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 = 30
sizeStates = 36
sizeConstants = 136
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 (minute)"
legend_states[0] = "mass in component mass (dimensionless)"
legend_constants[0] = "kg in component model_parameters (first_order_rate_constant)"
legend_states[1] = "Cln2 in component Cln2 (dimensionless)"
legend_constants[1] = "ks_n2_ in component model_parameters (first_order_rate_constant)"
legend_constants[2] = "ks_n2__ in component model_parameters (first_order_rate_constant)"
legend_constants[3] = "kd_n2 in component model_parameters (first_order_rate_constant)"
legend_algebraic[27] = "SBF in component SBF_MBF (dimensionless)"
legend_states[2] = "Clb5 in component Clb5 (dimensionless)"
legend_constants[4] = "ks_b5_ in component model_parameters (first_order_rate_constant)"
legend_constants[5] = "ks_b5__ in component model_parameters (first_order_rate_constant)"
legend_constants[6] = "kdi_f5 in component model_parameters (first_order_rate_constant)"
legend_constants[7] = "kdi_b5 in component model_parameters (first_order_rate_constant)"
legend_constants[8] = "kas_b5 in component model_parameters (first_order_rate_constant)"
legend_constants[9] = "kas_f5 in component model_parameters (first_order_rate_constant)"
legend_constants[10] = "kd3_f6 in component model_parameters (first_order_rate_constant)"
legend_constants[11] = "kd3_c1 in component model_parameters (first_order_rate_constant)"
legend_algebraic[20] = "Vd_b5 in component Vd_b5 (first_order_rate_constant)"
legend_algebraic[26] = "MBF in component SBF_MBF (dimensionless)"
legend_states[3] = "C5P in component C5P (dimensionless)"
legend_states[4] = "C5 in component C5 (dimensionless)"
legend_states[5] = "F5P in component F5P (dimensionless)"
legend_states[6] = "F5 in component F5 (dimensionless)"
legend_states[7] = "Sic1 in component Sic1 (dimensionless)"
legend_states[8] = "Cdc6 in component Cdc6 (dimensionless)"
legend_states[9] = "Clb2 in component Clb2 (dimensionless)"
legend_constants[12] = "ks_b2_ in component model_parameters (first_order_rate_constant)"
legend_constants[13] = "ks_b2__ in component model_parameters (first_order_rate_constant)"
legend_constants[14] = "kdi_b2 in component model_parameters (first_order_rate_constant)"
legend_constants[15] = "kdi_f2 in component model_parameters (first_order_rate_constant)"
legend_constants[16] = "kas_b2 in component model_parameters (first_order_rate_constant)"
legend_constants[17] = "kas_f2 in component model_parameters (first_order_rate_constant)"
legend_algebraic[21] = "Vd_b2 in component Vd_b2 (first_order_rate_constant)"
legend_algebraic[7] = "Mcm1 in component Mcm1 (dimensionless)"
legend_states[10] = "C2P in component C2P (dimensionless)"
legend_states[11] = "C2 in component C2 (dimensionless)"
legend_states[12] = "F2P in component F2P (dimensionless)"
legend_states[13] = "F2 in component F2 (dimensionless)"
legend_constants[18] = "ks_c1_ in component model_parameters (first_order_rate_constant)"
legend_constants[19] = "ks_c1__ in component model_parameters (first_order_rate_constant)"
legend_constants[20] = "kpp_c1 in component model_parameters (first_order_rate_constant)"
legend_algebraic[23] = "Vkp_c1 in component Vkp_c1 (first_order_rate_constant)"
legend_states[14] = "Swi5 in component Swi5 (dimensionless)"
legend_states[15] = "Cdc14 in component Cdc14 (dimensionless)"
legend_states[16] = "Sic1P in component Sic1P (dimensionless)"
legend_constants[21] = "ks_f6_ in component model_parameters (first_order_rate_constant)"
legend_constants[22] = "ks_f6__ in component model_parameters (first_order_rate_constant)"
