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calibrated_model.py
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calibrated_model.py
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# exported from PySB model 'model'
import numpy as np
from pysb.integrate import Solver
import pylab as pl
import csv
from process_earm_data import process_data
import math
from pysb import Model, Monomer, Parameter, Expression, Compartment, Rule, Observable, Initial, MatchOnce, Annotation, ANY, WILD
Model()
Monomer('Ligand', ['Receptor'])
Monomer('ParpU', ['C3A'])
Monomer('C8A', ['BidU', 'C3pro'])
Monomer('SmacM', ['BaxA'])
Monomer('BaxM', ['BidM', 'BaxA'])
Monomer('Apop', ['C3pro', 'Xiap'])
Monomer('Fadd', ['Receptor', 'C8pro'])
Monomer('SmacC', ['Xiap'])
Monomer('ParpC')
Monomer('Xiap', ['SmacC', 'Apop', 'C3A'])
Monomer('C9')
Monomer('C3ub')
Monomer('C8pro', ['Fadd', 'C6A'])
Monomer('Bcl2', ['BidM', 'BaxA', 'Bad'])
Monomer('C3pro', ['Apop', 'C8A'])
Monomer('CytoCM', ['BaxA'])
Monomer('CytoCC')
Monomer('BaxA', ['BaxM', 'Bcl2', 'BaxA_1', 'BaxA_2', 'SmacM', 'CytoCM'])
Monomer('ApafI')
Monomer('BidU', ['C8A'])
Monomer('BidT')
Monomer('C3A', ['Xiap', 'ParpU', 'C6pro'])
Monomer('Bad', ['Bcl2'])
Monomer('ApafA')
Monomer('BidM', ['BaxM', 'Bcl2'])
Monomer('Receptor', ['Ligand', 'Fadd'])
Monomer('C6A', ['C8pro'])
Monomer('C6pro', ['C3A'])
Parameter('bind_0_Ligand_binder_Receptor_binder_target_2kf', 4.655202642495754e-07)
Parameter('bind_0_Ligand_binder_Receptor_binder_target_1kr', 0.1457845296708275)
Parameter('bind_0_Receptor_binder_Fadd_binder_target_2kf', 2.335760012097258e-07)
Parameter('bind_0_Receptor_binder_Fadd_binder_target_1kr', 0.000658129342761922)
Parameter('substrate_binding_0_Fadd_catalyzer_C8pro_substrate_2kf', 2.929656593658715e-08)
Parameter('substrate_binding_0_Fadd_catalyzer_C8pro_substrate_1kr', 0.04264361976342899)
Parameter('catalytic_step_0_Fadd_catalyzer_C8pro_substrate_C8A_product_1kc', 5.464093466796126)
Parameter('catalysis_0_C8A_catalyzer_BidU_substrate_BidT_product_2kf', 5.473806214434406e-08)
Parameter('catalysis_0_C8A_catalyzer_BidU_substrate_BidT_product_1kr', 0.0110809722200617)
Parameter('catalysis_1_C8A_catalyzer_BidU_substrate_BidT_product_1kc', 0.15495921542194752)
Parameter('conversion_0_CytoCC_subunit_d_ApafI_subunit_c_ApafA_complex_2kf', 1.3085363046337758e-07)
Parameter('conversion_0_CytoCC_subunit_d_ApafI_subunit_c_ApafA_complex_1kr', 0.00030792684957474766)
Parameter('inhibition_0_SmacC_inhibitor_Xiap_inh_target_2kf', 9.034841243805095e-05)
Parameter('inhibition_0_SmacC_inhibitor_Xiap_inh_target_1kr', 0.04007223230950221)
