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 = 66
sizeStates = 42
sizeConstants = 94
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] = "Casp8 in component Casp8 (micromolar)"
legend_states[1] = "Casp8Bid in component Casp8 (micromolar)"
legend_states[2] = "FeLnNO in component FeLn (micromolar)"
legend_states[3] = "Bid in component Bid (micromolar)"
legend_algebraic[2] = "J_0 in component Casp8 (flux)"
legend_algebraic[0] = "J_f0 in component Casp8 (flux)"
legend_algebraic[1] = "J_Casp8 in component Casp8 (flux)"
legend_algebraic[3] = "r_20NO in component Casp8 (flux)"
legend_algebraic[61] = "r_19NO in component PTPC (flux)"
legend_constants[0] = "k_f0 in component model_constant (first_order_rate_constant)"
legend_constants[1] = "k_10 in component model_constant (second_order_rate_constant)"
legend_constants[2] = "k_00 in component model_constant (first_order_rate_constant)"
legend_constants[3] = "u in component model_constant (first_order_rate_constant)"
legend_constants[4] = "k_20NO in component model_constant (second_order_rate_constant)"
legend_states[4] = "Apaf_1 in component Apaf_1 (micromolar)"
legend_states[5] = "CytcApaf_1 in component CytcApaf_1 (micromolar)"
legend_states[6] = "Cytc in component Cytc (micromolar)"
legend_algebraic[4] = "J_Apaf_1 in component Apaf_1 (flux)"
legend_algebraic[5] = "J_1 in component Apaf_1 (flux)"
legend_constants[5] = "P_Apaf_1 in component model_constant (flux)"
legend_constants[6] = "k_11 in component model_constant (second_order_rate_constant)"
legend_constants[7] = "k_01 in component model_constant (first_order_rate_constant)"
legend_states[7] = "Apop in component Apop (micromolar)"
legend_algebraic[7] = "J_1b in component CytcApaf_1 (flux)"
legend_constants[8] = "k_11b in component model_constant (rate)"
legend_constants[9] = "k_01b in component model_constant (first_order_rate_constant)"
legend_constants[10] = "p in component model_constant (dimensionless)"
legend_states[8] = "Cytc_mito in component Cytc_mito (micromolar)"
legend_states[9] = "PTPC in component PTPC (micromolar)"
legend_algebraic[8] = "PTPC_act in component Cytc (micromolar)"
legend_constants[11] = "PTPC_0 in component model_constant (micromolar)"
legend_algebraic[12] = "J_14 in component Cytc_mito (flux)"
legend_algebraic[6] = "J_Cytc in component Cytc (flux)"
legend_constants[12] = "k_1 in component model_constant (second_order_rate_constant)"
legend_states[10] = "Bax_2 in component Bax_2 (micromolar)"
legend_algebraic[10] = "J_Cytc_mito in component Cytc_mito (flux)"
legend_constants[13] = "P_Cytc_mito in component model_constant (flux)"
legend_constants[14] = "k14 in component model_constant (second_order_rate_constant)"
legend_algebraic[17] = "J_12b in component tBidBax (flux)"
legend_algebraic[9] = "J_Bax_2 in component Bax_2 (flux)"
legend_states[11] = "tBid_mito in component tBid_mito (micromolar)"
legend_states[12] = "Bax in component Bax (micromolar)"
legend_algebraic[14] = "J_11 in component tBid (flux)"
legend_algebraic[13] = "J_12a in component tBid_mito (flux)"
legend_algebraic[11] = "J_tBid_mito in component tBid_mito (flux)"
legend_constants[15] = "k12a in component model_constant (second_order_rate_constant)"
legend_states[13] = "tBid in component tBid (micromolar)"
legend_algebraic[25] = "J_f8 in component Casp3Bid (flux)"
legend_algebraic[15] = "J_tBid in component tBid (flux)"
legend_constants[16] = "k11 in component model_constant (first_order_rate_constant)"
legend_states[14] = "tBidBax in component tBidBax (micromolar)"
legend_algebraic[16] = "J_tBidBax in component tBidBax (flux)"
legend_constants[17] = "k12b in component model_constant (second_order_rate_constant)"
legend_states[15] = "Bcl_2 in component Bcl_2 (micromolar)"
