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 = 76
sizeStates = 29
sizeConstants = 86
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] = "Vm in component Vm (millivolt)"
legend_constants[0] = "Cm in component model_parameters (picoF)"
legend_algebraic[31] = "i_CaT in component i_CaT (picoA)"
legend_algebraic[14] = "i_CaL in component i_CaL (picoA)"
legend_algebraic[49] = "i_f in component i_f (picoA)"
legend_algebraic[50] = "i_st in component i_st (picoA)"
legend_algebraic[37] = "i_Kr in component i_Kr (picoA)"
legend_algebraic[42] = "i_Ks in component i_Ks (picoA)"
legend_algebraic[44] = "i_to in component AP_sensitive_currents (picoA)"
legend_algebraic[46] = "i_sus in component AP_sensitive_currents (picoA)"
legend_algebraic[52] = "i_NaK in component i_NaK (picoA)"
legend_algebraic[66] = "i_NaCa in component i_NaCa (picoA)"
legend_algebraic[53] = "i_b_Ca in component i_b_Ca (picoA)"
legend_algebraic[51] = "i_b_Na in component i_b_Na (picoA)"
legend_constants[75] = "E_Na in component electric_potentials (millivolt)"
legend_constants[76] = "E_K in component electric_potentials (millivolt)"
legend_constants[77] = "E_Ks in component electric_potentials (millivolt)"
legend_constants[1] = "R in component model_parameters (joule_per_kilomole_kelvin)"
legend_constants[2] = "T in component model_parameters (kelvin)"
legend_constants[3] = "F in component model_parameters (coulomb_per_mole)"
legend_constants[4] = "Nai in component model_parameters (millimolar)"
legend_constants[5] = "Nao in component model_parameters (millimolar)"
legend_constants[6] = "Ki in component model_parameters (millimolar)"
legend_constants[7] = "Ko in component model_parameters (millimolar)"
legend_constants[8] = "E_CaL in component i_CaL (millivolt)"
legend_constants[9] = "g_CaL in component i_CaL (nanoS_per_picoF)"
legend_states[1] = "Ca_sub in component calcium_dynamics (millimolar)"
legend_states[2] = "dL in component i_CaL_dL_gate (dimensionless)"
legend_states[3] = "fL in component i_CaL_fL_gate (dimensionless)"
legend_states[4] = "fCa in component i_CaL_fCa_gate (dimensionless)"
legend_algebraic[0] = "dL_infinity in component i_CaL_dL_gate (dimensionless)"
legend_algebraic[45] = "tau_dL in component i_CaL_dL_gate (millisecond)"
legend_algebraic[32] = "alpha_dL in component i_CaL_dL_gate (per_millisecond)"
legend_algebraic[43] = "beta_dL in component i_CaL_dL_gate (per_millisecond)"
legend_algebraic[16] = "adVm in component i_CaL_dL_gate (millivolt)"
legend_algebraic[38] = "bdVm in component i_CaL_dL_gate (millivolt)"
legend_algebraic[1] = "fL_infinity in component i_CaL_fL_gate (dimensionless)"
legend_algebraic[17] = "tau_fL in component i_CaL_fL_gate (millisecond)"
legend_constants[10] = "alpha_fCa in component i_CaL_fCa_gate (per_millisecond)"
legend_algebraic[2] = "fCa_infinity in component i_CaL_fCa_gate (dimensionless)"
legend_algebraic[18] = "tau_fCa in component i_CaL_fCa_gate (millisecond)"
legend_constants[11] = "Km_fCa in component i_CaL_fCa_gate (millimolar)"
legend_constants[12] = "g_CaT in component i_CaT (nanoS_per_picoF)"
legend_constants[13] = "E_CaT in component i_CaT (millivolt)"
legend_states[5] = "dT in component i_CaT_dT_gate (dimensionless)"
legend_states[6] = "fT in component i_CaT_fT_gate (dimensionless)"
legend_algebraic[3] = "dT_infinity in component i_CaT_dT_gate (dimensionless)"
legend_algebraic[19] = "tau_dT in component i_CaT_dT_gate (millisecond)"
legend_algebraic[4] = "fT_infinity in component i_CaT_fT_gate (dimensionless)"
legend_algebraic[20] = "tau_fT in component i_CaT_fT_gate (millisecond)"
legend_constants[14] = "g_Kr in component i_Kr (nanoS_per_picoF)"
legend_states[7] = "paS in component i_Kr_pa_gate (dimensionless)"
legend_states[8] = "paF in component i_Kr_pa_gate (dimensionless)"
legend_states[9] = "pi_ in component i_Kr_pi_gate (dimensionless)"
legend_algebraic[5] = "pa_infinity in component i_Kr_pa_gate (dimensionless)"
legend_algebraic[21] = "tau_paS in component i_Kr_pa_gate (millisecond)"
legend_algebraic[22] = "tau_paF in component i_Kr_pa_gate (millisecond)"
legend_algebraic[6] = "pi_infinity in component i_Kr_pi_gate (dimensionless)"
legend_algebraic[23] = "tau_pi in component i_Kr_pi_gate (millisecond)"
legend_constants[15] = "g_Ks in component i_Ks (nanoS_per_picoF)"
legend_states[10] = "n in component i_Ks_n_gate (dimensionless)"
legend_algebraic[33] = "n_infinity in component i_Ks_n_gate (dimensionless)"