Parameter('conversion_0_C9_subunit_d_ApafA_subunit_c_Apop_complex_2kf', 1.431217076352107e-05)
Parameter('conversion_0_C9_subunit_d_ApafA_subunit_c_Apop_complex_1kr', 0.11869168113503258)
Parameter('catalysis_0_Apop_catalyzer_C3pro_substrate_C3A_product_2kf', 2.3826229700037067e-08)
Parameter('catalysis_0_Apop_catalyzer_C3pro_substrate_C3A_product_1kr', 0.00011338345449770337)
Parameter('catalysis_1_Apop_catalyzer_C3pro_substrate_C3A_product_1kc', 5.880898497457189)
Parameter('inhibition_0_Xiap_inhibitor_Apop_inh_target_2kf', 7.37323816079312e-07)
Parameter('inhibition_0_Xiap_inhibitor_Apop_inh_target_1kr', 0.0014598033851522514)
Parameter('catalysis_0_Xiap_catalyzer_C3A_substrate_C3ub_product_2kf', 5.078502366178455e-07)
Parameter('catalysis_0_Xiap_catalyzer_C3A_substrate_C3ub_product_1kr', 0.0033673450533724275)
Parameter('catalysis_1_Xiap_catalyzer_C3A_substrate_C3ub_product_1kc', 75.77798519660789)
Parameter('catalysis_0_C3A_catalyzer_ParpU_substrate_ParpC_product_2kf', 1.4255225485775024e-06)
Parameter('catalysis_0_C3A_catalyzer_ParpU_substrate_ParpC_product_1kr', 0.015348257625899637)
Parameter('catalysis_1_C3A_catalyzer_ParpU_substrate_ParpC_product_1kc', 61.15396981312076)
Parameter('equilibration_0_BidT_equil_a_BidM_equil_b_1kf', 0.005982429829136439)
Parameter('equilibration_0_BidT_equil_a_BidM_equil_b_1kr', 0.0030721621738467766)
Parameter('catalysis_0_BidM_catalyzer_BaxM_substrate_BaxA_product_2kf', 1.2561368814303568e-07)
Parameter('catalysis_0_BidM_catalyzer_BaxM_substrate_BaxA_product_1kr', 0.00045169555395432897)
Parameter('catalysis_1_BidM_catalyzer_BaxM_substrate_BaxA_product_1kc', 1.4990063211914924)
Parameter('self_catalyze_0_BaxA_self_catalyzer_BaxM_self_substrate_2kf', 6.414248924353486e-08)
Parameter('self_catalyze_0_BaxA_self_catalyzer_BaxM_self_substrate_1kr', 0.260502199202815)
Parameter('self_catalyze_1_BaxA_self_catalyzer_BaxM_self_substrate_1kc', 393.8387462257094)
Parameter('inhibition_0_Bcl2_inhibitor_BidM_inh_target_2kf', 3.7177347286701594e-05)
Parameter('inhibition_0_Bcl2_inhibitor_BidM_inh_target_1kr', 0.0007671724179540023)
Parameter('inhibition_0_Bcl2_inhibitor_BaxA_inh_target_2kf', 1.5242269222242064e-08)
Parameter('inhibition_0_Bcl2_inhibitor_BaxA_inh_target_1kr', 0.002107524867919698)
Parameter('inhibition_0_Bad_inhibitor_Bcl2_inh_target_2kf', 3.3296702483581507e-06)
Parameter('inhibition_0_Bad_inhibitor_Bcl2_inh_target_1kr', 0.42684569988843113)
Parameter('pore_formation_0_BaxA_pore_2kf', 8.07023114411227e-08)
