Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 75
sizeStates = 27
sizeConstants = 66
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (millisecond)"
legend_states[0] = "V in component membrane (millivolt)"
legend_constants[0] = "R in component membrane (attojoule_per_millimole_kelvin)"
legend_constants[1] = "T in component membrane (kelvin)"
legend_constants[2] = "F in component membrane (femtocoulomb_per_millimole)"
legend_constants[3] = "Cm in component membrane (picoF)"
legend_algebraic[39] = "i_CaT in component T_type_calcium_channel_current (picoA)"
legend_algebraic[34] = "i_CaL in component L_type_calcium_channel_current (picoA)"
legend_algebraic[40] = "i_Kr in component rapidly_activating_delayed_rectifier_potassium_current (picoA)"
legend_algebraic[42] = "i_Ks in component slowly_activating_delayed_rectifier_potassium_current (picoA)"
legend_algebraic[43] = "i_to in component AP_sensitive_currents (picoA)"
legend_algebraic[44] = "i_sus in component AP_sensitive_currents (picoA)"
legend_algebraic[47] = "i_h in component hyperpolarisation_activated_current (picoA)"
legend_algebraic[48] = "i_st in component sustained_inward_current (picoA)"
legend_algebraic[49] = "i_b_Na in component sodium_dependent_background_current (picoA)"
legend_algebraic[65] = "i_NaCa in component sodium_calcium_exchange_current (picoA)"
legend_algebraic[51] = "i_NaK in component sodium_potassium_pump_current (picoA)"
legend_algebraic[50] = "i_K_ACh in component background_muscarinic_potassium_channel_current (picoA)"
legend_algebraic[0] = "E_Na in component reversal_potentials (millivolt)"
legend_algebraic[29] = "E_K in component reversal_potentials (millivolt)"
legend_states[1] = "Nai in component intracellular_ion_concentrations (millimolar)"
legend_constants[4] = "Nao in component intracellular_ion_concentrations (millimolar)"
legend_states[2] = "Ki in component intracellular_ion_concentrations (millimolar)"
legend_constants[5] = "Ko in component intracellular_ion_concentrations (millimolar)"
legend_constants[6] = "g_CaL in component L_type_calcium_channel_current (nanoS)"
legend_constants[7] = "E_CaL in component L_type_calcium_channel_current (millivolt)"
legend_states[3] = "Ca_sub in component intracellular_ion_concentrations (millimolar)"
legend_states[4] = "d in component L_type_calcium_channel_current_d_gate (dimensionless)"
legend_states[5] = "f in component L_type_calcium_channel_current_f_gate (dimensionless)"
legend_states[6] = "fCa in component L_type_calcium_channel_current_fCa_gate (dimensionless)"
legend_algebraic[1] = "d_infinity in component L_type_calcium_channel_current_d_gate (dimensionless)"
legend_algebraic[35] = "tau_d in component L_type_calcium_channel_current_d_gate (millisecond)"
legend_algebraic[15] = "alpha_d in component L_type_calcium_channel_current_d_gate (per_millisecond)"
legend_algebraic[30] = "beta_d in component L_type_calcium_channel_current_d_gate (per_millisecond)"
legend_algebraic[2] = "f_infinity in component L_type_calcium_channel_current_f_gate (dimensionless)"
legend_algebraic[16] = "tau_f in component L_type_calcium_channel_current_f_gate (millisecond)"
legend_constants[62] = "alpha_fCa in component L_type_calcium_channel_current_fCa_gate (per_millisecond)"
legend_constants[8] = "beta_fCa in component L_type_calcium_channel_current_fCa_gate (per_millimolar_millisecond)"
legend_algebraic[3] = "fCa_infinity in component L_type_calcium_channel_current_fCa_gate (dimensionless)"
legend_algebraic[17] = "tau_fCa in component L_type_calcium_channel_current_fCa_gate (millisecond)"
legend_constants[9] = "Km_fCa in component L_type_calcium_channel_current_fCa_gate (millimolar)"
legend_constants[10] = "g_CaT in component T_type_calcium_channel_current (nanoS)"
legend_constants[11] = "E_CaT in component T_type_calcium_channel_current (millivolt)"
legend_states[7] = "d in component T_type_calcium_channel_current_d_gate (dimensionless)"
legend_states[8] = "f in component T_type_calcium_channel_current_f_gate (dimensionless)"
legend_algebraic[4] = "d_infinity in component T_type_calcium_channel_current_d_gate (dimensionless)"
legend_algebraic[18] = "tau_d in component T_type_calcium_channel_current_d_gate (millisecond)"
legend_algebraic[5] = "f_infinity in component T_type_calcium_channel_current_f_gate (dimensionless)"
legend_algebraic[19] = "tau_f in component T_type_calcium_channel_current_f_gate (millisecond)"
legend_constants[63] = "g_Kr in component rapidly_activating_delayed_rectifier_potassium_current (nanoS)"