legend_algebraic[39] = "tau_n in component i_Ks_n_gate (millisecond)"
legend_algebraic[7] = "alpha_n in component i_Ks_n_gate (per_millisecond)"
legend_algebraic[24] = "beta_n in component i_Ks_n_gate (per_millisecond)"
legend_constants[16] = "g_to in component AP_sensitive_currents (nanoS_per_picoF)"
legend_constants[17] = "g_sus in component AP_sensitive_currents (nanoS_per_picoF)"
legend_states[11] = "q in component AP_sensitive_currents_q_gate (dimensionless)"
legend_states[12] = "r in component AP_sensitive_currents_r_gate (dimensionless)"
legend_algebraic[8] = "q_infinity in component AP_sensitive_currents_q_gate (dimensionless)"
legend_algebraic[25] = "tau_q in component AP_sensitive_currents_q_gate (millisecond)"
legend_algebraic[9] = "r_infinity in component AP_sensitive_currents_r_gate (dimensionless)"
legend_algebraic[26] = "tau_r in component AP_sensitive_currents_r_gate (millisecond)"
legend_algebraic[47] = "i_f_Na in component i_f (picoA)"
legend_algebraic[48] = "i_f_K in component i_f (picoA)"
legend_constants[18] = "g_if in component i_f (nanoS_per_picoF)"
legend_states[13] = "y in component i_f_y_gate (dimensionless)"
legend_algebraic[10] = "y_infinity in component i_f_y_gate (dimensionless)"
legend_algebraic[27] = "tau_y in component i_f_y_gate (millisecond)"
legend_constants[19] = "VIf_half in component i_f_y_gate (millivolt)"
legend_constants[20] = "g_st in component i_st (nanoS_per_picoF)"
legend_constants[21] = "E_st in component i_st (millivolt)"
legend_states[14] = "qa in component i_st_qa_gate (dimensionless)"
legend_states[15] = "qi in component i_st_qi_gate (dimensionless)"
legend_algebraic[11] = "qa_infinity in component i_st_qa_gate (dimensionless)"
legend_algebraic[40] = "tau_qa in component i_st_qa_gate (millisecond)"
legend_algebraic[28] = "alpha_qa in component i_st_qa_gate (per_millisecond)"
legend_algebraic[34] = "beta_qa in component i_st_qa_gate (per_millisecond)"
legend_algebraic[35] = "qi_infinity in component i_st_qi_gate (dimensionless)"
legend_algebraic[41] = "tau_qi in component i_st_qi_gate (millisecond)"
legend_algebraic[12] = "alpha_qi in component i_st_qi_gate (per_millisecond)"
legend_algebraic[29] = "beta_qi in component i_st_qi_gate (per_millisecond)"
legend_constants[22] = "g_b_Na in component i_b_Na (nanoS_per_picoF)"
legend_constants[23] = "Km_Kp in component i_NaK (millimolar)"
legend_constants[24] = "Km_Nap in component i_NaK (millimolar)"
legend_constants[25] = "i_NaK_max in component i_NaK (picoA_per_picoF)"
legend_constants[26] = "g_b_Ca in component i_b_Ca (nanoS_per_picoF)"
legend_constants[27] = "kNaCa in component i_NaCa (picoA_per_picoF)"
legend_algebraic[63] = "x1 in component i_NaCa (dimensionless)"
legend_algebraic[59] = "x2 in component i_NaCa (dimensionless)"
legend_algebraic[64] = "x3 in component i_NaCa (dimensionless)"
legend_algebraic[65] = "x4 in component i_NaCa (dimensionless)"
legend_algebraic[54] = "k41 in component i_NaCa (dimensionless)"
legend_constants[80] = "k34 in component i_NaCa (dimensionless)"
legend_algebraic[62] = "k23 in component i_NaCa (dimensionless)"
legend_algebraic[61] = "k21 in component i_NaCa (dimensionless)"
legend_algebraic[58] = "k32 in component i_NaCa (dimensionless)"
legend_constants[79] = "k43 in component i_NaCa (dimensionless)"
legend_algebraic[56] = "k12 in component i_NaCa (dimensionless)"
legend_algebraic[57] = "k14 in component i_NaCa (dimensionless)"
legend_constants[28] = "Qci in component i_NaCa (dimensionless)"
legend_constants[29] = "Qn in component i_NaCa (dimensionless)"
legend_constants[30] = "Qco in component i_NaCa (dimensionless)"
legend_constants[31] = "K3ni in component i_NaCa (millimolar)"
legend_constants[32] = "Kci in component i_NaCa (millimolar)"
legend_constants[33] = "K1ni in component i_NaCa (millimolar)"
legend_constants[34] = "K2ni in component i_NaCa (millimolar)"
legend_constants[35] = "Kcni in component i_NaCa (millimolar)"
legend_constants[36] = "K3no in component i_NaCa (millimolar)"
legend_constants[37] = "K1no in component i_NaCa (millimolar)"
legend_constants[38] = "K2no in component i_NaCa (millimolar)"
legend_constants[39] = "Kco in component i_NaCa (millimolar)"
legend_constants[78] = "RTOnF in component i_NaCa (millivolt)"
legend_algebraic[60] = "do in component i_NaCa (dimensionless)"
legend_algebraic[55] = "di in component i_NaCa (dimensionless)"
legend_constants[40] = "Cao in component model_parameters (millimolar)"