Parameter('pore_formation_0_BaxA_pore_1kr', 0.011899201202356085)
Parameter('pore_formation_1_BaxA_pore_2kf', 1.6131025363600192e-05)
Parameter('pore_formation_1_BaxA_pore_1kr', 0.00020780382938987655)
Parameter('pore_formation_2_BaxA_pore_2kf', 4.291595130964981e-07)
Parameter('pore_formation_2_BaxA_pore_1kr', 0.0024785364174791102)
Parameter('transport_0_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C_2kf', 4.589550077614997e-05)
Parameter('transport_0_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C_1kr', 0.006192618697760851)
Parameter('transport_1_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C_1kc', 4.473105246763808)
Parameter('transport_0_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C_2kf', 2.2765860501909494e-08)
Parameter('transport_0_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C_1kr', 0.1698980612427414)
Parameter('transport_1_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C_1kc', 0.5302510554002018)
Parameter('catalysis_0_C8A_catalyzer_C3pro_substrate_C3A_product_2kf', 3.1272017331725167e-08)
Parameter('catalysis_0_C8A_catalyzer_C3pro_substrate_C3A_product_1kr', 0.6763673748790885)
Parameter('catalysis_1_C8A_catalyzer_C3pro_substrate_C3A_product_1kc', 0.21449813894117592)
Parameter('catalysis_0_C3A_catalyzer_C6pro_substrate_C6A_product_2kf', 1.0223167431468999e-06)
Parameter('catalysis_0_C3A_catalyzer_C6pro_substrate_C6A_product_1kr', 0.0007004282317895014)
Parameter('catalysis_1_C3A_catalyzer_C6pro_substrate_C6A_product_1kc', 7.161867765065879)
Parameter('catalysis_0_C6A_catalyzer_C8pro_substrate_C8A_product_2kf', 5.294791546454888e-06)
Parameter('catalysis_0_C6A_catalyzer_C8pro_substrate_C8A_product_1kr', 0.12411380336814638)
Parameter('catalysis_1_C6A_catalyzer_C8pro_substrate_C8A_product_1kc', 536.7760712534144)
Parameter('Ligand_0', 1000.0)
Parameter('ParpU_0', 1000000.0)
Parameter('C8A_0', 0.0)
Parameter('SmacM_0', 100000.0)
Parameter('BaxM_0', 40000.0)
Parameter('Apop_0', 0.0)
Parameter('Fadd_0', 130000.0)
Parameter('SmacC_0', 0.0)
Parameter('ParpC_0', 0.0)
Parameter('Xiap_0', 42000.0)
Parameter('C9_0', 100000.0)
Parameter('C3ub_0', 0.0)
Parameter('C8pro_0', 130000.0)
Parameter('Bcl2_0', 328000.0)
Parameter('C3pro_0', 21000.0)
Parameter('CytoCM_0', 500000.0)
Parameter('CytoCC_0', 0.0)
Parameter('BaxA_0', 0.0)
Parameter('ApafI_0', 100000.0)
Parameter('BidU_0', 171000.0)
Parameter('BidT_0', 0.0)
Parameter('C3A_0', 0.0)
Parameter('Bad_0', 53000.0)
Parameter('ApafA_0', 0.0)
Parameter('BidM_0', 0.0)
Parameter('Receptor_0', 100.0)
Parameter('C6A_0', 0.0)
Parameter('C6pro_0', 100.)