legend_states[9] = "paS in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (dimensionless)"
legend_states[10] = "paF in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (dimensionless)"
legend_states[11] = "piy in component rapidly_activating_delayed_rectifier_potassium_current_pi_gate (dimensionless)"
legend_algebraic[6] = "pa_infinity in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (dimensionless)"
legend_algebraic[20] = "tau_paS in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (millisecond)"
legend_algebraic[21] = "tau_paF in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (millisecond)"
legend_algebraic[7] = "pi_infinity in component rapidly_activating_delayed_rectifier_potassium_current_pi_gate (dimensionless)"
legend_algebraic[22] = "tau_pi in component rapidly_activating_delayed_rectifier_potassium_current_pi_gate (millisecond)"
legend_constants[12] = "g_Ks in component slowly_activating_delayed_rectifier_potassium_current (nanoS)"
legend_algebraic[41] = "E_Ks in component slowly_activating_delayed_rectifier_potassium_current (millivolt)"
legend_states[12] = "n in component slowly_activating_delayed_rectifier_potassium_current_n_gate (dimensionless)"
legend_algebraic[31] = "n_infinity in component slowly_activating_delayed_rectifier_potassium_current_n_gate (dimensionless)"
legend_algebraic[36] = "tau_n in component slowly_activating_delayed_rectifier_potassium_current_n_gate (millisecond)"
legend_algebraic[8] = "alpha_n in component slowly_activating_delayed_rectifier_potassium_current_n_gate (per_millisecond)"
legend_algebraic[23] = "beta_n in component slowly_activating_delayed_rectifier_potassium_current_n_gate (per_millisecond)"
legend_constants[13] = "g_to in component AP_sensitive_currents (nanoS)"
legend_constants[14] = "g_sus in component AP_sensitive_currents (nanoS)"
legend_states[13] = "q in component AP_sensitive_currents_q_gate (dimensionless)"
legend_states[14] = "r in component AP_sensitive_currents_r_gate (dimensionless)"
legend_algebraic[9] = "q_infinity in component AP_sensitive_currents_q_gate (dimensionless)"
legend_algebraic[24] = "tau_q in component AP_sensitive_currents_q_gate (millisecond)"
legend_algebraic[10] = "r_infinity in component AP_sensitive_currents_r_gate (dimensionless)"
legend_algebraic[25] = "tau_r in component AP_sensitive_currents_r_gate (millisecond)"
legend_algebraic[45] = "i_h_Na in component hyperpolarisation_activated_current (picoA)"
legend_algebraic[46] = "i_h_K in component hyperpolarisation_activated_current (picoA)"
legend_constants[15] = "g_h_Na in component hyperpolarisation_activated_current (nanoS)"
legend_constants[16] = "g_h_K in component hyperpolarisation_activated_current (nanoS)"
legend_states[15] = "y in component hyperpolarisation_activated_current_y_gate (dimensionless)"
legend_algebraic[11] = "y_infinity in component hyperpolarisation_activated_current_y_gate (dimensionless)"
legend_algebraic[26] = "tau_y in component hyperpolarisation_activated_current_y_gate (millisecond)"
legend_constants[17] = "g_st in component sustained_inward_current (nanoS)"
legend_constants[18] = "E_st in component sustained_inward_current (millivolt)"
legend_states[16] = "qa in component sustained_inward_current_qa_gate (dimensionless)"
legend_states[17] = "qi in component sustained_inward_current_qi_gate (dimensionless)"
legend_algebraic[12] = "qa_infinity in component sustained_inward_current_qa_gate (dimensionless)"
legend_algebraic[37] = "tau_qa in component sustained_inward_current_qa_gate (millisecond)"
legend_algebraic[27] = "alpha_qa in component sustained_inward_current_qa_gate (per_millisecond)"
legend_algebraic[32] = "beta_qa in component sustained_inward_current_qa_gate (per_millisecond)"
legend_algebraic[33] = "qi_infinity in component sustained_inward_current_qi_gate (dimensionless)"
legend_algebraic[38] = "tau_qi in component sustained_inward_current_qi_gate (millisecond)"
legend_algebraic[13] = "alpha_qi in component sustained_inward_current_qi_gate (per_millisecond)"
legend_algebraic[28] = "beta_qi in component sustained_inward_current_qi_gate (per_millisecond)"
legend_constants[19] = "g_b_Na in component sodium_dependent_background_current (nanoS)"
legend_constants[64] = "g_K_ACh in component background_muscarinic_potassium_channel_current (picoA)"
legend_constants[20] = "Km_Kp in component sodium_potassium_pump_current (millimolar)"
legend_constants[21] = "Km_Nap in component sodium_potassium_pump_current (millimolar)"
legend_constants[22] = "i_NaK_max in component sodium_potassium_pump_current (picoA)"