legend_algebraic[19] = "J_13 in component Bax (flux)"
legend_algebraic[18] = "J_Bax in component Bax (flux)"
legend_constants[91] = "P_Bax in component Bax (flux)"
legend_constants[18] = "k13 in component model_constant (second_order_rate_constant)"
legend_constants[19] = "P_oBax in component model_constant (flux)"
legend_constants[20] = "p53 in component model_constant (micromolar)"
legend_constants[21] = "p53_thresh in component model_constant (micromolar)"
legend_constants[22] = "u_Bax in component model_constant (first_order_rate_constant)"
legend_states[16] = "Casp3 in component Casp3 (micromolar)"
legend_states[17] = "Casp3Bcl_2 in component Casp3Bcl_2 (micromolar)"
legend_algebraic[20] = "J_9 in component Bcl_2 (flux)"
legend_algebraic[22] = "J_Bcl_2 in component Bcl_2 (flux)"
legend_constants[23] = "k_19 in component model_constant (second_order_rate_constant)"
legend_constants[24] = "k_09 in component model_constant (first_order_rate_constant)"
legend_constants[92] = "P_Bcl_2 in component Bcl_2 (flux)"
legend_constants[25] = "P_oBcl_2 in component model_constant (flux)"
legend_constants[26] = "u_Bcl_2 in component model_constant (first_order_rate_constant)"
legend_algebraic[21] = "J_f9 in component Casp3Bcl_2 (flux)"
legend_constants[27] = "k_f9 in component model_constant (first_order_rate_constant)"
legend_states[18] = "Casp3Bid in component Casp3Bid (micromolar)"
legend_algebraic[23] = "J_8 in component Casp3Bid (flux)"
legend_constants[28] = "k_18 in component model_constant (second_order_rate_constant)"
legend_constants[29] = "k_08 in component model_constant (first_order_rate_constant)"
legend_constants[30] = "k_f8 in component model_constant (first_order_rate_constant)"
legend_algebraic[24] = "J_Bid in component Bid (flux)"
legend_constants[31] = "P_Bid in component model_constant (flux)"
legend_states[19] = "IAP in component IAP (micromolar)"
legend_states[20] = "Casp3IAP in component Casp3 (micromolar)"
legend_algebraic[34] = "J_f6 in component Casp9Pro3 (flux)"
legend_algebraic[33] = "J_f6b in component ApopCasp9_2Pro3 (flux)"
legend_algebraic[27] = "J_7 in component Casp3 (flux)"
legend_algebraic[26] = "J_Casp3 in component Casp3 (flux)"
legend_algebraic[65] = "r_22NO in component FeLn (flux)"
legend_constants[32] = "k_17 in component model_constant (second_order_rate_constant)"
legend_constants[33] = "k_07 in component model_constant (first_order_rate_constant)"
legend_algebraic[29] = "J_2 in component Pro9 (flux)"
legend_algebraic[42] = "J_4b in component ApopCasp9 (flux)"
legend_states[21] = "Pro9 in component Pro9 (micromolar)"
legend_states[22] = "ApopPro9 in component Pro9 (micromolar)"
legend_states[23] = "ApopPro9_2 in component ApopPro9_2 (micromolar)"
legend_algebraic[30] = "J_3 in component Pro9 (flux)"
legend_algebraic[28] = "J_Pro9 in component Pro9 (flux)"
legend_constants[34] = "k_12 in component model_constant (second_order_rate_constant)"
legend_constants[35] = "k_02 in component model_constant (first_order_rate_constant)"
legend_constants[36] = "k_13 in component model_constant (second_order_rate_constant)"
legend_constants[37] = "k_03 in component model_constant (first_order_rate_constant)"
legend_constants[38] = "P_Pro9 in component model_constant (flux)"
legend_algebraic[31] = "J_f3 in component ApopPro9_2 (flux)"
legend_constants[39] = "k_f3 in component model_constant (first_order_rate_constant)"
legend_states[24] = "ApopCasp9_2Pro3 in component ApopCasp9_2Pro3 (micromolar)"
legend_states[25] = "ApopCasp9_2 in component ApopCasp9_2 (micromolar)"
legend_states[26] = "Pro3 in component Pro3 (micromolar)"
legend_algebraic[32] = "J_6b in component ApopCasp9_2Pro3 (flux)"
