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 = 35
sizeStates = 16
sizeConstants = 134
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 (second)"
legend_states[0] = "ADP_m in component ADP_m (millimolar)"
legend_algebraic[32] = "V_ANT in component calcium_dynamics (flux)"
legend_algebraic[30] = "V_ATPase in component oxidative_phosphorylation (flux)"
legend_algebraic[11] = "V_SL in component V_SL (flux)"
legend_states[1] = "NADH in component NADH (millimolar)"
legend_algebraic[26] = "V_O2 in component oxidative_phosphorylation (flux)"
legend_algebraic[9] = "V_IDH in component V_IDH (flux)"
legend_algebraic[10] = "V_KGDH in component V_KGDH (flux)"
legend_algebraic[13] = "V_MDH in component V_MDH (flux)"
legend_states[2] = "ISOC in component ISOC (millimolar)"
legend_algebraic[8] = "V_ACO in component V_ACO (flux)"
legend_states[3] = "alpha_KG in component alpha_KG (millimolar)"
legend_algebraic[15] = "V_AAT in component V_AAT (flux)"
legend_states[4] = "SCoA in component SCoA (millimolar)"
legend_states[5] = "Suc in component Suc (millimolar)"
legend_algebraic[12] = "V_SDH in component V_SDH (flux)"
legend_states[6] = "FUM in component FUM (millimolar)"
legend_algebraic[16] = "V_FH in component V_FH (flux)"
legend_states[7] = "MAL in component MAL (millimolar)"
legend_states[8] = "OAA in component OAA (millimolar)"
legend_algebraic[7] = "V_CS in component V_CS (flux)"
legend_states[9] = "ASP in component ASP (millimolar)"
legend_algebraic[18] = "V_C_ASP in component V_C_ASP (flux)"
legend_states[10] = "Ca_m in component Ca_m (micromolar)"
legend_constants[0] = "f in component Ca_m (dimensionless)"
legend_algebraic[33] = "V_uni in component calcium_dynamics (flux)"
legend_algebraic[34] = "V_NaCa in component calcium_dynamics (flux)"
legend_algebraic[1] = "Ca_i in component Ca_i (micromolar)"
legend_constants[1] = "stim_start in component Ca_i (second)"
legend_constants[2] = "stim_end in component Ca_i (second)"
legend_algebraic[0] = "stim_period in component Ca_i (second)"
legend_constants[3] = "stim_duration in component Ca_i (second)"
legend_constants[4] = "pulse_value in component Ca_i (micromolar)"
legend_constants[5] = "Na_i in component Na_i (millimolar)"
legend_constants[6] = "ATP_i in component ATP_i (millimolar)"
legend_algebraic[2] = "ATP_m in component ATP_m (millimolar)"
legend_constants[7] = "Cm in component ATP_m (millimolar)"
legend_algebraic[3] = "ADP_i in component ADP_i (millimolar)"
legend_constants[8] = "pulse_value in component ADP_i (millimolar)"
legend_constants[9] = "GLU in component GLU (millimolar)"
legend_constants[10] = "Mg in component Mg (millimolar)"
legend_constants[11] = "H in component H (millimolar)"
legend_constants[12] = "Pi in component Pi (millimolar)"
legend_constants[13] = "CoA in component CoA (millimolar)"
legend_constants[14] = "AcCoA in component AcCoA (millimolar)"
legend_constants[15] = "FAD in component FAD (millimolar)"
legend_constants[16] = "FADH2 in component FADH2 (millimolar)"
legend_algebraic[4] = "NAD in component NAD (millimolar)"
legend_constants[17] = "C_PN in component NAD (millimolar)"
legend_constants[18] = "NADPH in component NADPH (millimolar)"
legend_states[11] = "O2_m in component O2_m (millimolar)"
legend_constants[19] = "shunt in component O2_m (dimensionless)"
legend_algebraic[20] = "VTr_ROS in component VTr_ROS (flux)"
legend_states[12] = "O2_i in component O2_i (millimolar)"
legend_algebraic[14] = "V_SOD in component V_SOD (flux)"
legend_states[13] = "H2O2 in component H2O2 (millimolar)"
legend_algebraic[19] = "V_CAT in component V_CAT (flux)"
legend_algebraic[21] = "V_GPX in component V_GPX (flux)"
legend_states[14] = "GSH in component GSH (millimolar)"
legend_algebraic[23] = "V_GR in component V_GR (flux)"
legend_algebraic[5] = "GSSG in component GSSG (millimolar)"
legend_constants[20] = "GT in component GSSG (millimolar)"
legend_algebraic[6] = "CIT in component CIT (millimolar)"
legend_constants[21] = "C_Kint in component CIT (millimolar)"
legend_states[15] = "delta_psi_m in component mitochondrial_membrane (volt)"