legend_constants[23] = "kNaCa in component sodium_calcium_exchange_current (picoA)"
legend_algebraic[62] = "x1 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[58] = "x2 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[63] = "x3 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[64] = "x4 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[53] = "k41 in component sodium_calcium_exchange_current (dimensionless)"
legend_constants[65] = "k34 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[61] = "k23 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[60] = "k21 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[57] = "k32 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[52] = "k43 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[55] = "k12 in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[56] = "k14 in component sodium_calcium_exchange_current (dimensionless)"
legend_constants[24] = "Qci in component sodium_calcium_exchange_current (dimensionless)"
legend_constants[25] = "Qn in component sodium_calcium_exchange_current (dimensionless)"
legend_constants[26] = "Qco in component sodium_calcium_exchange_current (dimensionless)"
legend_constants[27] = "K3ni in component sodium_calcium_exchange_current (millimolar)"
legend_constants[28] = "Kci in component sodium_calcium_exchange_current (millimolar)"
legend_constants[29] = "K1ni in component sodium_calcium_exchange_current (millimolar)"
legend_constants[30] = "K2ni in component sodium_calcium_exchange_current (millimolar)"
legend_constants[31] = "Kcni in component sodium_calcium_exchange_current (millimolar)"
legend_constants[32] = "K3no in component sodium_calcium_exchange_current (millimolar)"
legend_constants[33] = "K1no in component sodium_calcium_exchange_current (millimolar)"
legend_constants[34] = "K2no in component sodium_calcium_exchange_current (millimolar)"
legend_constants[35] = "Kco in component sodium_calcium_exchange_current (millimolar)"
legend_algebraic[59] = "do in component sodium_calcium_exchange_current (dimensionless)"
legend_algebraic[54] = "di in component sodium_calcium_exchange_current (dimensionless)"
legend_constants[36] = "Cao in component intracellular_ion_concentrations (millimolar)"
legend_algebraic[66] = "j_Ca_dif in component intracellular_calcium_dynamics (millimolar_per_millisecond)"
legend_algebraic[67] = "j_rel in component intracellular_calcium_dynamics (millimolar_per_millisecond)"
legend_algebraic[68] = "j_up in component intracellular_calcium_dynamics (millimolar_per_millisecond)"
legend_algebraic[70] = "j_tr in component intracellular_calcium_dynamics (millimolar_per_millisecond)"
legend_constants[37] = "tau_dif_Ca in component intracellular_calcium_dynamics (millisecond)"
legend_constants[38] = "tau_tr in component intracellular_calcium_dynamics (millisecond)"
legend_constants[39] = "K_rel in component intracellular_calcium_dynamics (millimolar)"
legend_constants[40] = "P_up in component intracellular_calcium_dynamics (millimolar_per_millisecond)"
legend_constants[41] = "P_rel in component intracellular_calcium_dynamics (per_millisecond)"
legend_constants[42] = "K_up in component intracellular_calcium_dynamics (millimolar)"
legend_states[18] = "Ca_up in component intracellular_ion_concentrations (millimolar)"
legend_states[19] = "Cai in component intracellular_ion_concentrations (millimolar)"
legend_states[20] = "Ca_rel in component intracellular_ion_concentrations (millimolar)"
legend_constants[43] = "Mgi in component intracellular_ion_concentrations (millimolar)"
legend_constants[44] = "V_i in component intracellular_ion_concentrations (litre)"
legend_constants[45] = "V_rel in component intracellular_ion_concentrations (litre)"
legend_constants[46] = "V_up in component intracellular_ion_concentrations (litre)"
legend_constants[47] = "V_sub in component intracellular_ion_concentrations (litre)"
legend_constants[48] = "TMC_tot in component calcium_buffering (dimensionless)"
legend_constants[49] = "CM_tot in component calcium_buffering (dimensionless)"
legend_constants[50] = "TC_tot in component calcium_buffering (dimensionless)"
legend_constants[51] = "CQ_tot in component calcium_buffering (dimensionless)"
legend_algebraic[72] = "delta_fTMC in component calcium_buffering (millimolar_per_millisecond)"
legend_algebraic[74] = "delta_fCMi in component calcium_buffering (millimolar_per_millisecond)"
legend_algebraic[69] = "delta_fCMs in component calcium_buffering (millimolar_per_millisecond)"
legend_algebraic[71] = "delta_fTC in component calcium_buffering (millimolar_per_millisecond)"