legend_constants[40] = "k_16b in component model_constant (second_order_rate_constant)"
legend_constants[41] = "k_06b in component model_constant (first_order_rate_constant)"
legend_constants[42] = "k_f6b in component model_constant (first_order_rate_constant)"
legend_states[27] = "Casp9Pro3 in component Casp9Pro3 (micromolar)"
legend_algebraic[35] = "J_6 in component Pro3 (flux)"
legend_constants[43] = "k_f6 in component model_constant (first_order_rate_constant)"
legend_states[28] = "Casp9 in component Casp9 (micromolar)"
legend_algebraic[36] = "J_Pro3 in component Pro3 (flux)"
legend_constants[44] = "k_16 in component model_constant (second_order_rate_constant)"
legend_constants[45] = "k_06 in component model_constant (first_order_rate_constant)"
legend_constants[46] = "P_Pro3 in component model_constant (flux)"
legend_states[29] = "Casp9IAP in component IAP (micromolar)"
legend_states[30] = "ApopCasp9IAP in component IAP (micromolar)"
legend_states[31] = "ApopCasp9_2IAP in component IAP (micromolar)"
legend_states[32] = "ApopCasp9 in component ApopCasp9 (micromolar)"
legend_algebraic[37] = "J_5 in component IAP (flux)"
legend_algebraic[38] = "J_5b in component IAP (flux)"
legend_algebraic[39] = "J_5c in component IAP (flux)"
legend_algebraic[41] = "J_IAP in component IAP (flux)"
legend_constants[47] = "P_IAP in component model_constant (flux)"
legend_constants[48] = "k_15 in component model_constant (second_order_rate_constant)"
legend_constants[49] = "k_05 in component model_constant (first_order_rate_constant)"
legend_constants[50] = "k_15b in component model_constant (second_order_rate_constant)"
legend_constants[51] = "k_05b in component model_constant (first_order_rate_constant)"
legend_constants[52] = "k_15c in component model_constant (second_order_rate_constant)"
legend_constants[53] = "k_05c in component model_constant (first_order_rate_constant)"
legend_algebraic[40] = "J_4 in component ApopCasp9 (flux)"
legend_constants[54] = "k_14 in component model_constant (first_order_rate_constant)"
legend_constants[55] = "k_04 in component model_constant (second_order_rate_constant)"
legend_constants[56] = "k_14b in component model_constant (first_order_rate_constant)"
legend_constants[57] = "k_04b in component model_constant (second_order_rate_constant)"
legend_algebraic[43] = "J_Casp9 in component Casp9 (flux)"
legend_algebraic[64] = "r_21NO in component FeLn (flux)"
legend_states[33] = "NO in component NO (micromolar)"
legend_states[34] = "O_2m in component O_2m (micromolar)"
legend_constants[58] = "O_2 in component NO (micromolar)"
legend_states[35] = "NO_2 in component NO (micromolar)"
legend_states[36] = "N2O3 in component N2O3 (micromolar)"
legend_states[37] = "GSNO in component GSNO (micromolar)"
legend_states[38] = "CcOX in component NO (micromolar)"
legend_states[39] = "FeLn in component FeLn (micromolar)"
legend_constants[90] = "r_1NO in component NO (flux)"
legend_algebraic[44] = "r_4NO in component NO (flux)"
legend_algebraic[45] = "r_12aNO in component NO (flux)"
legend_algebraic[46] = "r_12bNOp in component NO (flux)"
legend_algebraic[47] = "r_12bNOm in component NO (flux)"
legend_algebraic[48] = "r_14NO in component NO (flux)"
legend_algebraic[49] = "r_15NO in component NO (flux)"
legend_algebraic[50] = "r_16NO in component NO (flux)"
legend_constants[59] = "k_1NO in component model_constant (flux)"
legend_constants[60] = "k_4NO in component model_constant (second_order_rate_constant)"
legend_constants[61] = "k_12aNO in component model_constant (rate2)"
legend_constants[62] = "k_12bNOp in component model_constant (second_order_rate_constant)"
legend_constants[63] = "k_12bNOm in component model_constant (first_order_rate_constant)"