legend_constants[22] = "R in component mitochondrial_membrane (volt_coulomb_per_mole_kelvin)"
legend_constants[23] = "T in component mitochondrial_membrane (kelvin)"
legend_constants[24] = "F in component mitochondrial_membrane (coulomb_per_mole)"
legend_constants[25] = "C_mito in component mitochondrial_membrane (millimolar_per_volt)"
legend_algebraic[25] = "V_He in component oxidative_phosphorylation (flux)"
legend_algebraic[27] = "V_He_F in component oxidative_phosphorylation (flux)"
legend_algebraic[31] = "V_Hu in component oxidative_phosphorylation (flux)"
legend_algebraic[28] = "V_Hleak in component oxidative_phosphorylation (flux)"
legend_constants[26] = "Km_AcCoA in component V_CS (millimolar)"
legend_constants[27] = "Km_OAA in component V_CS (millimolar)"
legend_constants[28] = "Kcat_CS in component V_CS (first_order_rate_constant)"
legend_constants[29] = "ET_CS in component V_CS (millimolar)"
legend_constants[30] = "Kf_ACO in component V_ACO (first_order_rate_constant)"
legend_constants[31] = "KE_ACO in component V_ACO (dimensionless)"
legend_constants[32] = "Kh_1 in component V_IDH (millimolar)"
legend_constants[33] = "Kh_2 in component V_IDH (millimolar)"
legend_constants[34] = "Km_ISOC in component V_IDH (millimolar)"
legend_constants[35] = "Ka_ADP in component V_IDH (millimolar)"
legend_constants[36] = "Ka_Ca in component V_IDH (micromolar)"
legend_constants[37] = "Km_NAD in component V_IDH (millimolar)"
legend_constants[38] = "Ki_NADH in component V_IDH (millimolar)"
legend_constants[39] = "Kcat_IDH in component V_IDH (first_order_rate_constant)"
legend_constants[40] = "ET_IDH in component V_IDH (millimolar)"
legend_constants[41] = "ni in component V_IDH (dimensionless)"
legend_constants[42] = "Km_alpha_KG in component V_KGDH (millimolar)"
legend_constants[43] = "Kcat_KGDH in component V_KGDH (first_order_rate_constant)"
legend_constants[44] = "ET_KGDH in component V_KGDH (millimolar)"
legend_constants[45] = "Kd_Mg in component V_KGDH (millimolar)"
legend_constants[46] = "Kd_Ca in component V_KGDH (micromolar)"
legend_constants[47] = "n_alpha_KG in component V_KGDH (dimensionless)"
legend_constants[48] = "Km_NAD in component V_KGDH (millimolar)"
legend_constants[49] = "kf_SL in component V_SL (second_order_rate_constant)"
legend_constants[50] = "Ke_SL in component V_SL (millimolar)"
legend_constants[51] = "Kisdh_OAA in component V_SDH (millimolar)"
legend_constants[52] = "Kcat_SDH in component V_SDH (first_order_rate_constant)"
legend_constants[53] = "ET_SDH in component V_SDH (millimolar)"
legend_constants[54] = "Km_Suc in component V_SDH (millimolar)"
legend_constants[55] = "Ki_FUM in component V_SDH (millimolar)"
legend_constants[56] = "Km_MAL in component V_MDH (millimolar)"
legend_constants[57] = "Kcat_MDH in component V_MDH (first_order_rate_constant)"
legend_constants[58] = "ET_MDH in component V_MDH (millimolar)"
legend_constants[59] = "Ki_OAA in component V_MDH (millimolar)"
legend_constants[132] = "fh_a in component V_MDH (dimensionless)"
legend_constants[133] = "fh_i in component V_MDH (dimensionless)"
legend_constants[60] = "Km_NAD in component V_MDH (millimolar)"
legend_constants[61] = "kh1 in component V_MDH (millimolar)"
legend_constants[62] = "kh2 in component V_MDH (millimolar)"
legend_constants[63] = "kh3 in component V_MDH (millimolar)"
legend_constants[64] = "kh4 in component V_MDH (millimolar)"
legend_constants[65] = "k_offset in component V_MDH (dimensionless)"
legend_constants[66] = "Ke_FH in component V_FH (dimensionless)"
legend_constants[67] = "kf_FH in component V_FH (first_order_rate_constant)"
legend_constants[68] = "Ke_AAT in component V_AAT (dimensionless)"
legend_constants[69] = "kf_AAT in component V_AAT (second_order_rate_constant)"
legend_constants[70] = "k_C_ASP in component V_C_ASP (first_order_rate_constant)"
legend_constants[71] = "k1_SOD in component V_SOD (second_order_rate_constant)"
legend_constants[72] = "k3_SOD in component V_SOD (second_order_rate_constant)"
legend_constants[73] = "k5_SOD in component V_SOD (first_order_rate_constant)"
legend_constants[74] = "ET_SOD in component V_SOD (millimolar)"