legend_algebraic[73] = "delta_fCQ in component calcium_buffering (millimolar_per_millisecond)"
legend_algebraic[14] = "delta_fTMM in component calcium_buffering (millimolar_per_millisecond)"
legend_states[21] = "fTMM in component calcium_buffering (millimolar)"
legend_states[22] = "fCMi in component calcium_buffering (millimolar)"
legend_states[23] = "fCMs in component calcium_buffering (millimolar)"
legend_states[24] = "fTC in component calcium_buffering (millimolar)"
legend_states[25] = "fTMC in component calcium_buffering (millimolar)"
legend_states[26] = "fCQ in component calcium_buffering (millimolar)"
legend_constants[52] = "kf_TC in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[53] = "kf_TMM in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[54] = "kf_TMC in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[55] = "kf_CM in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[56] = "kf_CQ in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[57] = "kb_TC in component calcium_buffering (per_millisecond)"
legend_constants[58] = "kb_TMC in component calcium_buffering (per_millisecond)"
legend_constants[59] = "kb_TMM in component calcium_buffering (per_millisecond)"
legend_constants[60] = "kb_CM in component calcium_buffering (per_millisecond)"
legend_constants[61] = "kb_CQ in component calcium_buffering (per_millisecond)"
legend_rates[0] = "d/dt V in component membrane (millivolt)"
legend_rates[4] = "d/dt d in component L_type_calcium_channel_current_d_gate (dimensionless)"
legend_rates[5] = "d/dt f in component L_type_calcium_channel_current_f_gate (dimensionless)"
legend_rates[6] = "d/dt fCa in component L_type_calcium_channel_current_fCa_gate (dimensionless)"
legend_rates[7] = "d/dt d in component T_type_calcium_channel_current_d_gate (dimensionless)"
legend_rates[8] = "d/dt f in component T_type_calcium_channel_current_f_gate (dimensionless)"
legend_rates[9] = "d/dt paS in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (dimensionless)"
legend_rates[10] = "d/dt paF in component rapidly_activating_delayed_rectifier_potassium_current_pa_gate (dimensionless)"
legend_rates[11] = "d/dt piy in component rapidly_activating_delayed_rectifier_potassium_current_pi_gate (dimensionless)"
legend_rates[12] = "d/dt n in component slowly_activating_delayed_rectifier_potassium_current_n_gate (dimensionless)"
legend_rates[13] = "d/dt q in component AP_sensitive_currents_q_gate (dimensionless)"
legend_rates[14] = "d/dt r in component AP_sensitive_currents_r_gate (dimensionless)"
legend_rates[15] = "d/dt y in component hyperpolarisation_activated_current_y_gate (dimensionless)"
legend_rates[16] = "d/dt qa in component sustained_inward_current_qa_gate (dimensionless)"
legend_rates[17] = "d/dt qi in component sustained_inward_current_qi_gate (dimensionless)"
legend_rates[1] = "d/dt Nai in component intracellular_ion_concentrations (millimolar)"
legend_rates[2] = "d/dt Ki in component intracellular_ion_concentrations (millimolar)"
legend_rates[19] = "d/dt Cai in component intracellular_ion_concentrations (millimolar)"
legend_rates[3] = "d/dt Ca_sub in component intracellular_ion_concentrations (millimolar)"
legend_rates[18] = "d/dt Ca_up in component intracellular_ion_concentrations (millimolar)"
legend_rates[20] = "d/dt Ca_rel in component intracellular_ion_concentrations (millimolar)"
legend_rates[24] = "d/dt fTC in component calcium_buffering (millimolar)"
legend_rates[25] = "d/dt fTMC in component calcium_buffering (millimolar)"
legend_rates[21] = "d/dt fTMM in component calcium_buffering (millimolar)"
legend_rates[22] = "d/dt fCMi in component calcium_buffering (millimolar)"
legend_rates[23] = "d/dt fCMs in component calcium_buffering (millimolar)"
legend_rates[26] = "d/dt fCQ in component calcium_buffering (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = -58.600291137693
constants[0] = 8314400000000000
constants[1] = 310.15
constants[2] = 96485000000000000
constants[3] = 32
states[1] = 9.438646305915
constants[4] = 140
states[2] = 139.984146485614
constants[5] = 5.4
constants[6] = 0.58
constants[7] = 45
states[3] = 0.00019074741
states[4] = 0.000602055134
states[5] = 0.626999773853
states[6] = 0.589580408056
constants[8] = 60
constants[9] = 0.00035
constants[10] = 0.458
constants[11] = 45
states[7] = 0.004571884917
states[8] = 0.249637570396
states[9] = 0.629323128348
states[10] = 0.3493633709533
states[11] = 0.852396631172
constants[12] = 0.0259
states[12] = 0.054409723782
constants[13] = 0.18
constants[14] = 0.02