legend_constants[23] = "ks_f6___ in component model_parameters (first_order_rate_constant)"
legend_constants[24] = "kpp_f6 in component model_parameters (first_order_rate_constant)"
legend_algebraic[28] = "Vkp_f6 in component Vkp_f6 (first_order_rate_constant)"
legend_states[17] = "Cdc6P in component Cdc6P (dimensionless)"
legend_states[18] = "Pds1 in component Pds1 (dimensionless)"
legend_constants[25] = "ks_pds_ in component model_parameters (first_order_rate_constant)"
legend_constants[26] = "ks1_pds__ in component model_parameters (first_order_rate_constant)"
legend_constants[27] = "ks2_pds__ in component model_parameters (first_order_rate_constant)"
legend_constants[28] = "kdi_esp in component model_parameters (first_order_rate_constant)"
legend_algebraic[29] = "Vd_pds in component Vd_pds (first_order_rate_constant)"
legend_constants[29] = "kas_esp in component model_parameters (first_order_rate_constant)"
legend_algebraic[18] = "PE in component PE (dimensionless)"
legend_states[19] = "Esp1 in component Esp1 (dimensionless)"
legend_states[20] = "ORI in component ORI (dimensionless)"
legend_constants[30] = "ks_ori in component model_parameters (first_order_rate_constant)"
legend_constants[31] = "kd_ori in component model_parameters (first_order_rate_constant)"
legend_constants[32] = "epsilon_ori_b5 in component model_parameters (dimensionless)"
legend_constants[33] = "epsilon_ori_b2 in component model_parameters (dimensionless)"
legend_states[21] = "BUD in component BUD (dimensionless)"
legend_constants[34] = "ks_bud in component model_parameters (first_order_rate_constant)"
legend_constants[35] = "kd_bud in component model_parameters (first_order_rate_constant)"
legend_constants[36] = "epsilon_bud_n2 in component model_parameters (dimensionless)"
legend_constants[37] = "epsilon_bud_n3 in component model_parameters (dimensionless)"
legend_constants[38] = "epsilon_bud_b5 in component model_parameters (dimensionless)"
legend_algebraic[10] = "Cln3 in component Cln3 (dimensionless)"
legend_states[22] = "SPN in component SPN (dimensionless)"
legend_constants[39] = "ks_spn in component model_parameters (first_order_rate_constant)"
legend_constants[40] = "kd_spn in component model_parameters (first_order_rate_constant)"
legend_constants[41] = "Jspn in component model_parameters (dimensionless)"
legend_algebraic[25] = "G_sbf in component G_sbf (dimensionless)"
legend_constants[42] = "Ji_sbf in component model_parameters (dimensionless)"
legend_constants[43] = "Ja_sbf in component model_parameters (dimensionless)"
legend_algebraic[24] = "Vi_sbf in component Vi_sbf (first_order_rate_constant)"
legend_algebraic[22] = "Va_sbf in component Va_sbf (first_order_rate_constant)"
legend_algebraic[0] = "G_mcm in component G_mcm (dimensionless)"
legend_constants[44] = "Ji_mcm in component model_parameters (dimensionless)"
legend_constants[45] = "Ja_mcm in component model_parameters (dimensionless)"
legend_constants[46] = "ki_mcm in component model_parameters (first_order_rate_constant)"
legend_constants[47] = "ka_mcm in component model_parameters (first_order_rate_constant)"
legend_constants[48] = "C0 in component model_parameters (dimensionless)"
legend_constants[49] = "Dn3 in component model_parameters (dimensionless)"
legend_constants[50] = "Jn3 in component model_parameters (dimensionless)"
legend_algebraic[12] = "Bck2 in component Bck2 (dimensionless)"
legend_constants[51] = "B0 in component model_parameters (dimensionless)"
legend_algebraic[1] = "Clb5_T in component Clb5_T (dimensionless)"
legend_algebraic[2] = "Clb2_T in component Clb2_T (dimensionless)"
legend_algebraic[15] = "Sic1_T in component Sic1_T (dimensionless)"