legend_constants[75] = "Ki_H2O2 in component V_SOD (millimolar)"
legend_constants[76] = "k1_CAT in component V_CAT (second_order_rate_constant)"
legend_constants[77] = "ET_CAT in component V_CAT (millimolar)"
legend_constants[78] = "fr in component V_CAT (per_millimolar)"
legend_constants[79] = "phi1_GPX in component V_GPX (millimolar_second)"
legend_constants[80] = "phi2_GPX in component V_GPX (millimolar_second)"
legend_constants[81] = "ET_GPX in component V_GPX (millimolar)"
legend_constants[82] = "k1_GR in component V_GR (first_order_rate_constant)"
legend_constants[83] = "KM_GSSG in component V_GR (millimolar)"
legend_constants[84] = "KM_NADPH in component V_GR (millimolar)"
legend_constants[85] = "ET_GR in component V_GR (millimolar)"
legend_algebraic[17] = "V_IMAC in component V_IMAC (flux)"
legend_constants[86] = "Gmax in component V_IMAC (millimolar_per_second_volt)"
legend_constants[87] = "GL in component V_IMAC (millimolar_per_second_volt)"
legend_constants[88] = "a in component V_IMAC (dimensionless)"
legend_constants[89] = "b in component V_IMAC (dimensionless)"
legend_constants[90] = "kappa in component V_IMAC (per_volt)"
legend_constants[91] = "delta_psi_bm in component V_IMAC (volt)"
legend_constants[92] = "Kcc in component V_IMAC (millimolar)"
legend_constants[93] = "j in component VTr_ROS (dimensionless)"
legend_constants[94] = "rho_res in component oxidative_phosphorylation (millimolar)"
legend_constants[95] = "rho_res_F in component oxidative_phosphorylation (millimolar)"
legend_constants[96] = "ra in component oxidative_phosphorylation (first_order_rate_constant)"
legend_constants[97] = "rc1 in component oxidative_phosphorylation (first_order_rate_constant)"
legend_algebraic[22] = "Ares in component oxidative_phosphorylation (volt)"
legend_constants[131] = "Ares_F in component oxidative_phosphorylation (volt)"
legend_constants[98] = "r1 in component oxidative_phosphorylation (dimensionless)"
legend_constants[99] = "r2 in component oxidative_phosphorylation (dimensionless)"
legend_constants[100] = "r3 in component oxidative_phosphorylation (dimensionless)"
legend_constants[101] = "rb in component oxidative_phosphorylation (first_order_rate_constant)"
legend_constants[102] = "rc2 in component oxidative_phosphorylation (first_order_rate_constant)"
legend_constants[103] = "Kres in component oxidative_phosphorylation (dimensionless)"
legend_constants[104] = "Kres_F in component oxidative_phosphorylation (dimensionless)"
legend_constants[105] = "gH in component oxidative_phosphorylation (millimolar_per_second_volt)"
legend_constants[106] = "delta_psi_B in component oxidative_phosphorylation (volt)"
legend_constants[107] = "g in component oxidative_phosphorylation (dimensionless)"
legend_algebraic[24] = "delta_mu_H in component oxidative_phosphorylation (volt)"
legend_constants[108] = "delta_pH in component oxidative_phosphorylation (dimensionless)"
legend_constants[109] = "rho_F1 in component oxidative_phosphorylation (millimolar)"
legend_constants[110] = "pa in component oxidative_phosphorylation (first_order_rate_constant)"
legend_constants[111] = "pc1 in component oxidative_phosphorylation (first_order_rate_constant)"
legend_algebraic[29] = "AF1 in component oxidative_phosphorylation (volt)"
legend_constants[112] = "p1 in component oxidative_phosphorylation (dimensionless)"
legend_constants[113] = "p2 in component oxidative_phosphorylation (dimensionless)"
legend_constants[114] = "p3 in component oxidative_phosphorylation (dimensionless)"
legend_constants[115] = "pb in component oxidative_phosphorylation (first_order_rate_constant)"
legend_constants[116] = "pc2 in component oxidative_phosphorylation (first_order_rate_constant)"
legend_constants[117] = "KF1 in component oxidative_phosphorylation (millimolar)"
legend_constants[118] = "h in component calcium_dynamics (dimensionless)"
legend_constants[119] = "delta_psi_0 in component calcium_dynamics (volt)"
legend_constants[120] = "Vmax_ANT in component calcium_dynamics (flux)"
legend_constants[121] = "L in component calcium_dynamics (dimensionless)"
legend_constants[122] = "na in component calcium_dynamics (dimensionless)"