Observable('Ligand_obs', Ligand())
Observable('ParpU_obs', ParpU())
Observable('C8A_obs', C8A())
Observable('SmacM_obs', SmacM())
Observable('BaxM_obs', BaxM())
Observable('Apop_obs', Apop())
Observable('Fadd_obs', Fadd())
Observable('SmacC_obs', SmacC())
Observable('ParpC_obs', ParpC())
Observable('Xiap_obs', Xiap())
Observable('C9_obs', C9())
Observable('C3ub_obs', C3ub())
Observable('C8pro_obs', C8pro())
Observable('Bcl2_obs', Bcl2())
Observable('C3pro_obs', C3pro())
Observable('CytoCM_obs', CytoCM())
Observable('CytoCC_obs', CytoCC())
Observable('BaxA_obs', BaxA())
Observable('ApafI_obs', ApafI())
Observable('BidU_obs', BidU())
Observable('BidT_obs', BidT())
Observable('C3A_obs', C3A())
Observable('Bad_obs', Bad())
Observable('ApafA_obs', ApafA())
Observable('BidM_obs', BidM())
Observable('Receptor_obs', Receptor())
Observable('C6A_obs', C6A())
Observable('C6pro_obs', C6pro())
Rule('bind_0_Ligand_binder_Receptor_binder_target', Ligand(Receptor=None) + Receptor(Ligand=None, Fadd=None) | Ligand(Receptor=1) % Receptor(Ligand=1, Fadd=None), bind_0_Ligand_binder_Receptor_binder_target_2kf, bind_0_Ligand_binder_Receptor_binder_target_1kr)
Rule('bind_0_Receptor_binder_Fadd_binder_target', Receptor(Ligand=ANY, Fadd=None) + Fadd(Receptor=None, C8pro=None) | Receptor(Ligand=ANY, Fadd=1) % Fadd(Receptor=1, C8pro=None), bind_0_Receptor_binder_Fadd_binder_target_2kf, bind_0_Receptor_binder_Fadd_binder_target_1kr)
Rule('substrate_binding_0_Fadd_catalyzer_C8pro_substrate', Fadd(Receptor=ANY, C8pro=None) + C8pro(Fadd=None, C6A=None) | Fadd(Receptor=ANY, C8pro=1) % C8pro(Fadd=1, C6A=None), substrate_binding_0_Fadd_catalyzer_C8pro_substrate_2kf, substrate_binding_0_Fadd_catalyzer_C8pro_substrate_1kr)
Rule('catalytic_step_0_Fadd_catalyzer_C8pro_substrate_C8A_product', Fadd(Receptor=ANY, C8pro=1) % C8pro(Fadd=1, C6A=None) >> Fadd(Receptor=ANY, C8pro=None) + C8A(BidU=None, C3pro=None), catalytic_step_0_Fadd_catalyzer_C8pro_substrate_C8A_product_1kc)
Rule('catalysis_0_C8A_catalyzer_BidU_substrate_BidT_product', C8A(BidU=None, C3pro=None) + BidU(C8A=None) | C8A(BidU=1, C3pro=None) % BidU(C8A=1), catalysis_0_C8A_catalyzer_BidU_substrate_BidT_product_2kf, catalysis_0_C8A_catalyzer_BidU_substrate_BidT_product_1kr)
Rule('catalysis_1_C8A_catalyzer_BidU_substrate_BidT_product', C8A(BidU=1, C3pro=None) % BidU(C8A=1) >> C8A(BidU=None, C3pro=None) + BidT(), catalysis_1_C8A_catalyzer_BidU_substrate_BidT_product_1kc)
Rule('conversion_0_CytoCC_subunit_d_ApafI_subunit_c_ApafA_complex', ApafI() + CytoCC() | ApafA(), conversion_0_CytoCC_subunit_d_ApafI_subunit_c_ApafA_complex_2kf, conversion_0_CytoCC_subunit_d_ApafI_subunit_c_ApafA_complex_1kr)
Rule('inhibition_0_SmacC_inhibitor_Xiap_inh_target', SmacC(Xiap=None) + Xiap(SmacC=None, Apop=None, C3A=None) | SmacC(Xiap=1) % Xiap(SmacC=1, Apop=None, C3A=None), inhibition_0_SmacC_inhibitor_Xiap_inh_target_2kf, inhibition_0_SmacC_inhibitor_Xiap_inh_target_1kr)