states[13] = 0.531446952485
states[14] = 0.005550489445
constants[15] = 0.1437375
constants[16] = 0.2312625
states[15] = 0.067156687129
constants[17] = 0.015
constants[18] = 37.4
states[16] = 0.426018100136
states[17] = 0.333330378068
constants[19] = 0.0054
constants[20] = 1.4
constants[21] = 14
constants[22] = 3.6
constants[23] = 125
constants[24] = 0.1369
constants[25] = 0.4315
constants[26] = 0
constants[27] = 26.44
constants[28] = 0.0207
constants[29] = 395.3
constants[30] = 2.289
constants[31] = 26.44
constants[32] = 4.663
constants[33] = 1628
constants[34] = 561.4
constants[35] = 3.663
constants[36] = 2
constants[37] = 0.04
constants[38] = 60
constants[39] = 0.0012
constants[40] = 0.005
constants[41] = 0.5
constants[42] = 0.0006
states[18] = 1.462338380106
states[19] = 0.000312494921
states[20] = 0.296742023718
constants[43] = 2.5
constants[44] = 0.0000000000015835
constants[45] = 0.0000000000000042223
constants[46] = 0.000000000000040816
constants[47] = 0.000000000000035098
constants[48] = 0.062
constants[49] = 0.045
constants[50] = 0.031
constants[51] = 10
states[21] = 0.350600895635
states[22] = 0.116947220413
states[23] = 0.074631965653
states[24] = 0.059206293446
states[25] = 0.602955114871
states[26] = 0.260317260703
constants[52] = 88.8
constants[53] = 2.277
constants[54] = 227.7
constants[55] = 227.7
constants[56] = 0.534
constants[57] = 0.446
constants[58] = 0.00751
constants[59] = 0.751
constants[60] = 0.542
constants[61] = 0.445
constants[62] = constants[9]*constants[8]
constants[63] = 0.0250000*(power(constants[5]/1.00000, 0.590000))
constants[64] = 0.00110000*(power(constants[5]/1.00000, 0.410000))
constants[65] = constants[4]/(constants[32]+constants[4])
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[14] = constants[53]*constants[43]*(1.00000-(states[25]+states[21]))-constants[59]*states[21]
rates[21] = algebraic[14]
algebraic[2] = 1.00000/(1.00000+exp((states[0]+30.0000)/5.00000))
algebraic[16] = 44.3000+257.100*exp(-(power((states[0]+32.5000)/13.9000, 2.00000)))
rates[5] = (algebraic[2]-states[5])/algebraic[16]
algebraic[3] = constants[9]/(constants[9]+states[3])
algebraic[17] = algebraic[3]/constants[62]
rates[6] = (algebraic[3]-states[6])/algebraic[17]
algebraic[4] = 1.00000/(1.00000+exp(-(states[0]+26.3000)/6.00000))
algebraic[18] = 1.00000/(1.06800*exp((states[0]+26.3000)/30.0000)+1.06800*exp(-(states[0]+26.3000)/30.0000))
rates[7] = (algebraic[4]-states[7])/algebraic[18]
algebraic[5] = 1.00000/(1.00000+exp((states[0]+61.7000)/5.60000))
algebraic[19] = 1.00000/(0.0153000*exp(-(states[0]+61.7000)/83.3000)+0.0150000*exp((states[0]+61.7000)/15.3800))
rates[8] = (algebraic[5]-states[8])/algebraic[19]
algebraic[6] = 1.00000/(1.00000+exp(-(states[0]+23.2000)/10.6000))
algebraic[20] = 0.846554/(0.00420000*exp(states[0]/17.0000)+0.000150000*exp(-states[0]/21.6000))
rates[9] = (algebraic[6]-states[9])/algebraic[20]
algebraic[21] = 0.846554/(0.0372000*exp(states[0]/15.9000)+0.000960000*exp(-states[0]/22.5000))
rates[10] = (algebraic[6]-states[10])/algebraic[21]
algebraic[7] = 1.00000/(1.00000+exp((states[0]+28.6000)/17.1000))
algebraic[22] = 1.00000/(0.100000*exp(-states[0]/54.6450)+0.656000*exp(states[0]/106.157))
rates[11] = (algebraic[7]-states[11])/algebraic[22]
algebraic[9] = 1.00000/(1.00000+exp((states[0]+49.0000)/13.0000))
algebraic[24] = 0.600000*(65.1700/(0.570000*exp(-0.0800000*(states[0]+44.0000))+0.0650000*exp(0.100000*(states[0]+45.9300)))+10.1000)
rates[13] = (algebraic[9]-states[13])/algebraic[24]
algebraic[10] = 1.00000/(1.00000+exp(-(states[0]-19.3000)/15.0000))
algebraic[25] = 0.660000*1.40000*(15.5900/(1.03700*exp(0.0900000*(states[0]+30.6100))+0.369000*exp(-0.120000*(states[0]+23.8400)))+2.98000)
rates[14] = (algebraic[10]-states[14])/algebraic[25]
algebraic[11] = 1.00000/(1.00000+exp((states[0]+64.0000)/13.5000))
algebraic[26] = 0.716653/(exp(-(states[0]+386.900)/45.3020)+exp((states[0]-73.0800)/19.2310))
rates[15] = (algebraic[11]-states[15])/algebraic[26]
algebraic[1] = 1.00000/(1.00000+exp(-(states[0]+14.1000)/6.00000))
algebraic[15] = (-0.0283900*(states[0]+35.0000))/(exp(-(states[0]+35.0000)/2.50000)-1.00000)-(0.0849000*states[0])/(exp(-states[0]/4.80800)-1.00000)
algebraic[30] = (0.0114300*(states[0]-5.00000))/(exp((states[0]-5.00000)/2.50000)-1.00000)
algebraic[35] = 1.00000/(algebraic[15]+algebraic[30])
rates[4] = (algebraic[1]-states[4])/algebraic[35]
algebraic[8] = 0.0140000/(1.00000+exp(-(states[0]-40.0000)/9.00000))
algebraic[23] = 0.00100000*exp(-states[0]/45.0000)
algebraic[31] = algebraic[8]/(algebraic[8]+algebraic[23])