legend_constants[123] = "Vmax_uni in component calcium_dynamics (flux)"
legend_constants[124] = "K_act in component calcium_dynamics (micromolar)"
legend_constants[125] = "K_trans in component calcium_dynamics (micromolar)"
legend_constants[126] = "n in component calcium_dynamics (dimensionless)"
legend_constants[127] = "Vmax_NaCa in component calcium_dynamics (flux)"
legend_constants[128] = "KNa in component calcium_dynamics (millimolar)"
legend_constants[129] = "KCa in component calcium_dynamics (micromolar)"
legend_constants[130] = "b in component calcium_dynamics (dimensionless)"
legend_rates[0] = "d/dt ADP_m in component ADP_m (millimolar)"
legend_rates[1] = "d/dt NADH in component NADH (millimolar)"
legend_rates[2] = "d/dt ISOC in component ISOC (millimolar)"
legend_rates[3] = "d/dt alpha_KG in component alpha_KG (millimolar)"
legend_rates[4] = "d/dt SCoA in component SCoA (millimolar)"
legend_rates[5] = "d/dt Suc in component Suc (millimolar)"
legend_rates[6] = "d/dt FUM in component FUM (millimolar)"
legend_rates[7] = "d/dt MAL in component MAL (millimolar)"
legend_rates[8] = "d/dt OAA in component OAA (millimolar)"
legend_rates[9] = "d/dt ASP in component ASP (millimolar)"
legend_rates[10] = "d/dt Ca_m in component Ca_m (micromolar)"
legend_rates[11] = "d/dt O2_m in component O2_m (millimolar)"
legend_rates[12] = "d/dt O2_i in component O2_i (millimolar)"
legend_rates[13] = "d/dt H2O2 in component H2O2 (millimolar)"
legend_rates[14] = "d/dt GSH in component GSH (millimolar)"
legend_rates[15] = "d/dt delta_psi_m in component mitochondrial_membrane (volt)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.1
states[1] = 0.01
states[2] = 0.01
states[3] = 0.01
states[4] = 0.01
states[5] = 0.01
states[6] = 0.01
states[7] = 0.01
states[8] = 0.01
states[9] = 0.01
states[10] = 0.01
constants[0] = 0.0003
constants[1] = 0
constants[2] = 10000
constants[3] = 0.4
constants[4] = 1
constants[5] = 10.0
constants[6] = 6.5
constants[7] = 15.0
constants[8] = 0.15
constants[9] = 20
constants[10] = 0.4
constants[11] = 2.5E-5
constants[12] = 20.0
constants[13] = 0.02
constants[14] = 0.0002
constants[15] = 0.01
constants[16] = 1.24
constants[17] = 10.0
constants[18] = 1.0
states[11] = 0.01
constants[19] = 0.05
states[12] = 0.01
states[13] = 0.01
states[14] = 0.01
constants[20] = 1.0
constants[21] = 1.0
states[15] = 0.01
constants[22] = 8.315
constants[23] = 310.16
constants[24] = 96480
constants[25] = 1.812
constants[26] = 1.26E-2
constants[27] = 6.4E-4
constants[28] = 3.2
constants[29] = 0.4
constants[30] = 12.5
constants[31] = 2.22
constants[32] = 8.1E-5
constants[33] = 5.98E-5
constants[34] = 1.52
constants[35] = 6.2E-2
constants[36] = 1.41
constants[37] = 0.923
constants[38] = 0.19
constants[39] = 1.94
constants[40] = 0.109
constants[41] = 1
constants[42] = 1.94
constants[43] = 0.15
constants[44] = 0.5
constants[45] = 0.0308
constants[46] = 1.27
constants[47] = 1.2
constants[48] = 38.7
constants[49] = 0.127
constants[50] = 3.115
constants[51] = 0.15
constants[52] = 1.0
constants[53] = 0.5
constants[54] = 3.0E-2
constants[55] = 1.3
constants[56] = 1.493
constants[57] = 2.775E1
constants[58] = 0.154
constants[59] = 3.1E-3
constants[60] = 0.2244
constants[61] = 1.13E-5
constants[62] = 26.7
constants[63] = 6.68E-9
constants[64] = 5.62E-6
constants[65] = 3.99E-2
constants[66] = 1.0
constants[67] = 0.83
constants[68] = 6.6
constants[69] = 0.644
constants[70] = 0.01
constants[71] = 2.4E6
constants[72] = 4.8E4
constants[73] = 5.0E-1
constants[74] = 0.4E-3
constants[75] = 0.5
constants[76] = 1.7E4
constants[77] = 0.001
constants[78] = 50.0
constants[79] = 0.15
constants[80] = 0.5
constants[81] = 0.00141
constants[82] = 0.0308
constants[83] = 1.94
constants[84] = 38.7
constants[85] = 1.27E-3
constants[86] = 7.82
constants[87] = 0.0782
constants[88] = 1.0E-3
constants[89] = 1.0E4
constants[90] = 70.0
constants[91] = 0.004
constants[92] = 0.01
constants[93] = 0.12
constants[94] = 0.0006
constants[95] = 0.0045
constants[96] = 6.394E-10
constants[97] = 2.656E-19
constants[98] = 2.077E-18
constants[99] = 1.728E-9
constants[100] = 1.059E-26