legend_constants[64] = "k_14NO in component model_constant (first_order_rate_constant)"
legend_constants[65] = "k_15NO in component model_constant (second_order_rate_constant)"
legend_constants[66] = "k_16NO in component model_constant (second_order_rate_constant)"
legend_constants[67] = "SOD in component O_2m (micromolar)"
legend_constants[93] = "r_2NO in component O_2m (flux)"
legend_algebraic[51] = "r_5NO in component O_2m (flux)"
legend_algebraic[52] = "r_10NO in component O_2m (flux)"
legend_constants[68] = "k_2NO in component model_constant (flux)"
legend_constants[69] = "k_5NO in component model_constant (second_order_rate_constant)"
legend_constants[70] = "k_10NO in component model_constant (rate2)"
legend_states[40] = "ONOO_m in component ONOO_m (micromolar)"
legend_states[41] = "GSH in component GSH (micromolar)"
legend_constants[71] = "GPX in component ONOO_m (micromolar)"
legend_constants[72] = "CO_2 in component ONOO_m (micromolar)"
legend_constants[73] = "Cyt_c in component ONOO_m (micromolar)"
legend_algebraic[53] = "r_6NO in component ONOO_m (flux)"
legend_algebraic[54] = "r_7NO in component ONOO_m (flux)"
legend_algebraic[57] = "r_8NO in component ONOO_m (flux)"
legend_algebraic[60] = "r_9NO in component ONOO_m (flux)"
legend_algebraic[63] = "r_18NO in component ONOO_m (flux)"
legend_constants[74] = "k_6NO in component model_constant (second_order_rate_constant)"
legend_constants[75] = "k_7NO in component model_constant (second_order_rate_constant)"
legend_constants[76] = "k_8NO in component model_constant (second_order_rate_constant)"
legend_constants[77] = "k_9NO in component model_constant (second_order_rate_constant)"
legend_constants[78] = "k_18NO in component model_constant (second_order_rate_constant)"
legend_algebraic[55] = "GSSG in component GSH (micromolar)"
legend_constants[79] = "FeLn_0 in component model_constant (micromolar)"
legend_constants[80] = "GSH_0 in component model_constant (micromolar)"
legend_algebraic[56] = "r_11NO in component GSH (flux)"
legend_algebraic[59] = "r_m in component GSH (flux)"
legend_algebraic[62] = "r_17NO in component GSH (flux)"
legend_constants[81] = "k_11NO in component model_constant (second_order_rate_constant)"
legend_constants[82] = "v_m in component model_constant (flux)"
legend_constants[83] = "k_m in component model_constant (micromolar)"
legend_constants[84] = "k_17NO in component model_constant (second_order_rate_constant)"
legend_algebraic[58] = "r_13NO in component N2O3 (flux)"
legend_constants[85] = "k_13NO in component model_constant (first_order_rate_constant)"
legend_constants[86] = "k_21NO in component model_constant (second_order_rate_constant)"
legend_constants[87] = "k_22NO in component model_constant (second_order_rate_constant)"
legend_constants[88] = "k_19NO in component model_constant (second_order_rate_constant)"
legend_constants[89] = "k_17bNO in component model_constant (second_order_rate_constant)"
legend_rates[0] = "d/dt Casp8 in component Casp8 (micromolar)"
legend_rates[1] = "d/dt Casp8Bid in component Casp8 (micromolar)"
legend_rates[4] = "d/dt Apaf_1 in component Apaf_1 (micromolar)"
legend_rates[5] = "d/dt CytcApaf_1 in component CytcApaf_1 (micromolar)"
legend_rates[6] = "d/dt Cytc in component Cytc (micromolar)"
legend_rates[8] = "d/dt Cytc_mito in component Cytc_mito (micromolar)"
legend_rates[10] = "d/dt Bax_2 in component Bax_2 (micromolar)"
legend_rates[11] = "d/dt tBid_mito in component tBid_mito (micromolar)"
legend_rates[13] = "d/dt tBid in component tBid (micromolar)"
legend_rates[14] = "d/dt tBidBax in component tBidBax (micromolar)"
legend_rates[12] = "d/dt Bax in component Bax (micromolar)"
legend_rates[15] = "d/dt Bcl_2 in component Bcl_2 (micromolar)"