legend_algebraic[67] = "j_SRCarel in component j_SRCarel (millimolar_per_millisecond)"
legend_states[16] = "R in component j_SRCarel (dimensionless)"
legend_states[17] = "O in component j_SRCarel (dimensionless)"
legend_states[18] = "I in component j_SRCarel (dimensionless)"
legend_states[19] = "RI in component j_SRCarel (dimensionless)"
legend_constants[41] = "ks in component j_SRCarel (per_millisecond)"
legend_constants[42] = "MaxSR in component j_SRCarel (dimensionless)"
legend_constants[43] = "MinSR in component j_SRCarel (dimensionless)"
legend_constants[44] = "EC50_SR in component j_SRCarel (millimolar)"
legend_constants[45] = "HSR in component j_SRCarel (dimensionless)"
legend_algebraic[30] = "koSRCa in component j_SRCarel (per_millimolar2_millisecond)"
legend_algebraic[36] = "kiSRCa in component j_SRCarel (per_millimolar_millisecond)"
legend_constants[46] = "koCa in component j_SRCarel (per_millimolar2_millisecond)"
legend_constants[47] = "kiCa in component j_SRCarel (per_millimolar_millisecond)"
legend_algebraic[13] = "kCaSR in component j_SRCarel (dimensionless)"
legend_constants[48] = "kim in component j_SRCarel (per_millisecond)"
legend_constants[49] = "kom in component j_SRCarel (per_millisecond)"
legend_states[20] = "Ca_jsr in component calcium_dynamics (millimolar)"
legend_algebraic[68] = "j_Ca_dif in component intracellular_calcium_fluxes (millimolar_per_millisecond)"
legend_algebraic[70] = "j_up in component intracellular_calcium_fluxes (millimolar_per_millisecond)"
legend_algebraic[72] = "j_tr in component intracellular_calcium_fluxes (millimolar_per_millisecond)"
legend_constants[50] = "tau_dif_Ca in component intracellular_calcium_fluxes (millisecond)"
legend_constants[51] = "tau_tr in component intracellular_calcium_fluxes (millisecond)"
legend_constants[52] = "P_up in component intracellular_calcium_fluxes (millimolar_per_millisecond)"
legend_constants[53] = "K_up in component intracellular_calcium_fluxes (millimolar)"
legend_states[21] = "Ca_nsr in component calcium_dynamics (millimolar)"
legend_states[22] = "Cai in component calcium_dynamics (millimolar)"
legend_constants[54] = "TC_tot in component calcium_buffering (millimolar)"
legend_constants[55] = "TMC_tot in component calcium_buffering (millimolar)"
legend_constants[56] = "CM_tot in component calcium_buffering (millimolar)"
legend_constants[57] = "CQ_tot in component calcium_buffering (millimolar)"
legend_algebraic[71] = "delta_fTC in component calcium_buffering (per_millisecond)"
legend_algebraic[73] = "delta_fTMC in component calcium_buffering (per_millisecond)"
legend_algebraic[69] = "delta_fCMs in component calcium_buffering (per_millisecond)"
legend_algebraic[75] = "delta_fCMi in component calcium_buffering (per_millisecond)"
legend_algebraic[74] = "delta_fCQ in component calcium_buffering (per_millisecond)"
legend_algebraic[15] = "delta_fTMM in component calcium_buffering (per_millisecond)"
legend_states[23] = "fTMM in component calcium_buffering (dimensionless)"
legend_states[24] = "fCMi in component calcium_buffering (dimensionless)"
legend_states[25] = "fCMs in component calcium_buffering (dimensionless)"
legend_states[26] = "fTC in component calcium_buffering (dimensionless)"
legend_states[27] = "fTMC in component calcium_buffering (dimensionless)"
legend_states[28] = "fCQ in component calcium_buffering (dimensionless)"
legend_constants[58] = "kf_TC in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[59] = "kf_TMM in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[60] = "kf_TMC in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[61] = "kf_CM in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[62] = "kf_CQ in component calcium_buffering (per_millimolar_millisecond)"
legend_constants[63] = "kb_TC in component calcium_buffering (per_millisecond)"
legend_constants[64] = "kb_TMC in component calcium_buffering (per_millisecond)"
legend_constants[65] = "kb_TMM in component calcium_buffering (per_millisecond)"
legend_constants[66] = "kb_CM in component calcium_buffering (per_millisecond)"
legend_constants[67] = "kb_CQ in component calcium_buffering (per_millisecond)"
legend_constants[68] = "Mgi in component model_parameters (millimolar)"
legend_constants[84] = "V_i in component model_parameters (picolitre)"
legend_constants[83] = "V_jsr in component model_parameters (picolitre)"
legend_constants[85] = "V_nsr in component model_parameters (picolitre)"
legend_constants[82] = "V_sub in component model_parameters (picolitre)"