constants[101] = 1.762E-13
constants[102] = 8.632E-27
constants[103] = 1.35E18
constants[104] = 5.765E13
constants[105] = 0.01
constants[106] = 0.05
constants[107] = 0.85
constants[108] = -0.6
constants[109] = 0.06
constants[110] = 1.656E-5
constants[111] = 9.651E-14
constants[112] = 1.346E-8
constants[113] = 7.739E-7
constants[114] = 6.65E-15
constants[115] = 3.373E-7
constants[116] = 4.585E-14
constants[117] = 1.71E6
constants[118] = 0.5
constants[119] = 0.091
constants[120] = 0.05
constants[121] = 110.0
constants[122] = 2.8
constants[123] = 0.000625
constants[124] = 0.38
constants[125] = 19.0
constants[126] = 3.0
constants[127] = 0.005
constants[128] = 9.4
constants[129] = 3.75E-1
constants[130] = 0.5
constants[131] = ((constants[22]*constants[23])/constants[24])*log(constants[104]*(power(constants[16]/constants[15], 0.500000)))
constants[132] = 1.00000/(1.00000+constants[11]/constants[61]+(power(constants[11], 2.00000))/(constants[61]*constants[62]))+constants[65]
constants[133] = power(1.00000/(1.00000+constants[63]/constants[11]+(constants[63]*constants[64])/(power(constants[11], 2.00000))), 2.00000)
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[4] = constants[17]-states[1]
algebraic[9] = (constants[39]*constants[40])/(1.00000+constants[11]/constants[32]+constants[33]/constants[11]+(power(constants[34]/states[2], constants[41]))/((1.00000+states[0]/constants[35])*(1.00000+states[10]/constants[36]))+(constants[37]/algebraic[4])*(1.00000+states[1]/constants[38])+((power(constants[34]/states[2], constants[41]))*(constants[37]/algebraic[4])*(1.00000+states[1]/constants[38]))/((1.00000+states[0]/constants[35])*(1.00000+states[10]/constants[36])))
algebraic[6] = constants[21]-(states[2]+states[3]+states[4]+states[5]+states[6]+states[7]+states[8])
algebraic[8] = constants[30]*(algebraic[6]-states[2]/constants[31])
rates[2] = algebraic[8]-algebraic[9]
algebraic[2] = constants[7]-states[0]
algebraic[11] = constants[49]*(states[4]*states[0]-(states[5]*algebraic[2]*constants[13])/constants[50])
algebraic[10] = (constants[43]*constants[44])/(1.00000+(power(constants[42]/states[3], constants[47]))/((1.00000+constants[10]/constants[45])*(1.00000+states[10]/constants[46]))+(constants[48]/algebraic[4])/((1.00000+constants[10]/constants[45])*(1.00000+states[10]/constants[46])))
rates[4] = algebraic[10]-algebraic[11]
algebraic[12] = (constants[52]*constants[53])/(1.00000+(constants[54]/states[5])*(1.00000+states[8]/constants[51])*(1.00000+states[6]/constants[55]))
rates[5] = algebraic[11]-algebraic[12]
algebraic[15] = constants[69]*(states[8]*constants[9]-(states[3]*states[9])/constants[68])
rates[3] = algebraic[15]+algebraic[9]+-algebraic[10]
algebraic[16] = constants[67]*(states[6]-states[7]/constants[66])
rates[6] = algebraic[12]-algebraic[16]
algebraic[13] = (constants[57]*constants[58]*constants[132]*constants[133])/(1.00000+(constants[56]/states[7])*(1.00000+states[8]/constants[59])+constants[60]/algebraic[4]+(constants[56]/states[7])*(1.00000+states[8]/constants[59])*(constants[60]/algebraic[4]))
rates[7] = algebraic[16]-algebraic[13]
algebraic[7] = (constants[28]*constants[29])/(1.00000+constants[26]/constants[14]+constants[27]/states[8]+(constants[26]/constants[14])*(constants[27]/states[8]))
rates[8] = algebraic[13]-(algebraic[7]+algebraic[15])
algebraic[18] = constants[70]*states[9]
rates[9] = algebraic[15]-algebraic[18]
algebraic[17] = (constants[88]+constants[89]/(1.00000+constants[92]/states[12]))*(constants[87]+constants[86]/(1.00000+exp(constants[90]*(constants[91]-states[15]))))*states[15]
algebraic[20] = constants[93]*(algebraic[17]/states[15])*(states[15]-((constants[22]*constants[23])/constants[24])*log(states[11]/states[12], 10))
algebraic[14] = (2.00000*constants[71]*constants[73]*(constants[71]+constants[72]*(1.00000+states[13]/constants[75]))*constants[74]*states[12])/(constants[73]*(2.00000*constants[71]+constants[72]*(1.00000+states[13]/constants[75]))+states[12]*constants[71]*constants[72]*(1.00000+states[13]/constants[75]))
rates[12] = algebraic[20]-algebraic[14]