Rule('conversion_0_C9_subunit_d_ApafA_subunit_c_Apop_complex', ApafA() + C9() | Apop(C3pro=None, Xiap=None), conversion_0_C9_subunit_d_ApafA_subunit_c_Apop_complex_2kf, conversion_0_C9_subunit_d_ApafA_subunit_c_Apop_complex_1kr)
Rule('catalysis_0_Apop_catalyzer_C3pro_substrate_C3A_product', Apop(C3pro=None, Xiap=None) + C3pro(Apop=None, C8A=None) | Apop(C3pro=1, Xiap=None) % C3pro(Apop=1, C8A=None), catalysis_0_Apop_catalyzer_C3pro_substrate_C3A_product_2kf, catalysis_0_Apop_catalyzer_C3pro_substrate_C3A_product_1kr)
Rule('catalysis_1_Apop_catalyzer_C3pro_substrate_C3A_product', Apop(C3pro=1, Xiap=None) % C3pro(Apop=1, C8A=None) >> Apop(C3pro=None, Xiap=None) + C3A(Xiap=None, ParpU=None, C6pro=None), catalysis_1_Apop_catalyzer_C3pro_substrate_C3A_product_1kc)
Rule('inhibition_0_Xiap_inhibitor_Apop_inh_target', Xiap(SmacC=None, Apop=None, C3A=None) + Apop(C3pro=None, Xiap=None) | Xiap(SmacC=None, Apop=1, C3A=None) % Apop(C3pro=None, Xiap=1), inhibition_0_Xiap_inhibitor_Apop_inh_target_2kf, inhibition_0_Xiap_inhibitor_Apop_inh_target_1kr)
Rule('catalysis_0_Xiap_catalyzer_C3A_substrate_C3ub_product', Xiap(SmacC=None, Apop=None, C3A=None) + C3A(Xiap=None, ParpU=None, C6pro=None) | Xiap(SmacC=None, Apop=None, C3A=1) % C3A(Xiap=1, ParpU=None, C6pro=None), catalysis_0_Xiap_catalyzer_C3A_substrate_C3ub_product_2kf, catalysis_0_Xiap_catalyzer_C3A_substrate_C3ub_product_1kr)
Rule('catalysis_1_Xiap_catalyzer_C3A_substrate_C3ub_product', Xiap(SmacC=None, Apop=None, C3A=1) % C3A(Xiap=1, ParpU=None, C6pro=None) >> Xiap(SmacC=None, Apop=None, C3A=None) + C3ub(), catalysis_1_Xiap_catalyzer_C3A_substrate_C3ub_product_1kc)
Rule('catalysis_0_C3A_catalyzer_ParpU_substrate_ParpC_product', C3A(Xiap=None, ParpU=None, C6pro=None) + ParpU(C3A=None) | C3A(Xiap=None, ParpU=1, C6pro=None) % ParpU(C3A=1), catalysis_0_C3A_catalyzer_ParpU_substrate_ParpC_product_2kf, catalysis_0_C3A_catalyzer_ParpU_substrate_ParpC_product_1kr)
Rule('catalysis_1_C3A_catalyzer_ParpU_substrate_ParpC_product', C3A(Xiap=None, ParpU=1, C6pro=None) % ParpU(C3A=1) >> C3A(Xiap=None, ParpU=None, C6pro=None) + ParpC(), catalysis_1_C3A_catalyzer_ParpU_substrate_ParpC_product_1kc)
Rule('equilibration_0_BidT_equil_a_BidM_equil_b', BidT() | BidM(BaxM=None, Bcl2=None), equilibration_0_BidT_equil_a_BidM_equil_b_1kf, equilibration_0_BidT_equil_a_BidM_equil_b_1kr)
Rule('catalysis_0_BidM_catalyzer_BaxM_substrate_BaxA_product', BidM(BaxM=None, Bcl2=None) + BaxM(BidM=None, BaxA=None) | BidM(BaxM=1, Bcl2=None) % BaxM(BidM=1, BaxA=None), catalysis_0_BidM_catalyzer_BaxM_substrate_BaxA_product_2kf, catalysis_0_BidM_catalyzer_BaxM_substrate_BaxA_product_1kr)
Rule('catalysis_1_BidM_catalyzer_BaxM_substrate_BaxA_product', BidM(BaxM=1, Bcl2=None) % BaxM(BidM=1, BaxA=None) >> BidM(BaxM=None, Bcl2=None) + BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None), catalysis_1_BidM_catalyzer_BaxM_substrate_BaxA_product_1kc)