legend_constants[81] = "V_cell in component model_parameters (picolitre)"
legend_constants[69] = "V_jsr_part in component model_parameters (dimensionless)"
legend_constants[70] = "V_i_part in component model_parameters (dimensionless)"
legend_constants[71] = "V_nsr_part in component model_parameters (dimensionless)"
legend_constants[72] = "R_cell in component model_parameters (micrometre)"
legend_constants[73] = "L_cell in component model_parameters (micrometre)"
legend_constants[74] = "L_sub in component model_parameters (micrometre)"
legend_rates[0] = "d/dt Vm in component Vm (millivolt)"
legend_rates[2] = "d/dt dL in component i_CaL_dL_gate (dimensionless)"
legend_rates[3] = "d/dt fL in component i_CaL_fL_gate (dimensionless)"
legend_rates[4] = "d/dt fCa in component i_CaL_fCa_gate (dimensionless)"
legend_rates[5] = "d/dt dT in component i_CaT_dT_gate (dimensionless)"
legend_rates[6] = "d/dt fT in component i_CaT_fT_gate (dimensionless)"
legend_rates[7] = "d/dt paS in component i_Kr_pa_gate (dimensionless)"
legend_rates[8] = "d/dt paF in component i_Kr_pa_gate (dimensionless)"
legend_rates[9] = "d/dt pi_ in component i_Kr_pi_gate (dimensionless)"
legend_rates[10] = "d/dt n in component i_Ks_n_gate (dimensionless)"
legend_rates[11] = "d/dt q in component AP_sensitive_currents_q_gate (dimensionless)"
legend_rates[12] = "d/dt r in component AP_sensitive_currents_r_gate (dimensionless)"
legend_rates[13] = "d/dt y in component i_f_y_gate (dimensionless)"
legend_rates[14] = "d/dt qa in component i_st_qa_gate (dimensionless)"
legend_rates[15] = "d/dt qi in component i_st_qi_gate (dimensionless)"
legend_rates[16] = "d/dt R in component j_SRCarel (dimensionless)"
legend_rates[17] = "d/dt O in component j_SRCarel (dimensionless)"
legend_rates[18] = "d/dt I in component j_SRCarel (dimensionless)"
legend_rates[19] = "d/dt RI in component j_SRCarel (dimensionless)"
legend_rates[26] = "d/dt fTC in component calcium_buffering (dimensionless)"
legend_rates[27] = "d/dt fTMC in component calcium_buffering (dimensionless)"
legend_rates[23] = "d/dt fTMM in component calcium_buffering (dimensionless)"
legend_rates[24] = "d/dt fCMi in component calcium_buffering (dimensionless)"
legend_rates[25] = "d/dt fCMs in component calcium_buffering (dimensionless)"
legend_rates[28] = "d/dt fCQ in component calcium_buffering (dimensionless)"
legend_rates[22] = "d/dt Cai in component calcium_dynamics (millimolar)"
legend_rates[1] = "d/dt Ca_sub in component calcium_dynamics (millimolar)"
legend_rates[21] = "d/dt Ca_nsr in component calcium_dynamics (millimolar)"
legend_rates[20] = "d/dt Ca_jsr in component calcium_dynamics (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = -65
constants[0] = 32
constants[1] = 8314.4
constants[2] = 310.15
constants[3] = 96485
constants[4] = 10
constants[5] = 140
constants[6] = 140
constants[7] = 5.4
constants[8] = 45
constants[9] = 0.464
states[1] = 0.000223
states[2] = 0
states[3] = 1
states[4] = 1
constants[10] = 0.021
constants[11] = 0.00035
constants[12] = 0.1832
constants[13] = 45
states[5] = 0
states[6] = 1
constants[14] = 0.08113973
states[7] = 0
states[8] = 0
states[9] = 1
constants[15] = 0.0259
states[10] = 0
constants[16] = 0.252
constants[17] = 0.02
states[11] = 1
states[12] = 0
constants[18] = 0.15
states[13] = 1
constants[19] = -64
constants[20] = 0.003
constants[21] = 37.4
states[14] = 0
states[15] = 1
constants[22] = 0.00486
constants[23] = 1.4
constants[24] = 14
constants[25] = 2.88
constants[26] = 0.0006
constants[27] = 187.5
constants[28] = 0.1369
constants[29] = 0.4315
constants[30] = 0
constants[31] = 26.44
constants[32] = 0.0207
constants[33] = 395.3
constants[34] = 2.289
constants[35] = 26.44
constants[36] = 4.663
constants[37] = 1628
constants[38] = 561.4
constants[39] = 3.663
constants[40] = 2
states[16] = 0.7499955
states[17] = 3.4e-6
states[18] = 1.1e-6
states[19] = 0.25
constants[41] = 250000
constants[42] = 15
constants[43] = 1
constants[44] = 0.45
constants[45] = 2.5
constants[46] = 10
constants[47] = 0.5
constants[48] = 0.005
constants[49] = 0.06
states[20] = 0.029
constants[50] = 0.04
constants[51] = 40
constants[52] = 0.012
constants[53] = 0.0006
states[21] = 1.35
states[22] = 0.0001
constants[54] = 0.031
constants[55] = 0.062
constants[56] = 0.045
constants[57] = 10
states[23] = 0.69
states[24] = 0.042
states[25] = 0.089
states[26] = 0.02
states[27] = 0.22
states[28] = 0.032
constants[58] = 88.8
constants[59] = 2.277