algebraic[36] = 1.00000/(algebraic[8]+algebraic[23])
rates[12] = (algebraic[31]-states[12])/algebraic[36]
algebraic[12] = 1.00000/(1.00000+exp(-(states[0]+57.0000)/5.00000))
algebraic[27] = 1.00000/(0.150000*exp(-states[0]/11.0000)+0.200000*exp(-states[0]/700.000))
algebraic[32] = 1.00000/(16.0000*exp(states[0]/8.00000)+15.0000*exp(states[0]/50.0000))
algebraic[37] = 1.00000/(algebraic[27]+algebraic[32])
rates[16] = (algebraic[12]-states[16])/algebraic[37]
algebraic[13] = 1.00000/(3100.00*exp(states[0]/13.0000)+700.000*exp(states[0]/70.0000))
algebraic[28] = 1.00000/(95.0000*exp(-states[0]/10.0000)+50.0000*exp(-states[0]/700.000))+0.000229000/(1.00000+exp(-states[0]/5.00000))
algebraic[33] = algebraic[13]/(algebraic[13]+algebraic[28])
algebraic[38] = 6.65000/(algebraic[13]+algebraic[28])
rates[17] = (algebraic[33]-states[17])/algebraic[38]
algebraic[29] = ((constants[0]*constants[1])/constants[2])*log(constants[5]/states[2])
algebraic[40] = constants[63]*(states[0]-algebraic[29])*(0.600000*states[10]+0.400000*states[9])*states[11]
algebraic[41] = ((constants[0]*constants[1])/constants[2])*log((constants[5]+0.120000*constants[4])/(states[2]+0.120000*states[1]))
algebraic[42] = constants[12]*(states[0]-algebraic[41])*(power(states[12], 2.00000))
algebraic[43] = constants[13]*(states[0]-algebraic[29])*states[13]*states[14]
algebraic[44] = constants[14]*(states[0]-algebraic[29])*states[14]
algebraic[0] = ((constants[0]*constants[1])/constants[2])*log(constants[4]/states[1])
algebraic[51] = constants[22]*(power(1.00000+power(constants[20]/constants[5], 1.20000), -1.00000))*(power(1.00000+power(constants[21]/states[1], 1.30000), -1.00000))*(power(1.00000+exp(-((states[0]-algebraic[0])+120.000)/30.0000), -1.00000))
algebraic[50] = (constants[64]*(states[2]-constants[5]*exp((-states[0]*constants[2])/(constants[0]*constants[1]))))/1.00000
algebraic[46] = constants[16]*(states[0]-algebraic[29])*(power(states[15], 2.00000))
rates[2] = (-(algebraic[40]+algebraic[42]+algebraic[43]+algebraic[44]+algebraic[46]+algebraic[50]+-2.00000*algebraic[51])*constants[3])/(1.00000*constants[2]*(constants[44]+constants[47]))
algebraic[39] = constants[10]*(states[0]-constants[11])*states[7]*states[8]
algebraic[34] = constants[6]*(states[0]-constants[7])*states[4]*states[5]*states[6]
algebraic[45] = constants[15]*(states[0]-algebraic[0])*(power(states[15], 2.00000))
algebraic[47] = algebraic[45]+algebraic[46]
algebraic[48] = constants[17]*(states[0]-constants[18])*states[16]*states[17]
algebraic[49] = constants[19]*(states[0]-algebraic[0])
algebraic[53] = exp((-constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1]))
algebraic[59] = 1.00000+(constants[36]/constants[35])*(1.00000+exp((constants[26]*states[0]*constants[2])/(constants[0]*constants[1])))+(constants[4]/constants[33])*(1.00000+constants[4]/constants[34])*(1.00000+constants[4]/constants[32])
algebraic[61] = ((((constants[4]/constants[33])*constants[4])/constants[34])*(1.00000+constants[4]/constants[32])*exp((-constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1])))/algebraic[59]
algebraic[60] = ((constants[36]/constants[35])*exp((constants[26]*states[0]*constants[2])/(constants[0]*constants[1])))/algebraic[59]
algebraic[57] = exp((constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1]))
algebraic[52] = states[1]/(constants[27]+states[1])
algebraic[62] = algebraic[53]*constants[65]*(algebraic[61]+algebraic[60])+algebraic[60]*algebraic[57]*(algebraic[52]+algebraic[53])
algebraic[54] = 1.00000+(states[3]/constants[28])*(1.00000+exp((-constants[24]*states[0]*constants[2])/(constants[0]*constants[1]))+states[1]/constants[31])+(states[1]/constants[29])*(1.00000+(states[1]/constants[30])*(1.00000+states[1]/constants[27]))
algebraic[55] = ((states[3]/constants[28])*exp((-constants[24]*states[0]*constants[2])/(constants[0]*constants[1])))/algebraic[54]
algebraic[56] = ((((states[1]/constants[29])*states[1])/constants[30])*(1.00000+states[1]/constants[27])*exp((constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1])))/algebraic[54]
algebraic[58] = algebraic[57]*algebraic[52]*(algebraic[56]+algebraic[55])+algebraic[53]*algebraic[55]*(constants[65]+algebraic[57])
algebraic[63] = algebraic[56]*algebraic[52]*(algebraic[61]+algebraic[60])+algebraic[55]*algebraic[61]*(algebraic[52]+algebraic[53])
algebraic[64] = algebraic[61]*constants[65]*(algebraic[56]+algebraic[55])+algebraic[56]*algebraic[60]*(constants[65]+algebraic[57])
algebraic[65] = (constants[23]*(algebraic[58]*algebraic[60]-algebraic[62]*algebraic[55]))/(algebraic[62]+algebraic[58]+algebraic[63]+algebraic[64])