Rule('self_catalyze_0_BaxA_self_catalyzer_BaxM_self_substrate', BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) + BaxM(BidM=None, BaxA=None) | BaxA(BaxM=1, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) % BaxM(BidM=None, BaxA=1), self_catalyze_0_BaxA_self_catalyzer_BaxM_self_substrate_2kf, self_catalyze_0_BaxA_self_catalyzer_BaxM_self_substrate_1kr)
Rule('self_catalyze_1_BaxA_self_catalyzer_BaxM_self_substrate', BaxA(BaxM=1, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) % BaxM(BidM=None, BaxA=1) >> BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) + BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None), self_catalyze_1_BaxA_self_catalyzer_BaxM_self_substrate_1kc)
Rule('inhibition_0_Bcl2_inhibitor_BidM_inh_target', Bcl2(BidM=None, BaxA=None, Bad=None) + BidM(BaxM=None, Bcl2=None) | Bcl2(BidM=1, BaxA=None, Bad=None) % BidM(BaxM=None, Bcl2=1), inhibition_0_Bcl2_inhibitor_BidM_inh_target_2kf, inhibition_0_Bcl2_inhibitor_BidM_inh_target_1kr)
Rule('inhibition_0_Bcl2_inhibitor_BaxA_inh_target', Bcl2(BidM=None, BaxA=None, Bad=None) + BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) | Bcl2(BidM=None, BaxA=1, Bad=None) % BaxA(BaxM=None, Bcl2=1, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None), inhibition_0_Bcl2_inhibitor_BaxA_inh_target_2kf, inhibition_0_Bcl2_inhibitor_BaxA_inh_target_1kr)
Rule('inhibition_0_Bad_inhibitor_Bcl2_inh_target', Bad(Bcl2=None) + Bcl2(BidM=None, BaxA=None, Bad=None) | Bad(Bcl2=1) % Bcl2(BidM=None, BaxA=None, Bad=1), inhibition_0_Bad_inhibitor_Bcl2_inh_target_2kf, inhibition_0_Bad_inhibitor_Bcl2_inh_target_1kr)
Rule('pore_formation_0_BaxA_pore', BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) + BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) | BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=None, SmacM=None, CytoCM=None), pore_formation_0_BaxA_pore_2kf, pore_formation_0_BaxA_pore_1kr)
Rule('pore_formation_1_BaxA_pore', BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) + BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=None, SmacM=None, CytoCM=None) | BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None), pore_formation_1_BaxA_pore_2kf, pore_formation_1_BaxA_pore_1kr)
Rule('pore_formation_2_BaxA_pore', BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None) + BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) | BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=None), pore_formation_2_BaxA_pore_2kf, pore_formation_2_BaxA_pore_1kr)
Rule('transport_0_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C', BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=None) + SmacM(BaxA=None) | BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=5, CytoCM=None) % SmacM(BaxA=5), transport_0_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C_2kf, transport_0_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C_1kr)
Rule('transport_1_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C', BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=5, CytoCM=None) % SmacM(BaxA=5) >> BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=None) + SmacC(Xiap=None), transport_1_BaxA_pore_SmacM_cargo_M_SmacC_cargo_C_1kc)