legend_states[23] = "Swi5_T in component Swi5_T (dimensionless)"
legend_constants[52] = "ks_swi_ in component model_parameters (first_order_rate_constant)"
legend_constants[53] = "ks_swi__ in component model_parameters (first_order_rate_constant)"
legend_constants[54] = "kd_swi in component model_parameters (first_order_rate_constant)"
legend_constants[55] = "ka_swi in component model_parameters (first_order_rate_constant)"
legend_constants[56] = "ki_swi in component model_parameters (first_order_rate_constant)"
legend_states[24] = "APC_P in component APC_P (dimensionless)"
legend_constants[57] = "ka_apc in component model_parameters (first_order_rate_constant)"
legend_constants[58] = "ki_apc in component model_parameters (first_order_rate_constant)"
legend_constants[59] = "Ja_apc in component model_parameters (dimensionless)"
legend_constants[60] = "Ji_apc in component model_parameters (dimensionless)"
legend_states[25] = "Cdc20_T in component Cdc20_T (dimensionless)"
legend_constants[61] = "ks_20_ in component model_parameters (first_order_rate_constant)"
legend_constants[62] = "ks_20__ in component model_parameters (first_order_rate_constant)"
legend_constants[63] = "kd_20 in component model_parameters (first_order_rate_constant)"
legend_states[26] = "Cdc20_A in component Cdc20_A (dimensionless)"
legend_constants[64] = "ka_20_ in component model_parameters (first_order_rate_constant)"
legend_constants[65] = "ka_20__ in component model_parameters (first_order_rate_constant)"
legend_algebraic[3] = "kmad2 in component model_parameters (first_order_rate_constant)"
legend_states[27] = "Cdh1_T in component Cdh1_T (dimensionless)"
legend_constants[66] = "ks_cdh in component model_parameters (first_order_rate_constant)"
legend_constants[67] = "kd_cdh in component model_parameters (first_order_rate_constant)"
legend_states[28] = "Cdh1 in component Cdh1 (dimensionless)"
legend_constants[68] = "Ja_cdh in component model_parameters (dimensionless)"
legend_constants[69] = "Ji_cdh in component model_parameters (dimensionless)"
legend_algebraic[13] = "Va_cdh in component Va_cdh (first_order_rate_constant)"
legend_algebraic[16] = "Vi_cdh in component Vi_cdh (first_order_rate_constant)"
legend_states[29] = "Tem1 in component Tem1 (dimensionless)"
legend_algebraic[4] = "kbub2 in component model_parameters (first_order_rate_constant)"
legend_algebraic[8] = "klte1 in component model_parameters (first_order_rate_constant)"
legend_constants[70] = "Ja_tem in component model_parameters (dimensionless)"
legend_constants[71] = "Ji_tem in component model_parameters (dimensionless)"
legend_constants[72] = "Tem1_T in component model_parameters (dimensionless)"
legend_states[30] = "Cdc15 in component Cdc15 (dimensionless)"
legend_constants[73] = "ka_15_ in component model_parameters (first_order_rate_constant)"
legend_constants[74] = "ka_15__ in component model_parameters (first_order_rate_constant)"
legend_constants[75] = "ka_15___ in component model_parameters (first_order_rate_constant)"
legend_constants[76] = "ki_15 in component model_parameters (first_order_rate_constant)"
legend_constants[77] = "Cdc15_T in component model_parameters (dimensionless)"
legend_states[31] = "Cdc14_T in component Cdc14_T (dimensionless)"
legend_constants[78] = "ks_14 in component model_parameters (first_order_rate_constant)"
legend_constants[79] = "kd_14 in component model_parameters (first_order_rate_constant)"
legend_constants[80] = "kd_net in component model_parameters (first_order_rate_constant)"
legend_constants[81] = "kdi_rent in component model_parameters (first_order_rate_constant)"
legend_constants[82] = "kdi_rentp in component model_parameters (first_order_rate_constant)"