rates[0] = -(algebraic[34]+algebraic[39]+algebraic[40]+algebraic[42]+algebraic[43]+algebraic[44]+algebraic[47]+algebraic[48]+algebraic[49]+algebraic[50]+algebraic[51]+algebraic[65])/1.00000
rates[1] = (-(algebraic[45]+algebraic[48]+algebraic[49]+3.00000*algebraic[51]+3.00000*algebraic[65])*constants[3])/(1.00000*constants[2]*(constants[44]+constants[47]))
algebraic[66] = (states[3]-states[19])/constants[37]
algebraic[67] = (constants[41]*(states[20]-states[3]))/(1.00000+power(constants[39]/states[3], 2.00000))
algebraic[69] = constants[55]*states[3]*(1.00000-states[23])-constants[60]*states[23]
rates[3] = ((-((algebraic[34]+algebraic[39])-2.00000*algebraic[65])*constants[3])/(1.00000*2.00000*constants[2])+algebraic[67]*constants[45])/constants[47]-(algebraic[66]+constants[49]*algebraic[69])
rates[23] = algebraic[69]
algebraic[68] = constants[40]/(1.00000+constants[42]/states[19])
algebraic[70] = (states[18]-states[20])/constants[38]
rates[18] = algebraic[68]-(algebraic[70]*constants[45])/constants[46]
algebraic[71] = constants[52]*states[19]*(1.00000-states[24])-constants[57]*states[24]
rates[24] = algebraic[71]
algebraic[73] = constants[56]*states[20]*(1.00000-states[26])-constants[61]*states[26]
rates[20] = algebraic[70]-(algebraic[67]+constants[51]*algebraic[73])
algebraic[72] = constants[54]*states[19]*(1.00000-(states[25]+states[21]))-constants[58]*states[25]
rates[25] = algebraic[72]
rates[26] = algebraic[73]
algebraic[74] = constants[55]*states[19]*(1.00000-states[22])-constants[60]*states[22]
rates[19] = (algebraic[66]*constants[47]-algebraic[68]*constants[46])/constants[44]-(constants[49]*algebraic[74]+constants[50]*algebraic[71]+constants[48]*algebraic[72])
rates[22] = algebraic[74]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[14] = constants[53]*constants[43]*(1.00000-(states[25]+states[21]))-constants[59]*states[21]
algebraic[2] = 1.00000/(1.00000+exp((states[0]+30.0000)/5.00000))
algebraic[16] = 44.3000+257.100*exp(-(power((states[0]+32.5000)/13.9000, 2.00000)))
algebraic[3] = constants[9]/(constants[9]+states[3])
algebraic[17] = algebraic[3]/constants[62]
algebraic[4] = 1.00000/(1.00000+exp(-(states[0]+26.3000)/6.00000))
algebraic[18] = 1.00000/(1.06800*exp((states[0]+26.3000)/30.0000)+1.06800*exp(-(states[0]+26.3000)/30.0000))
algebraic[5] = 1.00000/(1.00000+exp((states[0]+61.7000)/5.60000))
algebraic[19] = 1.00000/(0.0153000*exp(-(states[0]+61.7000)/83.3000)+0.0150000*exp((states[0]+61.7000)/15.3800))
algebraic[6] = 1.00000/(1.00000+exp(-(states[0]+23.2000)/10.6000))
algebraic[20] = 0.846554/(0.00420000*exp(states[0]/17.0000)+0.000150000*exp(-states[0]/21.6000))
algebraic[21] = 0.846554/(0.0372000*exp(states[0]/15.9000)+0.000960000*exp(-states[0]/22.5000))
algebraic[7] = 1.00000/(1.00000+exp((states[0]+28.6000)/17.1000))
algebraic[22] = 1.00000/(0.100000*exp(-states[0]/54.6450)+0.656000*exp(states[0]/106.157))
algebraic[9] = 1.00000/(1.00000+exp((states[0]+49.0000)/13.0000))
algebraic[24] = 0.600000*(65.1700/(0.570000*exp(-0.0800000*(states[0]+44.0000))+0.0650000*exp(0.100000*(states[0]+45.9300)))+10.1000)
algebraic[10] = 1.00000/(1.00000+exp(-(states[0]-19.3000)/15.0000))
algebraic[25] = 0.660000*1.40000*(15.5900/(1.03700*exp(0.0900000*(states[0]+30.6100))+0.369000*exp(-0.120000*(states[0]+23.8400)))+2.98000)
algebraic[11] = 1.00000/(1.00000+exp((states[0]+64.0000)/13.5000))
algebraic[26] = 0.716653/(exp(-(states[0]+386.900)/45.3020)+exp((states[0]-73.0800)/19.2310))
algebraic[1] = 1.00000/(1.00000+exp(-(states[0]+14.1000)/6.00000))
algebraic[15] = (-0.0283900*(states[0]+35.0000))/(exp(-(states[0]+35.0000)/2.50000)-1.00000)-(0.0849000*states[0])/(exp(-states[0]/4.80800)-1.00000)
algebraic[30] = (0.0114300*(states[0]-5.00000))/(exp((states[0]-5.00000)/2.50000)-1.00000)
algebraic[35] = 1.00000/(algebraic[15]+algebraic[30])
algebraic[8] = 0.0140000/(1.00000+exp(-(states[0]-40.0000)/9.00000))
algebraic[23] = 0.00100000*exp(-states[0]/45.0000)
algebraic[31] = algebraic[8]/(algebraic[8]+algebraic[23])
algebraic[36] = 1.00000/(algebraic[8]+algebraic[23])
algebraic[12] = 1.00000/(1.00000+exp(-(states[0]+57.0000)/5.00000))
algebraic[27] = 1.00000/(0.150000*exp(-states[0]/11.0000)+0.200000*exp(-states[0]/700.000))
algebraic[32] = 1.00000/(16.0000*exp(states[0]/8.00000)+15.0000*exp(states[0]/50.0000))
algebraic[37] = 1.00000/(algebraic[27]+algebraic[32])
algebraic[13] = 1.00000/(3100.00*exp(states[0]/13.0000)+700.000*exp(states[0]/70.0000))