constants[60] = 227.7
constants[61] = 227.7
constants[62] = 0.534
constants[63] = 0.446
constants[64] = 0.00751
constants[65] = 0.751
constants[66] = 0.542
constants[67] = 0.445
constants[68] = 2.5
constants[69] = 0.0012
constants[70] = 0.46
constants[71] = 0.0116
constants[72] = 4
constants[73] = 70
constants[74] = 0.02
constants[75] = ((constants[1]*constants[2])/constants[3])*log(constants[5]/constants[4])
constants[76] = ((constants[1]*constants[2])/constants[3])*log(constants[7]/constants[6])
constants[77] = ((constants[1]*constants[2])/constants[3])*log((constants[7]+0.120000*constants[5])/(constants[6]+0.120000*constants[4]))
constants[78] = (constants[1]*constants[2])/constants[3]
constants[79] = constants[4]/(constants[31]+constants[4])
constants[80] = constants[5]/(constants[36]+constants[5])
constants[81] = 0.00100000* pi*(power(constants[72], 2.00000))*constants[73]
constants[82] = 0.00100000*2.00000* pi*constants[74]*(constants[72]-constants[74]/2.00000)*constants[73]
constants[83] = constants[69]*constants[81]
constants[84] = constants[70]*constants[81]-constants[82]
constants[85] = constants[71]*constants[81]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[15] = constants[59]*constants[68]*(1.00000-(states[27]+states[23]))-constants[65]*states[23]
rates[23] = algebraic[15]
algebraic[1] = 1.00000/(1.00000+exp((states[0]+35.0000)/7.30000))
algebraic[17] = 44.3000+257.100*exp(-(power((states[0]+32.5000)/13.9000, 2.00000)))
rates[3] = (algebraic[1]-states[3])/algebraic[17]
algebraic[2] = constants[11]/(constants[11]+states[1])
algebraic[18] = algebraic[2]/constants[10]
rates[4] = (algebraic[2]-states[4])/algebraic[18]
algebraic[3] = 1.00000/(1.00000+exp(-(states[0]+26.3000)/6.00000))
algebraic[19] = 1.00000/(1.06800*exp((states[0]+26.3000)/30.0000)+1.06800*exp(-(states[0]+26.3000)/30.0000))
rates[5] = (algebraic[3]-states[5])/algebraic[19]
algebraic[4] = 1.00000/(1.00000+exp((states[0]+61.7000)/5.60000))
algebraic[20] = 1.00000/(0.0153000*exp(-(states[0]+61.7000)/83.3000)+0.0150000*exp((states[0]+61.7000)/15.3800))
rates[6] = (algebraic[4]-states[6])/algebraic[20]
algebraic[5] = 1.00000/(1.00000+exp(-(states[0]+23.2000)/10.6000))
algebraic[21] = 0.846554/(0.00420000*exp(states[0]/17.0000)+0.000150000*exp(-states[0]/21.6000))
rates[7] = (algebraic[5]-states[7])/algebraic[21]
algebraic[22] = 0.846554/(0.0372000*exp(states[0]/15.9000)+0.000960000*exp(-states[0]/22.5000))
rates[8] = (algebraic[5]-states[8])/algebraic[22]
algebraic[6] = 1.00000/(1.00000+exp((states[0]+28.6000)/17.1000))
algebraic[23] = 1.00000/(0.100000*exp(-states[0]/54.6450)+0.656000*exp(states[0]/106.157))
rates[9] = (algebraic[6]-states[9])/algebraic[23]
algebraic[8] = 1.00000/(1.00000+exp((states[0]+49.0000)/13.0000))
algebraic[25] = 6.06000+39.1020/(0.570000*exp(-0.0800000*(states[0]+44.0000))+0.0650000*exp(0.100000*(states[0]+45.9300)))
rates[11] = (algebraic[8]-states[11])/algebraic[25]
algebraic[9] = 1.00000/(1.00000+exp(-(states[0]-19.3000)/15.0000))
algebraic[26] = 2.75352+14.4052/(1.03700*exp(0.0900000*(states[0]+30.6100))+0.369000*exp(-0.120000*(states[0]+23.8400)))
rates[12] = (algebraic[9]-states[12])/algebraic[26]
algebraic[10] = 1.00000/(1.00000+exp((states[0]-constants[19])/13.5000))
algebraic[27] = 0.716653/(exp(-(states[0]+386.900)/45.3020)+exp((states[0]-73.0800)/19.2310))
rates[13] = (algebraic[10]-states[13])/algebraic[27]
algebraic[13] = constants[42]-(constants[42]-constants[43])/(1.00000+power(constants[44]/states[20], constants[45]))
algebraic[30] = constants[46]/algebraic[13]
algebraic[36] = constants[47]*algebraic[13]
rates[16] = (constants[48]*states[19]-algebraic[36]*states[1]*states[16])-(algebraic[30]*(power(states[1], 2.00000))*states[16]-constants[49]*states[17])
rates[17] = (algebraic[30]*(power(states[1], 2.00000))*states[16]-constants[49]*states[17])-(algebraic[36]*states[1]*states[17]-constants[48]*states[18])
rates[18] = (algebraic[36]*states[1]*states[17]-constants[48]*states[18])-(constants[49]*states[18]-algebraic[30]*(power(states[1], 2.00000))*states[19])
rates[19] = (constants[49]*states[18]-algebraic[30]*(power(states[1], 2.00000))*states[19])-(constants[48]*states[19]-algebraic[36]*states[1]*states[16])
algebraic[7] = 0.0140000/(1.00000+exp(-(states[0]-40.0000)/9.00000))
algebraic[24] = 0.00100000*exp(-states[0]/45.0000)
algebraic[33] = algebraic[7]/(algebraic[7]+algebraic[24])
algebraic[39] = 1.00000/(algebraic[7]+algebraic[24])