legend_rates[17] = "d/dt Casp3Bcl_2 in component Casp3Bcl_2 (micromolar)"
legend_rates[18] = "d/dt Casp3Bid in component Casp3Bid (micromolar)"
legend_rates[3] = "d/dt Bid in component Bid (micromolar)"
legend_rates[20] = "d/dt Casp3IAP in component Casp3 (micromolar)"
legend_rates[16] = "d/dt Casp3 in component Casp3 (micromolar)"
legend_rates[7] = "d/dt Apop in component Apop (micromolar)"
legend_rates[21] = "d/dt Pro9 in component Pro9 (micromolar)"
legend_rates[22] = "d/dt ApopPro9 in component Pro9 (micromolar)"
legend_rates[23] = "d/dt ApopPro9_2 in component ApopPro9_2 (micromolar)"
legend_rates[24] = "d/dt ApopCasp9_2Pro3 in component ApopCasp9_2Pro3 (micromolar)"
legend_rates[27] = "d/dt Casp9Pro3 in component Casp9Pro3 (micromolar)"
legend_rates[26] = "d/dt Pro3 in component Pro3 (micromolar)"
legend_rates[29] = "d/dt Casp9IAP in component IAP (micromolar)"
legend_rates[30] = "d/dt ApopCasp9IAP in component IAP (micromolar)"
legend_rates[31] = "d/dt ApopCasp9_2IAP in component IAP (micromolar)"
legend_rates[19] = "d/dt IAP in component IAP (micromolar)"
legend_rates[32] = "d/dt ApopCasp9 in component ApopCasp9 (micromolar)"
legend_rates[28] = "d/dt Casp9 in component Casp9 (micromolar)"
legend_rates[25] = "d/dt ApopCasp9_2 in component ApopCasp9_2 (micromolar)"
legend_rates[33] = "d/dt NO in component NO (micromolar)"
legend_rates[38] = "d/dt CcOX in component NO (micromolar)"
legend_rates[35] = "d/dt NO_2 in component NO (micromolar)"
legend_rates[34] = "d/dt O_2m in component O_2m (micromolar)"
legend_rates[40] = "d/dt ONOO_m in component ONOO_m (micromolar)"
legend_rates[41] = "d/dt GSH in component GSH (micromolar)"
legend_rates[37] = "d/dt GSNO in component GSNO (micromolar)"
legend_rates[36] = "d/dt N2O3 in component N2O3 (micromolar)"
legend_rates[39] = "d/dt FeLn in component FeLn (micromolar)"
legend_rates[2] = "d/dt FeLnNO in component FeLn (micromolar)"
legend_rates[9] = "d/dt PTPC in component PTPC (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0
states[1] = 0
states[2] = 0
states[3] = 0.004
constants[0] = 0.1
constants[1] = 10
constants[2] = 0.5
constants[3] = 0.006
constants[4] = 66
states[4] = 0.004
states[5] = 0
states[6] = 0
constants[5] = 0.0003
constants[6] = 5
constants[7] = 0.5
states[7] = 0
constants[8] = 50000
constants[9] = 0.5
constants[10] = 4
states[8] = 0.004
states[9] = 0
constants[11] = 0
constants[12] = 1
states[10] = 0
constants[13] = 0.0003
constants[14] = 10
states[11] = 0
states[12] = 0.004
constants[15] = 10
states[13] = 0
constants[16] = 10
states[14] = 0
constants[17] = 10
states[15] = 0.004
constants[18] = 10
constants[19] = 0.00003
constants[20] = 0.0066
constants[21] = 0.004
constants[22] = 0.006
states[16] = 0
states[17] = 0
constants[23] = 10
constants[24] = 0.5
constants[25] = 0.00008
constants[26] = 0.006
constants[27] = 0.1
states[18] = 0
constants[28] = 10
constants[29] = 0.5
constants[30] = 0.1
constants[31] = 0.00003
states[19] = 0.004
states[20] = 0
constants[32] = 5
constants[33] = 0.0035
states[21] = 0.004
states[22] = 0
states[23] = 0
constants[34] = 10
constants[35] = 0.5
constants[36] = 10
constants[37] = 0.5
constants[38] = 0.0003
constants[39] = 0.1
states[24] = 0
states[25] = 0
states[26] = 0.004
constants[40] = 10
constants[41] = 0.5
constants[42] = 0.1
states[27] = 0
constants[43] = 0.001
states[28] = 0
constants[44] = 10
constants[45] = 0.5
constants[46] = 0.0003
states[29] = 0
states[30] = 0
states[31] = 0
states[32] = 0
constants[47] = 0.00003
constants[48] = 5
constants[49] = 0.0035
constants[50] = 5
constants[51] = 0.0035
constants[52] = 5
constants[53] = 0.0035
constants[54] = 5
constants[55] = 0.5
constants[56] = 5
constants[57] = 0.5
states[33] = 0
states[34] = 35
constants[58] = 35
states[35] = 0