algebraic[19] = 2.00000*constants[76]*constants[77]*states[13]*exp(-constants[78]*states[13])
algebraic[21] = (constants[81]*states[13]*states[14])/(constants[79]*states[14]+constants[80]*states[13])
rates[13] = algebraic[14]-(algebraic[19]+algebraic[21])
algebraic[5] = 2.00000*(constants[20]-states[14])
algebraic[23] = (constants[82]*constants[85])/(1.00000+constants[83]/algebraic[5]+constants[84]/constants[18]+(constants[83]/algebraic[5])*(constants[84]/constants[18]))
rates[14] = algebraic[23]-algebraic[21]
algebraic[22] = ((constants[22]*constants[23])/constants[24])*log(constants[103]*(power(states[1]/algebraic[4], 0.500000)))
algebraic[24] = ((constants[22]*constants[23])/constants[24])*constants[108]+states[15]
algebraic[26] = 0.500000*constants[94]*((((constants[96]+constants[97]*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23])))*exp((algebraic[22]*constants[24])/(constants[22]*constants[23]))-constants[96]*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))+constants[102]*exp((algebraic[22]*constants[24])/(constants[22]*constants[23]))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[98]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[99]+constants[100]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
rates[1] = -algebraic[26]+algebraic[9]+algebraic[10]+algebraic[13]
rates[11] = constants[19]*algebraic[26]-algebraic[20]
algebraic[3] = custom_piecewise([greater_equal(voi , 100.000) & less(voi , 300.000), constants[8] , True, 0.0500000])
algebraic[32] = constants[120]*((1.00000-(0.0500000*constants[6]*0.450000*0.800000*states[0])/(0.450000*algebraic[3]*0.0500000*algebraic[2]))/((1.00000+((0.0500000*constants[6])/(0.450000*algebraic[3]))*exp((-constants[118]*constants[24]*constants[119])/(constants[22]*constants[23])))*(1.00000+(0.450000*0.800000*states[0])/(0.0500000*algebraic[2]))))
algebraic[29] = ((constants[22]*constants[23])/constants[24])*log(constants[117]*(algebraic[2]/(states[0]*constants[12])))
algebraic[30] = -constants[109]*(((100.000*constants[110]+constants[111]*exp((3.00000*constants[24]*constants[106])/(constants[22]*constants[23])))*exp((algebraic[29]*constants[24])/(constants[22]*constants[23]))-(constants[110]*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))+constants[116]*exp((algebraic[29]*constants[24])/(constants[22]*constants[23]))*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))/((1.00000+constants[112]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[113]+constants[114]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
rates[0] = algebraic[32]-(algebraic[30]+algebraic[11])
algebraic[0] = custom_piecewise([greater_equal(voi , 100.000) & less(voi , 300.000), 0.500000 , True, 4.00000])
algebraic[1] = custom_piecewise([greater_equal(voi , constants[1]) & less_equal(voi , constants[2]) & less_equal((voi-constants[1])-floor((voi-constants[1])/algebraic[0])*algebraic[0] , constants[3]), constants[4] , True, 0.100000])
algebraic[33] = constants[123]*(((algebraic[1]/constants[125])*(power(1.00000+algebraic[1]/constants[125], 3.00000))*((2.00000*constants[24]*(states[15]-constants[119]))/(constants[22]*constants[23])))/(power(1.00000+algebraic[1]/constants[125], 4.00000)+(constants[121]/(power(1.00000+algebraic[1]/constants[124], constants[122])))*(1.00000-exp((-2.00000*constants[24]*(states[15]-constants[119]))/(constants[22]*constants[23])))))
algebraic[34] = constants[127]*((exp((constants[130]*constants[24]*(states[15]-constants[119]))/(constants[22]*constants[23]))*exp(log(algebraic[1]/states[10])))/((power(1.00000+constants[128]/constants[5], constants[126]))*(1.00000+constants[129]/states[10])))
rates[10] = constants[0]*1.00000*(algebraic[33]-algebraic[34])