algebraic[28] = 1.00000/(95.0000*exp(-states[0]/10.0000)+50.0000*exp(-states[0]/700.000))+0.000229000/(1.00000+exp(-states[0]/5.00000))
algebraic[33] = algebraic[13]/(algebraic[13]+algebraic[28])
algebraic[38] = 6.65000/(algebraic[13]+algebraic[28])
algebraic[29] = ((constants[0]*constants[1])/constants[2])*log(constants[5]/states[2])
algebraic[40] = constants[63]*(states[0]-algebraic[29])*(0.600000*states[10]+0.400000*states[9])*states[11]
algebraic[41] = ((constants[0]*constants[1])/constants[2])*log((constants[5]+0.120000*constants[4])/(states[2]+0.120000*states[1]))
algebraic[42] = constants[12]*(states[0]-algebraic[41])*(power(states[12], 2.00000))
algebraic[43] = constants[13]*(states[0]-algebraic[29])*states[13]*states[14]
algebraic[44] = constants[14]*(states[0]-algebraic[29])*states[14]
algebraic[0] = ((constants[0]*constants[1])/constants[2])*log(constants[4]/states[1])
algebraic[51] = constants[22]*(power(1.00000+power(constants[20]/constants[5], 1.20000), -1.00000))*(power(1.00000+power(constants[21]/states[1], 1.30000), -1.00000))*(power(1.00000+exp(-((states[0]-algebraic[0])+120.000)/30.0000), -1.00000))
algebraic[50] = (constants[64]*(states[2]-constants[5]*exp((-states[0]*constants[2])/(constants[0]*constants[1]))))/1.00000
algebraic[46] = constants[16]*(states[0]-algebraic[29])*(power(states[15], 2.00000))
algebraic[39] = constants[10]*(states[0]-constants[11])*states[7]*states[8]
algebraic[34] = constants[6]*(states[0]-constants[7])*states[4]*states[5]*states[6]
algebraic[45] = constants[15]*(states[0]-algebraic[0])*(power(states[15], 2.00000))
algebraic[47] = algebraic[45]+algebraic[46]
algebraic[48] = constants[17]*(states[0]-constants[18])*states[16]*states[17]
algebraic[49] = constants[19]*(states[0]-algebraic[0])
algebraic[53] = exp((-constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1]))
algebraic[59] = 1.00000+(constants[36]/constants[35])*(1.00000+exp((constants[26]*states[0]*constants[2])/(constants[0]*constants[1])))+(constants[4]/constants[33])*(1.00000+constants[4]/constants[34])*(1.00000+constants[4]/constants[32])
algebraic[61] = ((((constants[4]/constants[33])*constants[4])/constants[34])*(1.00000+constants[4]/constants[32])*exp((-constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1])))/algebraic[59]
algebraic[60] = ((constants[36]/constants[35])*exp((constants[26]*states[0]*constants[2])/(constants[0]*constants[1])))/algebraic[59]
algebraic[57] = exp((constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1]))
algebraic[52] = states[1]/(constants[27]+states[1])
algebraic[62] = algebraic[53]*constants[65]*(algebraic[61]+algebraic[60])+algebraic[60]*algebraic[57]*(algebraic[52]+algebraic[53])
algebraic[54] = 1.00000+(states[3]/constants[28])*(1.00000+exp((-constants[24]*states[0]*constants[2])/(constants[0]*constants[1]))+states[1]/constants[31])+(states[1]/constants[29])*(1.00000+(states[1]/constants[30])*(1.00000+states[1]/constants[27]))
algebraic[55] = ((states[3]/constants[28])*exp((-constants[24]*states[0]*constants[2])/(constants[0]*constants[1])))/algebraic[54]
algebraic[56] = ((((states[1]/constants[29])*states[1])/constants[30])*(1.00000+states[1]/constants[27])*exp((constants[25]*states[0]*constants[2])/(2.00000*constants[0]*constants[1])))/algebraic[54]
algebraic[58] = algebraic[57]*algebraic[52]*(algebraic[56]+algebraic[55])+algebraic[53]*algebraic[55]*(constants[65]+algebraic[57])
algebraic[63] = algebraic[56]*algebraic[52]*(algebraic[61]+algebraic[60])+algebraic[55]*algebraic[61]*(algebraic[52]+algebraic[53])
algebraic[64] = algebraic[61]*constants[65]*(algebraic[56]+algebraic[55])+algebraic[56]*algebraic[60]*(constants[65]+algebraic[57])
algebraic[65] = (constants[23]*(algebraic[58]*algebraic[60]-algebraic[62]*algebraic[55]))/(algebraic[62]+algebraic[58]+algebraic[63]+algebraic[64])
algebraic[66] = (states[3]-states[19])/constants[37]
algebraic[67] = (constants[41]*(states[20]-states[3]))/(1.00000+power(constants[39]/states[3], 2.00000))
algebraic[69] = constants[55]*states[3]*(1.00000-states[23])-constants[60]*states[23]
algebraic[68] = constants[40]/(1.00000+constants[42]/states[19])
algebraic[70] = (states[18]-states[20])/constants[38]
algebraic[71] = constants[52]*states[19]*(1.00000-states[24])-constants[57]*states[24]
algebraic[73] = constants[56]*states[20]*(1.00000-states[26])-constants[61]*states[26]
algebraic[72] = constants[54]*states[19]*(1.00000-(states[25]+states[21]))-constants[58]*states[25]
algebraic[74] = constants[55]*states[19]*(1.00000-states[22])-constants[60]*states[22]
return algebraic
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)