states[36] = 0
states[37] = 0
states[38] = 0.1
states[39] = 0.05
constants[59] = 1
constants[60] = 6700
constants[61] = 0.000006
constants[62] = 1100
constants[63] = 81000
constants[64] = 0.0002
constants[65] = 100
constants[66] = 1.21
constants[67] = 10
constants[68] = 0.1
constants[69] = 2400
constants[70] = 0.0006
states[40] = 0
states[41] = 10000
constants[71] = 5.8
constants[72] = 1000
constants[73] = 400
constants[74] = 0.00135
constants[75] = 2
constants[76] = 0.058
constants[77] = 0.025
constants[78] = 1
constants[79] = 0.05
constants[80] = 10000
constants[81] = 66
constants[82] = 320
constants[83] = 50
constants[84] = 66
constants[85] = 1600
constants[86] = 66
constants[87] = 66
constants[88] = 10
constants[89] = 0.0002
constants[90] = constants[59]
constants[91] = constants[19]*(1.00000+(power(constants[20], 4.00000))/(power(constants[20], 4.00000)+power(constants[21], 4.00000)))
constants[92] = (constants[25]*(power(constants[21], 4.00000)))/(power(constants[20], 4.00000)+power(constants[21], 4.00000))
constants[93] = constants[68]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[2] = constants[1]*states[0]*states[3]-constants[2]*states[1]
algebraic[0] = constants[0]*states[1]
rates[1] = algebraic[2]-algebraic[0]
algebraic[4] = constants[5]-constants[3]*states[4]
algebraic[5] = constants[6]*states[6]*states[4]-constants[7]*states[5]
rates[4] = -algebraic[5]+algebraic[4]
algebraic[7] = constants[8]*(power(states[5], constants[10]))-constants[9]*states[7]
rates[5] = algebraic[5]-7.00000*algebraic[7]
algebraic[8] = constants[11]-states[9]
algebraic[12] = constants[14]*states[10]*states[8]
algebraic[6] = -constants[3]*states[6]
rates[6] = (algebraic[12]-algebraic[5])+algebraic[6]+constants[12]*algebraic[8]*states[8]
algebraic[10] = constants[13]-constants[3]*states[8]
rates[8] = -algebraic[12]+algebraic[10]
algebraic[14] = constants[16]*states[13]
algebraic[13] = constants[15]*states[11]*states[12]
algebraic[11] = -constants[3]*states[11]
rates[11] = (algebraic[14]-algebraic[13])+algebraic[11]
algebraic[17] = constants[17]*states[14]*states[12]
algebraic[9] = -constants[3]*states[10]
rates[10] = algebraic[17]+algebraic[9]
algebraic[16] = -constants[3]*states[14]
rates[14] = (algebraic[13]-algebraic[17])+algebraic[16]
algebraic[19] = constants[18]*states[15]*states[12]
algebraic[18] = constants[91]-constants[22]*states[12]
rates[12] = ((-algebraic[13]-algebraic[17])-algebraic[19])+algebraic[18]
algebraic[20] = constants[23]*states[16]*states[15]-constants[24]*states[17]
algebraic[22] = constants[92]-constants[26]*states[15]
rates[15] = (-algebraic[20]-algebraic[19])+algebraic[22]
algebraic[21] = constants[27]*states[17]
rates[17] = algebraic[20]-algebraic[21]
algebraic[25] = constants[30]*states[18]
algebraic[15] = -constants[3]*states[13]
rates[13] = ((algebraic[0]+algebraic[25])-algebraic[14])+algebraic[17]+algebraic[15]
algebraic[23] = constants[28]*states[16]*states[3]-constants[29]*states[18]
rates[18] = algebraic[23]-algebraic[25]
algebraic[24] = constants[31]-constants[3]*states[3]
rates[3] = (-algebraic[2]-algebraic[23])+algebraic[24]
algebraic[27] = constants[32]*states[16]*states[19]-constants[33]*states[20]
rates[20] = algebraic[27]
algebraic[29] = constants[34]*states[7]*states[21]-constants[35]*states[22]
algebraic[30] = constants[36]*states[22]*states[21]-constants[37]*states[23]
algebraic[28] = constants[38]-constants[3]*states[21]
rates[21] = (-algebraic[29]-algebraic[30])+algebraic[28]
rates[22] = algebraic[29]-algebraic[30]
algebraic[31] = constants[39]*states[23]
rates[23] = algebraic[30]-algebraic[31]
algebraic[33] = constants[42]*states[24]
algebraic[32] = constants[40]*states[25]*states[26]-constants[41]*states[24]
