Obs_MLKL', 'Obs_CytoC'
])

p.ion()
p.plot(sims.tspan, yout[:, 0], label='Cleaved Parp')
p.plot(sims.tspan, yout[:, 1], label='MLKL')
예제 #7
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from pysb.integrate import odesolve
from anrm.irvin_anrm_bid_experiment_0 import model

#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0, 86400,
                         1000)  #24hrs converted to seconds (1000 timepoints)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-3
sims.atol = 1e-6

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params = model.parameters_initial_conditions()
conditions = ct.initial_conditions(['Bak_0', 'Bax_0', 'Bid_0'], [0, 0, 0],
                                   ic_params)
ysim = solve.simulate(position=None, observables=True, initial_conc=conditions)

yout = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL'])

p.ion()
p.plot(sims.tspan, yout[:, 0], label='Cleaved Parp')
p.plot(sims.tspan, yout[:, 1], label='MLKL')

p.xlabel('time [sec]')
p.ylabel('PARP and MLKL concentration [molecules per cell]')
p.legend()
예제 #8
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solve = sim.Solver(sims)
solve.run()

delta_td = []
apopt_td = []
necro_td = []

condition_variable = 'RIP1_0'
graph_name = 'RIP1'
rangecv = range_RIP1

for i in rangecv:
    #-----------Initial Conditions--------------------------
    ic_params  = model.parameters_initial_conditions()
    conditions = ct.initial_conditions([condition_variable], [i], ic_params)
    ysim = solve.simulate(position = position, observables=True, initial_conc = conditions)

    #-----------Calculate Time Delays-----------------------
    PARP_MLKL_signals   = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL'])
    td_PARP = ct.calculate_time_delay(PARP_MLKL_signals[:,0], sims.tspan)
    td_MLKL = ct.calculate_time_delay(PARP_MLKL_signals[:,1], sims.tspan)

    #-----------Time Delay vs. procaspase 8-----------------
    if (td_PARP is not None) & (td_MLKL is not None):
        delta_td.append(td_MLKL[0] - td_PARP[0])
        apopt_td.append(td_PARP[0])
        necro_td.append(td_MLKL[0])

#------------Plot Results--------------------------------
pl.ion()
예제 #9
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파일: fit_3_0.py 프로젝트: clopezx/anrm 
#----Data and conditions----
ydata = ydata_fn()
#init_conc = {'Apop1':{'TNFa_0': 600}}
init_conc = {'Apop1':{'TNFa_0': 600}, 'Apop2':{'TNFa_0': 1200}, 'Necr1':{'TNFa_0':1800, 'zVad_0':9.6e6, 'FADD_0':0}} #600 = 10ng/ml TNFa, 9.6e6 = 20uM

#----Normalize--------------
ynorm = ydata.copy()
normalize = ct.normalize_array
for k in ynorm.keys():
    ynorm[k] = [normalize(ynorm[k][0], option = 1), ynorm[k][1]]

#----Initial Protein Concetrations----
conditions = {}
ic_params  = model.parameters_initial_conditions()
for k in init_conc.keys():
    conditions[k] = ct.initial_conditions(init_conc[k].keys(), init_conc[k].values(), ic_params)

#----Simulator Settings----
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0,36000,1000) #10hrs converted to seconds (1000 timepoints)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-5
sims.atol = 1e-5

solve = sim.Solver(sims)
solve.run()



#----Bayesian and MCMC Options----
예제 #10
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from pysb.integrate  import odesolve

#-----------Calibrated Parameters-----------------------
position = pickle.load(open('CompII_Hypthesis_123_addeddata_4run_v23_Position.pkl'))

#-----------Simulator Settings--------------------------
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0,20000,1000)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-3
sims.atol = 1e-6

solve = sim.Solver(sims)
solve.run()

#-----------Initial Conditions--------------------------
ic_params  = model.parameters_initial_conditions()
conditions = ct.initial_conditions(['Bak_0', 'Bax_0', 'Bid_0', 'zVad_0'], [0.2e5, 40165, 12044, 9.6e6], ic_params)
#20uM zVad == 9.6e6 zVad per cell for a cell volume of 8e-13m3
ysim = solve.simulate(position, observables=True, initial_conc = conditions)

yout = ct.extract_records(ysim, ['Obs_cPARP', 'Obs_MLKL','Obs_TNFa','Obs_NFkB', 'ComplexI','ComplexI_ub', 'ComplexI_TRAF', 'TRADD_RIP1', 'TRADD_RIP1_2','Obs_FADD_Sole', 'ComplexII','Bid_Trunc', 'Bid_PO4','Obs_RIP1', 'RIP1_Trunc', 'RIP3_Trunc', 'Necrosome','Obs_proC8', 'Obs_C8', 'Obs_C3ub', 'Obs_C3', 'Obs_pC3', 'RIP1_FADD','Obs_cPARP', 'Obs_PARP', 'Obs_MLKL','Obs_CytoC'])

p.ion()
p.plot(sims.tspan, yout[:,0], label = 'Cleaved Parp')
p.plot(sims.tspan, yout[:,1], label = 'MLKL')

p.xlabel('time [sec]')
p.ylabel('PARP and MLKL concentration [molecules per cell]')
p.legend()
예제 #11
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    },
    'Apop2': {
        'TNFa_0': 1200
    },
    'Necr1': {
        'TNFa_0': 1800,
        'zVad_0': 9.6e6,
        'FADD_0': 0
    },
    'BidKO': {
        'Bid_0': 0
    }
}
ic_params = model.parameters_initial_conditions()
for k in init_conc.keys():
    conditions[k] = ct.initial_conditions(init_conc[k].keys(),
                                          init_conc[k].values(), ic_params)

#----Simulator Settings----
sims = sim.Settings()
sims.model = model
sims.tspan = np.linspace(0, 36000,
                         1000)  #10hrs converted to seconds (1000 timepoints)
sims.estimate_params = model.parameters_rules()
sims.rtol = 1e-5
sims.atol = 1e-5

solve = sim.Solver(sims)
solve.run()

#----Bayesian and MCMC Options----
opts = bmc.MCMCOpts()