algebraic[25] = 6.00000*constants[94]*((constants[96]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23]))-(constants[96]+constants[101])*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[98]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[99]+constants[100]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[27] = 6.00000*constants[95]*((constants[96]*exp((constants[24]*constants[131])/(constants[22]*constants[23]))-(constants[96]+constants[101])*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[98]*exp((constants[24]*constants[131])/(constants[22]*constants[23])))*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[99]+constants[100]*exp((constants[24]*constants[131])/(constants[22]*constants[23])))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[31] = -3.00000*constants[109]*((100.000*constants[110]*(1.00000+exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))-(constants[110]+constants[115])*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[112]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[113]+constants[114]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[28] = constants[105]*algebraic[24]
rates[15] = (algebraic[25]+algebraic[27]+-(algebraic[31]+algebraic[32]+algebraic[28]+algebraic[34]+2.00000*algebraic[33]))/constants[25]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[4] = constants[17]-states[1]
algebraic[9] = (constants[39]*constants[40])/(1.00000+constants[11]/constants[32]+constants[33]/constants[11]+(power(constants[34]/states[2], constants[41]))/((1.00000+states[0]/constants[35])*(1.00000+states[10]/constants[36]))+(constants[37]/algebraic[4])*(1.00000+states[1]/constants[38])+((power(constants[34]/states[2], constants[41]))*(constants[37]/algebraic[4])*(1.00000+states[1]/constants[38]))/((1.00000+states[0]/constants[35])*(1.00000+states[10]/constants[36])))
algebraic[6] = constants[21]-(states[2]+states[3]+states[4]+states[5]+states[6]+states[7]+states[8])
algebraic[8] = constants[30]*(algebraic[6]-states[2]/constants[31])
algebraic[2] = constants[7]-states[0]
algebraic[11] = constants[49]*(states[4]*states[0]-(states[5]*algebraic[2]*constants[13])/constants[50])
algebraic[10] = (constants[43]*constants[44])/(1.00000+(power(constants[42]/states[3], constants[47]))/((1.00000+constants[10]/constants[45])*(1.00000+states[10]/constants[46]))+(constants[48]/algebraic[4])/((1.00000+constants[10]/constants[45])*(1.00000+states[10]/constants[46])))
algebraic[12] = (constants[52]*constants[53])/(1.00000+(constants[54]/states[5])*(1.00000+states[8]/constants[51])*(1.00000+states[6]/constants[55]))
algebraic[15] = constants[69]*(states[8]*constants[9]-(states[3]*states[9])/constants[68])
algebraic[16] = constants[67]*(states[6]-states[7]/constants[66])
algebraic[13] = (constants[57]*constants[58]*constants[132]*constants[133])/(1.00000+(constants[56]/states[7])*(1.00000+states[8]/constants[59])+constants[60]/algebraic[4]+(constants[56]/states[7])*(1.00000+states[8]/constants[59])*(constants[60]/algebraic[4]))
algebraic[7] = (constants[28]*constants[29])/(1.00000+constants[26]/constants[14]+constants[27]/states[8]+(constants[26]/constants[14])*(constants[27]/states[8]))
algebraic[18] = constants[70]*states[9]
algebraic[17] = (constants[88]+constants[89]/(1.00000+constants[92]/states[12]))*(constants[87]+constants[86]/(1.00000+exp(constants[90]*(constants[91]-states[15]))))*states[15]
algebraic[20] = constants[93]*(algebraic[17]/states[15])*(states[15]-((constants[22]*constants[23])/constants[24])*log(states[11]/states[12], 10))
algebraic[14] = (2.00000*constants[71]*constants[73]*(constants[71]+constants[72]*(1.00000+states[13]/constants[75]))*constants[74]*states[12])/(constants[73]*(2.00000*constants[71]+constants[72]*(1.00000+states[13]/constants[75]))+states[12]*constants[71]*constants[72]*(1.00000+states[13]/constants[75]))
algebraic[19] = 2.00000*constants[76]*constants[77]*states[13]*exp(-constants[78]*states[13])
algebraic[21] = (constants[81]*states[13]*states[14])/(constants[79]*states[14]+constants[80]*states[13])
algebraic[5] = 2.00000*(constants[20]-states[14])
algebraic[23] = (constants[82]*constants[85])/(1.00000+constants[83]/algebraic[5]+constants[84]/constants[18]+(constants[83]/algebraic[5])*(constants[84]/constants[18]))
algebraic[22] = ((constants[22]*constants[23])/constants[24])*log(constants[103]*(power(states[1]/algebraic[4], 0.500000)))
algebraic[24] = ((constants[22]*constants[23])/constants[24])*constants[108]+states[15]