rates[24] = algebraic[32]-algebraic[33]
algebraic[34] = constants[43]*states[27]
algebraic[35] = constants[44]*states[28]*states[26]-constants[45]*states[27]
rates[27] = algebraic[35]-algebraic[34]
algebraic[36] = constants[46]-constants[3]*states[26]
rates[26] = (-algebraic[35]-algebraic[32])+algebraic[36]
algebraic[37] = constants[48]*states[28]*states[19]-constants[49]*states[29]
rates[29] = algebraic[37]
algebraic[38] = constants[50]*states[32]*states[19]-constants[51]*states[30]
rates[30] = algebraic[38]
algebraic[39] = constants[52]*states[25]*states[19]-constants[53]*states[31]
rates[31] = algebraic[39]
algebraic[41] = constants[47]-constants[3]*states[19]
rates[19] = (((-algebraic[37]-algebraic[38])-algebraic[39])-algebraic[27])+algebraic[41]
algebraic[40] = constants[54]*states[25]-constants[55]*states[32]*states[28]
rates[25] = (((algebraic[31]-algebraic[40])-algebraic[39])-algebraic[32])+algebraic[33]
algebraic[42] = constants[56]*states[32]-constants[57]*states[7]*states[28]
rates[7] = (algebraic[7]-algebraic[29])+algebraic[42]
rates[32] = (algebraic[40]-algebraic[42])-algebraic[38]
algebraic[45] = constants[61]*(power(states[33], 2.00000))*constants[58]
algebraic[46] = constants[62]*states[35]*states[33]
algebraic[47] = constants[63]*states[36]
rates[35] = (2.00000*algebraic[45]-algebraic[46])+algebraic[47]
algebraic[49] = constants[65]*states[38]*states[33]
rates[38] = -algebraic[49]
algebraic[44] = constants[60]*states[33]*states[34]
algebraic[48] = constants[64]*states[37]
algebraic[50] = constants[66]*states[39]*states[33]
rates[33] = (((((constants[90]-algebraic[44])-2.00000*algebraic[45])-algebraic[46])+algebraic[47]+algebraic[48])-algebraic[49])-algebraic[50]
algebraic[51] = constants[69]*constants[67]*states[34]
algebraic[52] = constants[70]*(power(states[37], 2.00000))*states[34]
rates[34] = ((constants[93]-algebraic[44])-algebraic[51])-algebraic[52]
algebraic[1] = -constants[3]*states[0]
algebraic[3] = constants[4]*states[2]*states[0]
algebraic[61] = constants[88]*states[36]*states[0]
rates[0] = ((-algebraic[2]+algebraic[0]+algebraic[1])-algebraic[61])-algebraic[3]
algebraic[53] = constants[74]*states[40]*states[41]
algebraic[54] = constants[75]*states[40]*constants[71]
algebraic[57] = constants[76]*states[40]*constants[72]
algebraic[60] = constants[77]*states[40]*constants[73]
algebraic[63] = constants[78]*states[40]*states[9]
rates[40] = ((((algebraic[44]-algebraic[53])-algebraic[54])-algebraic[57])-algebraic[60])-algebraic[63]
algebraic[56] = constants[81]*states[36]*states[41]
algebraic[55] = ((constants[80]-states[41])-states[37])/2.00000
algebraic[59] = (constants[82]*algebraic[55])/(constants[83]+algebraic[55])
algebraic[62] = constants[84]*states[2]*states[41]
rates[41] = ((-algebraic[53]-algebraic[56])+2.00000*algebraic[59])-algebraic[62]
rates[37] = (((algebraic[53]-2.00000*algebraic[52])+algebraic[56])-algebraic[48])+algebraic[62]
algebraic[58] = constants[85]*states[36]
rates[36] = (((-algebraic[56]+algebraic[46])-algebraic[47])-algebraic[58])-algebraic[61]
rates[9] = -algebraic[61]
algebraic[43] = -constants[3]*states[28]
algebraic[64] = constants[86]*states[2]*states[28]
rates[28] = ((((algebraic[40]+algebraic[42])-algebraic[37])-algebraic[35])+algebraic[34]+algebraic[43])-algebraic[64]
algebraic[26] = -constants[3]*states[16]
algebraic[65] = constants[87]*states[2]*states[16]
rates[16] = ((((((algebraic[34]+algebraic[33])-algebraic[27])-algebraic[23])+algebraic[25])-algebraic[20])+algebraic[21]+algebraic[26])-algebraic[65]
rates[39] = -algebraic[50]+algebraic[62]+algebraic[3]+algebraic[64]+algebraic[65]
rates[2] = (((algebraic[50]-algebraic[62])-algebraic[3])-algebraic[64])-algebraic[65]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[2] = constants[1]*states[0]*states[3]-constants[2]*states[1]