Rule('transport_0_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C', BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=None) + CytoCM(BaxA=None) | BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=5) % CytoCM(BaxA=5), transport_0_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C_2kf, transport_0_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C_1kr)
Rule('transport_1_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C', BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=5) % CytoCM(BaxA=5) >> BaxA(BaxM=None, Bcl2=None, BaxA_1=4, BaxA_2=1, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=1, BaxA_2=2, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=2, BaxA_2=3, SmacM=None, CytoCM=None) % BaxA(BaxM=None, Bcl2=None, BaxA_1=3, BaxA_2=4, SmacM=None, CytoCM=None) + CytoCC(), transport_1_BaxA_pore_CytoCM_cargo_M_CytoCC_cargo_C_1kc)
Rule('catalysis_0_C8A_catalyzer_C3pro_substrate_C3A_product', C8A(BidU=None, C3pro=None) + C3pro(Apop=None, C8A=None) | C8A(BidU=None, C3pro=1) % C3pro(Apop=None, C8A=1), catalysis_0_C8A_catalyzer_C3pro_substrate_C3A_product_2kf, catalysis_0_C8A_catalyzer_C3pro_substrate_C3A_product_1kr)
Rule('catalysis_1_C8A_catalyzer_C3pro_substrate_C3A_product', C8A(BidU=None, C3pro=1) % C3pro(Apop=None, C8A=1) >> C8A(BidU=None, C3pro=None) + C3A(Xiap=None, ParpU=None, C6pro=None), catalysis_1_C8A_catalyzer_C3pro_substrate_C3A_product_1kc)
Rule('catalysis_0_C3A_catalyzer_C6pro_substrate_C6A_product', C3A(Xiap=None, ParpU=None, C6pro=None) + C6pro(C3A=None) | C3A(Xiap=None, ParpU=None, C6pro=1) % C6pro(C3A=1), catalysis_0_C3A_catalyzer_C6pro_substrate_C6A_product_2kf, catalysis_0_C3A_catalyzer_C6pro_substrate_C6A_product_1kr)
Rule('catalysis_1_C3A_catalyzer_C6pro_substrate_C6A_product', C3A(Xiap=None, ParpU=None, C6pro=1) % C6pro(C3A=1) >> C3A(Xiap=None, ParpU=None, C6pro=None) + C6A(C8pro=None), catalysis_1_C3A_catalyzer_C6pro_substrate_C6A_product_1kc)
Rule('catalysis_0_C6A_catalyzer_C8pro_substrate_C8A_product', C6A(C8pro=None) + C8pro(Fadd=None, C6A=None) | C6A(C8pro=1) % C8pro(Fadd=None, C6A=1), catalysis_0_C6A_catalyzer_C8pro_substrate_C8A_product_2kf, catalysis_0_C6A_catalyzer_C8pro_substrate_C8A_product_1kr)
Rule('catalysis_1_C6A_catalyzer_C8pro_substrate_C8A_product', C6A(C8pro=1) % C8pro(Fadd=None, C6A=1) >> C6A(C8pro=None) + C8A(BidU=None, C3pro=None), catalysis_1_C6A_catalyzer_C8pro_substrate_C8A_product_1kc)
Initial(Ligand(Receptor=None), Ligand_0)
Initial(ParpU(C3A=None), ParpU_0)
Initial(C8A(BidU=None, C3pro=None), C8A_0)
Initial(SmacM(BaxA=None), SmacM_0)
Initial(BaxM(BidM=None, BaxA=None), BaxM_0)
Initial(Apop(C3pro=None, Xiap=None), Apop_0)
Initial(Fadd(Receptor=None, C8pro=None), Fadd_0)
Initial(SmacC(Xiap=None), SmacC_0)
Initial(ParpC(), ParpC_0)
Initial(Xiap(SmacC=None, Apop=None, C3A=None), Xiap_0)
Initial(C9(), C9_0)
Initial(C3ub(), C3ub_0)