rates[10] = (algebraic[33]-states[10])/algebraic[39]
algebraic[11] = 1.00000/(1.00000+exp(-(states[0]+57.0000)/5.00000))
algebraic[28] = 1.00000/(0.150000*exp(-states[0]/11.0000)+0.200000*exp(-states[0]/700.000))
algebraic[34] = 1.00000/(16.0000*exp(states[0]/8.00000)+15.0000*exp(states[0]/50.0000))
algebraic[40] = 1.00000/(algebraic[28]+algebraic[34])
rates[14] = (algebraic[11]-states[14])/algebraic[40]
algebraic[12] = 1.00000/(3100.00*exp(states[0]/13.0000)+700.000*exp(states[0]/70.0000))
algebraic[29] = 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[35] = algebraic[12]/(algebraic[12]+algebraic[29])
algebraic[41] = 6.65000/(algebraic[12]+algebraic[29])
rates[15] = (algebraic[35]-states[15])/algebraic[41]
algebraic[0] = 1.00000/(1.00000+exp(-(states[0]+13.5000)/6.00000))
algebraic[16] = custom_piecewise([equal(states[0] , -35.0000), -35.0000 , equal(states[0] , 0.00000), 1.00000e-05 , True, states[0]])
algebraic[32] = (-0.0283900*(algebraic[16]+35.0000))/(exp(-(algebraic[16]+35.0000)/2.50000)-1.00000)-(0.0849000*algebraic[16])/(exp(-algebraic[16]/4.80000)-1.00000)
algebraic[38] = custom_piecewise([equal(states[0] , 5.00000), 5.00001 , True, states[0]])
algebraic[43] = (0.0114300*(algebraic[38]-5.00000))/(exp((algebraic[38]-5.00000)/2.50000)-1.00000)
algebraic[45] = 1.00000/(algebraic[32]+algebraic[43])
rates[2] = (algebraic[0]-states[2])/algebraic[45]
algebraic[31] = constants[0]*constants[12]*(states[0]-constants[13])*states[5]*states[6]
algebraic[14] = constants[0]*constants[9]*(states[0]-constants[8])*states[2]*states[3]*states[4]
algebraic[47] = constants[0]*0.383300*constants[18]*(states[0]-constants[75])*(power(states[13], 2.00000))
algebraic[48] = constants[0]*0.616700*constants[18]*(states[0]-constants[76])*(power(states[13], 2.00000))
algebraic[49] = algebraic[47]+algebraic[48]
algebraic[50] = constants[0]*constants[20]*(states[0]-constants[21])*states[14]*states[15]
algebraic[37] = constants[0]*constants[14]*(states[0]-constants[76])*(0.600000*states[8]+0.400000*states[7])*states[9]
algebraic[42] = constants[0]*constants[15]*(states[0]-constants[77])*(power(states[10], 2.00000))
algebraic[44] = constants[0]*constants[16]*(states[0]-constants[76])*states[11]*states[12]
algebraic[46] = constants[0]*constants[17]*(states[0]-constants[76])*states[12]
algebraic[52] = (constants[0]*constants[25])/((1.00000+power(constants[23]/constants[7], 1.20000))*(1.00000+power(constants[24]/constants[4], 1.30000))*(1.00000+exp(-((states[0]-constants[75])+120.000)/30.0000)))
algebraic[54] = exp((-constants[29]*states[0])/(2.00000*constants[78]))
algebraic[60] = 1.00000+(constants[40]/constants[39])*(1.00000+exp((constants[30]*states[0])/constants[78]))+(constants[5]/constants[37])*(1.00000+(constants[5]/constants[38])*(1.00000+constants[5]/constants[36]))
algebraic[62] = ((((constants[5]/constants[37])*constants[5])/constants[38])*(1.00000+constants[5]/constants[36])*exp((-constants[29]*states[0])/(2.00000*constants[78])))/algebraic[60]
algebraic[61] = ((constants[40]/constants[39])*exp((constants[30]*states[0])/constants[78]))/algebraic[60]
algebraic[58] = exp((constants[29]*states[0])/(2.00000*constants[78]))
algebraic[63] = algebraic[54]*constants[80]*(algebraic[62]+algebraic[61])+algebraic[61]*algebraic[58]*(constants[79]+algebraic[54])
algebraic[55] = 1.00000+(states[1]/constants[32])*(1.00000+exp((-constants[28]*states[0])/constants[78])+constants[4]/constants[35])+(constants[4]/constants[33])*(1.00000+(constants[4]/constants[34])*(1.00000+constants[4]/constants[31]))
algebraic[56] = ((states[1]/constants[32])*exp((-constants[28]*states[0])/constants[78]))/algebraic[55]
algebraic[57] = ((((constants[4]/constants[33])*constants[4])/constants[34])*(1.00000+constants[4]/constants[31])*exp((constants[29]*states[0])/(2.00000*constants[78])))/algebraic[55]
algebraic[59] = algebraic[58]*constants[79]*(algebraic[57]+algebraic[56])+algebraic[54]*algebraic[56]*(constants[80]+algebraic[58])
algebraic[64] = algebraic[57]*constants[79]*(algebraic[62]+algebraic[61])+algebraic[56]*algebraic[62]*(constants[79]+algebraic[54])
algebraic[65] = algebraic[62]*constants[80]*(algebraic[57]+algebraic[56])+algebraic[57]*algebraic[61]*(constants[80]+algebraic[58])
algebraic[66] = (constants[0]*constants[27]*(algebraic[59]*algebraic[61]-algebraic[63]*algebraic[56]))/(algebraic[63]+algebraic[59]+algebraic[64]+algebraic[65])
algebraic[53] = constants[0]*constants[26]*(states[0]-constants[8])