algebraic[0] = constants[0]*states[1]
algebraic[4] = constants[5]-constants[3]*states[4]
algebraic[5] = constants[6]*states[6]*states[4]-constants[7]*states[5]
algebraic[7] = constants[8]*(power(states[5], constants[10]))-constants[9]*states[7]
algebraic[8] = constants[11]-states[9]
algebraic[12] = constants[14]*states[10]*states[8]
algebraic[6] = -constants[3]*states[6]
algebraic[10] = constants[13]-constants[3]*states[8]
algebraic[14] = constants[16]*states[13]
algebraic[13] = constants[15]*states[11]*states[12]
algebraic[11] = -constants[3]*states[11]
algebraic[17] = constants[17]*states[14]*states[12]
algebraic[9] = -constants[3]*states[10]
algebraic[16] = -constants[3]*states[14]
algebraic[19] = constants[18]*states[15]*states[12]
algebraic[18] = constants[91]-constants[22]*states[12]
algebraic[20] = constants[23]*states[16]*states[15]-constants[24]*states[17]
algebraic[22] = constants[92]-constants[26]*states[15]
algebraic[21] = constants[27]*states[17]
algebraic[25] = constants[30]*states[18]
algebraic[15] = -constants[3]*states[13]
algebraic[23] = constants[28]*states[16]*states[3]-constants[29]*states[18]
algebraic[24] = constants[31]-constants[3]*states[3]
algebraic[27] = constants[32]*states[16]*states[19]-constants[33]*states[20]
algebraic[29] = constants[34]*states[7]*states[21]-constants[35]*states[22]
algebraic[30] = constants[36]*states[22]*states[21]-constants[37]*states[23]
algebraic[28] = constants[38]-constants[3]*states[21]
algebraic[31] = constants[39]*states[23]
algebraic[33] = constants[42]*states[24]
algebraic[32] = constants[40]*states[25]*states[26]-constants[41]*states[24]
algebraic[34] = constants[43]*states[27]
algebraic[35] = constants[44]*states[28]*states[26]-constants[45]*states[27]
algebraic[36] = constants[46]-constants[3]*states[26]
algebraic[37] = constants[48]*states[28]*states[19]-constants[49]*states[29]
algebraic[38] = constants[50]*states[32]*states[19]-constants[51]*states[30]
algebraic[39] = constants[52]*states[25]*states[19]-constants[53]*states[31]
algebraic[41] = constants[47]-constants[3]*states[19]
algebraic[40] = constants[54]*states[25]-constants[55]*states[32]*states[28]
algebraic[42] = constants[56]*states[32]-constants[57]*states[7]*states[28]
algebraic[45] = constants[61]*(power(states[33], 2.00000))*constants[58]
algebraic[46] = constants[62]*states[35]*states[33]
algebraic[47] = constants[63]*states[36]
algebraic[49] = constants[65]*states[38]*states[33]
algebraic[44] = constants[60]*states[33]*states[34]
algebraic[48] = constants[64]*states[37]
algebraic[50] = constants[66]*states[39]*states[33]
algebraic[51] = constants[69]*constants[67]*states[34]
algebraic[52] = constants[70]*(power(states[37], 2.00000))*states[34]
algebraic[1] = -constants[3]*states[0]
algebraic[3] = constants[4]*states[2]*states[0]
algebraic[61] = constants[88]*states[36]*states[0]
algebraic[53] = constants[74]*states[40]*states[41]
algebraic[54] = constants[75]*states[40]*constants[71]
algebraic[57] = constants[76]*states[40]*constants[72]
algebraic[60] = constants[77]*states[40]*constants[73]
algebraic[63] = constants[78]*states[40]*states[9]
algebraic[56] = constants[81]*states[36]*states[41]
algebraic[55] = ((constants[80]-states[41])-states[37])/2.00000
algebraic[59] = (constants[82]*algebraic[55])/(constants[83]+algebraic[55])
algebraic[62] = constants[84]*states[2]*states[41]
algebraic[58] = constants[85]*states[36]
algebraic[43] = -constants[3]*states[28]
algebraic[64] = constants[86]*states[2]*states[28]
algebraic[26] = -constants[3]*states[16]
algebraic[65] = constants[87]*states[2]*states[16]
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)