Initial(C8pro(Fadd=None, C6A=None), C8pro_0)
Initial(Bcl2(BidM=None, BaxA=None, Bad=None), Bcl2_0)
Initial(C3pro(Apop=None, C8A=None), C3pro_0)
Initial(CytoCM(BaxA=None), CytoCM_0)
Initial(CytoCC(), CytoCC_0)
Initial(BaxA(BaxM=None, Bcl2=None, BaxA_1=None, BaxA_2=None, SmacM=None, CytoCM=None), BaxA_0)
Initial(ApafI(), ApafI_0)
Initial(BidU(C8A=None), BidU_0)
Initial(BidT(), BidT_0)
Initial(C3A(Xiap=None, ParpU=None, C6pro=None), C3A_0)
Initial(Bad(Bcl2=None), Bad_0)
Initial(ApafA(), ApafA_0)
Initial(BidM(BaxM=None, Bcl2=None), BidM_0)
Initial(Receptor(Ligand=None, Fadd=None), Receptor_0)
Initial(C6A(C8pro=None), C6A_0)
Initial(C6pro(C3A=None), C6pro_0)
data_object = []
with open('earm_data.csv') as data_file:
reader = csv.reader(data_file)
line = list(reader)
for each in line:
data_object.append(each)
for i, each in enumerate(data_object):
if i > 0:
for j, item in enumerate(each):
data_object[i][j] = float(data_object[i][j])
t = []
for each in data_object[1:]:
t.append(each.pop(0))
data_object.pop(0)
# t = np.linspace(0,20000, 20001)
solve_mod = Solver(model, t)
solve_mod.run()
# temp = list()
# temp.append(list(solve_mod.yobs['BidM_obs']/(solve_mod.yobs['BidM_obs'] + solve_mod.yobs['BidU_obs'] + solve_mod.yobs['BidT_obs'])))
# temp.append(list(solve_mod.yobs['SmacC_obs']/(solve_mod.yobs['SmacC_obs'] + solve_mod.yobs['SmacM_obs'])))
# temp.append(list(solve_mod.yobs['ParpC_obs']/(solve_mod.yobs['ParpC_obs'] + solve_mod.yobs['ParpU_obs'])))
# print t
pl.figure(figsize=(16, 12))
pl.plot(t, solve_mod.yobs['BidM_obs']/(solve_mod.yobs['BidM_obs'] + solve_mod.yobs['BidU_obs'] + solve_mod.yobs['BidT_obs']), label="mBid/Bid")
pl.plot(t, solve_mod.yobs['SmacC_obs']/(solve_mod.yobs['SmacC_obs'] + solve_mod.yobs['SmacM_obs']), label="aSmac/Smac")
pl.plot(t, solve_mod.yobs['ParpC_obs']/(solve_mod.yobs['ParpC_obs'] + solve_mod.yobs['ParpU_obs']), label="cPARP/PARP")
data = process_data('earm_data_var.csv')
data = map(list, zip(*data))
# print data[3]
for i, each in enumerate(data[3]):
data[3][i] = math.sqrt(data[3][i])
for i, each in enumerate(data[9]):
data[9][i] = math.sqrt(data[9][i])
# pl.errorbar(t, data[2], yerr=data[3], c='b', solid_capstyle='projecting', capsize=3, label="IC-RP (Bid)")
# pl.errorbar(t, data[5], yerr=data[6], c='r', ms=2, label="IMS-RP (Smac)")
# pl.errorbar(t, data[8], yerr=data[9], c='g', solid_capstyle='projecting', capsize=3, label="EC-RP (Parp)")
pl.plot(t, data[2], 'ro', c='b', ms=3, label="IC-RP (Bid)")
pl.plot(t, data[4], 'ro', c='r', ms=3, label="IMS-RP (Smac)")
pl.plot(t, data[8], 'ro', c='g', ms=3, label="EC-RP (Parp)")
# pl.legend(loc='lower right', fontsize=20, numpoints=1)
pl.xlabel("Time (s)", fontsize=20)
pl.ylabel("Molecules/cell", fontsize=20)
pl.title('Calibration of modified EARM model over chosen priors (parameter ranges)', fontsize=22)
# pl.title('Bid error bars', fontsize=22)
# pl.title('Parp error bars', fontsize=22)
pl.tick_params(labelsize=16)
pl.tight_layout()
pl.show()