algebraic[51] = constants[0]*constants[22]*(states[0]-constants[75])
rates[0] = -(algebraic[14]+algebraic[31]+algebraic[49]+algebraic[50]+algebraic[37]+algebraic[42]+algebraic[44]+algebraic[46]+algebraic[52]+algebraic[66]+algebraic[53]+algebraic[51])/constants[0]
algebraic[69] = constants[61]*states[1]*(1.00000-states[25])-constants[66]*states[25]
rates[25] = algebraic[69]
algebraic[67] = constants[41]*states[17]*(states[20]-states[1])
algebraic[68] = (states[1]-states[22])/constants[50]
rates[1] = (algebraic[67]*constants[83])/constants[82]-(((algebraic[14]+algebraic[31]+algebraic[53])-2.00000*algebraic[66])/(2.00000*constants[3]*constants[82])+algebraic[68]+constants[56]*algebraic[69])
algebraic[71] = constants[58]*states[22]*(1.00000-states[26])-constants[63]*states[26]
rates[26] = algebraic[71]
algebraic[70] = constants[52]/(1.00000+constants[53]/states[22])
algebraic[72] = (states[21]-states[20])/constants[51]
rates[21] = algebraic[70]-(algebraic[72]*constants[83])/constants[85]
algebraic[73] = constants[60]*states[22]*(1.00000-(states[27]+states[23]))-constants[64]*states[27]
rates[27] = algebraic[73]
algebraic[74] = constants[62]*states[20]*(1.00000-states[28])-constants[67]*states[28]
rates[28] = algebraic[74]
rates[20] = algebraic[72]-(algebraic[67]+constants[57]*algebraic[74])
algebraic[75] = constants[61]*states[22]*(1.00000-states[24])-constants[66]*states[24]
rates[24] = algebraic[75]
rates[22] = (algebraic[68]*constants[82]-algebraic[70]*constants[85])/constants[84]-(constants[56]*algebraic[75]+constants[54]*algebraic[71]+constants[55]*algebraic[73])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[15] = constants[59]*constants[68]*(1.00000-(states[27]+states[23]))-constants[65]*states[23]
algebraic[1] = 1.00000/(1.00000+exp((states[0]+35.0000)/7.30000))
algebraic[17] = 44.3000+257.100*exp(-(power((states[0]+32.5000)/13.9000, 2.00000)))
algebraic[2] = constants[11]/(constants[11]+states[1])
algebraic[18] = algebraic[2]/constants[10]
algebraic[3] = 1.00000/(1.00000+exp(-(states[0]+26.3000)/6.00000))
algebraic[19] = 1.00000/(1.06800*exp((states[0]+26.3000)/30.0000)+1.06800*exp(-(states[0]+26.3000)/30.0000))
algebraic[4] = 1.00000/(1.00000+exp((states[0]+61.7000)/5.60000))
algebraic[20] = 1.00000/(0.0153000*exp(-(states[0]+61.7000)/83.3000)+0.0150000*exp((states[0]+61.7000)/15.3800))
algebraic[5] = 1.00000/(1.00000+exp(-(states[0]+23.2000)/10.6000))
algebraic[21] = 0.846554/(0.00420000*exp(states[0]/17.0000)+0.000150000*exp(-states[0]/21.6000))
algebraic[22] = 0.846554/(0.0372000*exp(states[0]/15.9000)+0.000960000*exp(-states[0]/22.5000))
algebraic[6] = 1.00000/(1.00000+exp((states[0]+28.6000)/17.1000))
algebraic[23] = 1.00000/(0.100000*exp(-states[0]/54.6450)+0.656000*exp(states[0]/106.157))
algebraic[8] = 1.00000/(1.00000+exp((states[0]+49.0000)/13.0000))
algebraic[25] = 6.06000+39.1020/(0.570000*exp(-0.0800000*(states[0]+44.0000))+0.0650000*exp(0.100000*(states[0]+45.9300)))
algebraic[9] = 1.00000/(1.00000+exp(-(states[0]-19.3000)/15.0000))
algebraic[26] = 2.75352+14.4052/(1.03700*exp(0.0900000*(states[0]+30.6100))+0.369000*exp(-0.120000*(states[0]+23.8400)))
algebraic[10] = 1.00000/(1.00000+exp((states[0]-constants[19])/13.5000))
algebraic[27] = 0.716653/(exp(-(states[0]+386.900)/45.3020)+exp((states[0]-73.0800)/19.2310))
algebraic[13] = constants[42]-(constants[42]-constants[43])/(1.00000+power(constants[44]/states[20], constants[45]))
algebraic[30] = constants[46]/algebraic[13]
algebraic[36] = constants[47]*algebraic[13]
algebraic[7] = 0.0140000/(1.00000+exp(-(states[0]-40.0000)/9.00000))
algebraic[24] = 0.00100000*exp(-states[0]/45.0000)
algebraic[33] = algebraic[7]/(algebraic[7]+algebraic[24])
algebraic[39] = 1.00000/(algebraic[7]+algebraic[24])
algebraic[11] = 1.00000/(1.00000+exp(-(states[0]+57.0000)/5.00000))
algebraic[28] = 1.00000/(0.150000*exp(-states[0]/11.0000)+0.200000*exp(-states[0]/700.000))
algebraic[34] = 1.00000/(16.0000*exp(states[0]/8.00000)+15.0000*exp(states[0]/50.0000))
algebraic[40] = 1.00000/(algebraic[28]+algebraic[34])
algebraic[12] = 1.00000/(3100.00*exp(states[0]/13.0000)+700.000*exp(states[0]/70.0000))
algebraic[29] = 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[35] = algebraic[12]/(algebraic[12]+algebraic[29])
algebraic[41] = 6.65000/(algebraic[12]+algebraic[29])
algebraic[0] = 1.00000/(1.00000+exp(-(states[0]+13.5000)/6.00000))
algebraic[16] = custom_piecewise([equal(states[0] , -35.0000), -35.0000 , equal(states[0] , 0.00000), 1.00000e-05 , True, states[0]])