algebraic[26] = 0.500000*constants[94]*((((constants[96]+constants[97]*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23])))*exp((algebraic[22]*constants[24])/(constants[22]*constants[23]))-constants[96]*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))+constants[102]*exp((algebraic[22]*constants[24])/(constants[22]*constants[23]))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[98]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[99]+constants[100]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[3] = custom_piecewise([greater_equal(voi , 100.000) & less(voi , 300.000), constants[8] , True, 0.0500000])
algebraic[32] = constants[120]*((1.00000-(0.0500000*constants[6]*0.450000*0.800000*states[0])/(0.450000*algebraic[3]*0.0500000*algebraic[2]))/((1.00000+((0.0500000*constants[6])/(0.450000*algebraic[3]))*exp((-constants[118]*constants[24]*constants[119])/(constants[22]*constants[23])))*(1.00000+(0.450000*0.800000*states[0])/(0.0500000*algebraic[2]))))
algebraic[29] = ((constants[22]*constants[23])/constants[24])*log(constants[117]*(algebraic[2]/(states[0]*constants[12])))
algebraic[30] = -constants[109]*(((100.000*constants[110]+constants[111]*exp((3.00000*constants[24]*constants[106])/(constants[22]*constants[23])))*exp((algebraic[29]*constants[24])/(constants[22]*constants[23]))-(constants[110]*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))+constants[116]*exp((algebraic[29]*constants[24])/(constants[22]*constants[23]))*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))/((1.00000+constants[112]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[113]+constants[114]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[0] = custom_piecewise([greater_equal(voi , 100.000) & less(voi , 300.000), 0.500000 , True, 4.00000])
algebraic[1] = custom_piecewise([greater_equal(voi , constants[1]) & less_equal(voi , constants[2]) & less_equal((voi-constants[1])-floor((voi-constants[1])/algebraic[0])*algebraic[0] , constants[3]), constants[4] , True, 0.100000])
algebraic[33] = constants[123]*(((algebraic[1]/constants[125])*(power(1.00000+algebraic[1]/constants[125], 3.00000))*((2.00000*constants[24]*(states[15]-constants[119]))/(constants[22]*constants[23])))/(power(1.00000+algebraic[1]/constants[125], 4.00000)+(constants[121]/(power(1.00000+algebraic[1]/constants[124], constants[122])))*(1.00000-exp((-2.00000*constants[24]*(states[15]-constants[119]))/(constants[22]*constants[23])))))
algebraic[34] = constants[127]*((exp((constants[130]*constants[24]*(states[15]-constants[119]))/(constants[22]*constants[23]))*exp(log(algebraic[1]/states[10])))/((power(1.00000+constants[128]/constants[5], constants[126]))*(1.00000+constants[129]/states[10])))
algebraic[25] = 6.00000*constants[94]*((constants[96]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23]))-(constants[96]+constants[101])*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[98]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[99]+constants[100]*exp((constants[24]*algebraic[22])/(constants[22]*constants[23])))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[27] = 6.00000*constants[95]*((constants[96]*exp((constants[24]*constants[131])/(constants[22]*constants[23]))-(constants[96]+constants[101])*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[98]*exp((constants[24]*constants[131])/(constants[22]*constants[23])))*exp((6.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[99]+constants[100]*exp((constants[24]*constants[131])/(constants[22]*constants[23])))*exp((constants[107]*6.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[31] = -3.00000*constants[109]*((100.000*constants[110]*(1.00000+exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))-(constants[110]+constants[115])*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23])))/((1.00000+constants[112]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*constants[106])/(constants[22]*constants[23]))+(constants[113]+constants[114]*exp((constants[24]*algebraic[29])/(constants[22]*constants[23])))*exp((3.00000*constants[24]*algebraic[24])/(constants[22]*constants[23]))))
algebraic[28] = constants[105]*algebraic[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)