algebraic[32] = (-0.0283900*(algebraic[16]+35.0000))/(exp(-(algebraic[16]+35.0000)/2.50000)-1.00000)-(0.0849000*algebraic[16])/(exp(-algebraic[16]/4.80000)-1.00000)
algebraic[38] = custom_piecewise([equal(states[0] , 5.00000), 5.00001 , True, states[0]])
algebraic[43] = (0.0114300*(algebraic[38]-5.00000))/(exp((algebraic[38]-5.00000)/2.50000)-1.00000)
algebraic[45] = 1.00000/(algebraic[32]+algebraic[43])
algebraic[31] = constants[0]*constants[12]*(states[0]-constants[13])*states[5]*states[6]
algebraic[14] = constants[0]*constants[9]*(states[0]-constants[8])*states[2]*states[3]*states[4]
algebraic[47] = constants[0]*0.383300*constants[18]*(states[0]-constants[75])*(power(states[13], 2.00000))
algebraic[48] = constants[0]*0.616700*constants[18]*(states[0]-constants[76])*(power(states[13], 2.00000))
algebraic[49] = algebraic[47]+algebraic[48]
algebraic[50] = constants[0]*constants[20]*(states[0]-constants[21])*states[14]*states[15]
algebraic[37] = constants[0]*constants[14]*(states[0]-constants[76])*(0.600000*states[8]+0.400000*states[7])*states[9]
algebraic[42] = constants[0]*constants[15]*(states[0]-constants[77])*(power(states[10], 2.00000))
algebraic[44] = constants[0]*constants[16]*(states[0]-constants[76])*states[11]*states[12]
algebraic[46] = constants[0]*constants[17]*(states[0]-constants[76])*states[12]
algebraic[52] = (constants[0]*constants[25])/((1.00000+power(constants[23]/constants[7], 1.20000))*(1.00000+power(constants[24]/constants[4], 1.30000))*(1.00000+exp(-((states[0]-constants[75])+120.000)/30.0000)))
algebraic[54] = exp((-constants[29]*states[0])/(2.00000*constants[78]))
algebraic[60] = 1.00000+(constants[40]/constants[39])*(1.00000+exp((constants[30]*states[0])/constants[78]))+(constants[5]/constants[37])*(1.00000+(constants[5]/constants[38])*(1.00000+constants[5]/constants[36]))
algebraic[62] = ((((constants[5]/constants[37])*constants[5])/constants[38])*(1.00000+constants[5]/constants[36])*exp((-constants[29]*states[0])/(2.00000*constants[78])))/algebraic[60]
algebraic[61] = ((constants[40]/constants[39])*exp((constants[30]*states[0])/constants[78]))/algebraic[60]
algebraic[58] = exp((constants[29]*states[0])/(2.00000*constants[78]))
algebraic[63] = algebraic[54]*constants[80]*(algebraic[62]+algebraic[61])+algebraic[61]*algebraic[58]*(constants[79]+algebraic[54])
algebraic[55] = 1.00000+(states[1]/constants[32])*(1.00000+exp((-constants[28]*states[0])/constants[78])+constants[4]/constants[35])+(constants[4]/constants[33])*(1.00000+(constants[4]/constants[34])*(1.00000+constants[4]/constants[31]))
algebraic[56] = ((states[1]/constants[32])*exp((-constants[28]*states[0])/constants[78]))/algebraic[55]
algebraic[57] = ((((constants[4]/constants[33])*constants[4])/constants[34])*(1.00000+constants[4]/constants[31])*exp((constants[29]*states[0])/(2.00000*constants[78])))/algebraic[55]
algebraic[59] = algebraic[58]*constants[79]*(algebraic[57]+algebraic[56])+algebraic[54]*algebraic[56]*(constants[80]+algebraic[58])
algebraic[64] = algebraic[57]*constants[79]*(algebraic[62]+algebraic[61])+algebraic[56]*algebraic[62]*(constants[79]+algebraic[54])
algebraic[65] = algebraic[62]*constants[80]*(algebraic[57]+algebraic[56])+algebraic[57]*algebraic[61]*(constants[80]+algebraic[58])
algebraic[66] = (constants[0]*constants[27]*(algebraic[59]*algebraic[61]-algebraic[63]*algebraic[56]))/(algebraic[63]+algebraic[59]+algebraic[64]+algebraic[65])
algebraic[53] = constants[0]*constants[26]*(states[0]-constants[8])
algebraic[51] = constants[0]*constants[22]*(states[0]-constants[75])
algebraic[69] = constants[61]*states[1]*(1.00000-states[25])-constants[66]*states[25]
algebraic[67] = constants[41]*states[17]*(states[20]-states[1])
algebraic[68] = (states[1]-states[22])/constants[50]
algebraic[71] = constants[58]*states[22]*(1.00000-states[26])-constants[63]*states[26]
algebraic[70] = constants[52]/(1.00000+constants[53]/states[22])
algebraic[72] = (states[21]-states[20])/constants[51]
algebraic[73] = constants[60]*states[22]*(1.00000-(states[27]+states[23]))-constants[64]*states[27]
algebraic[74] = constants[62]*states[20]*(1.00000-states[28])-constants[67]*states[28]
algebraic[75] = constants[61]*states[22]*(1.00000-states[24])-constants[66]*states[24]
return algebraic
def custom_piecewise(cases):
"""Compute result of a piecewise function"""
return select(cases[0::2],cases[1::2])
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)