legend_constants[83] = "kas_rent in component model_parameters (first_order_rate_constant)"
legend_constants[84] = "kas_rentp in component model_parameters (first_order_rate_constant)"
legend_states[32] = "RENT in component RENT (dimensionless)"
legend_algebraic[5] = "RENTP in component RENTP (dimensionless)"
legend_states[33] = "Net1 in component Net1 (dimensionless)"
legend_algebraic[9] = "Net1P in component Net1P (dimensionless)"
legend_states[34] = "Net1_T in component Net1_T (dimensionless)"
legend_constants[85] = "ks_net in component model_parameters (first_order_rate_constant)"
legend_algebraic[17] = "Cdc6_T in component Cdc6_T (dimensionless)"
legend_algebraic[19] = "CKI_T in component CKI_T (dimensionless)"
legend_constants[86] = "Esp1_T in component model_parameters (dimensionless)"
legend_constants[87] = "kd_b5_ in component model_parameters (first_order_rate_constant)"
legend_constants[88] = "kd_b5__ in component model_parameters (first_order_rate_constant)"
legend_constants[89] = "kd_b2_ in component model_parameters (first_order_rate_constant)"
legend_constants[90] = "kd_b2__ in component model_parameters (first_order_rate_constant)"
legend_constants[91] = "kd_b2p in component model_parameters (first_order_rate_constant)"
legend_constants[92] = "ka_sbf in component model_parameters (first_order_rate_constant)"
legend_constants[93] = "epsilon_sbf_n2 in component model_parameters (dimensionless)"
legend_constants[94] = "epsilon_sbf_n3 in component model_parameters (dimensionless)"
legend_constants[95] = "epsilon_sbf_b5 in component model_parameters (dimensionless)"
legend_constants[96] = "ki_sbf_ in component model_parameters (first_order_rate_constant)"
legend_constants[97] = "ki_sbf__ in component model_parameters (first_order_rate_constant)"
legend_constants[98] = "kd1_c1 in component model_parameters (first_order_rate_constant)"
legend_constants[99] = "kd2_c1 in component model_parameters (first_order_rate_constant)"
legend_constants[100] = "Jd2_c1 in component model_parameters (dimensionless)"
legend_constants[101] = "epsilon_c1_n2 in component model_parameters (dimensionless)"
legend_constants[102] = "epsilon_c1_n3 in component model_parameters (dimensionless)"
legend_constants[103] = "epsilon_c1_k2 in component model_parameters (dimensionless)"
legend_constants[104] = "epsilon_c1_b5 in component model_parameters (dimensionless)"
legend_constants[105] = "epsilon_c1_b2 in component model_parameters (dimensionless)"
legend_constants[106] = "Jd2_f6 in component model_parameters (dimensionless)"
legend_constants[107] = "kd1_f6 in component model_parameters (first_order_rate_constant)"
legend_constants[108] = "kd2_f6 in component model_parameters (first_order_rate_constant)"
legend_constants[109] = "epsilon_f6_n2 in component model_parameters (dimensionless)"
legend_constants[110] = "epsilon_f6_n3 in component model_parameters (dimensionless)"
legend_constants[111] = "epsilon_f6_k2 in component model_parameters (dimensionless)"
legend_constants[112] = "epsilon_f6_b5 in component model_parameters (dimensionless)"
legend_constants[113] = "epsilon_f6_b2 in component model_parameters (dimensionless)"
legend_constants[114] = "ka_cdh_ in component model_parameters (first_order_rate_constant)"
legend_constants[115] = "ka_cdh__ in component model_parameters (first_order_rate_constant)"
legend_constants[116] = "ki_cdh_ in component model_parameters (first_order_rate_constant)"
legend_constants[117] = "ki_cdh__ in component model_parameters (first_order_rate_constant)"
legend_constants[118] = "epsilon_cdh_n2 in component model_parameters (dimensionless)"
legend_constants[119] = "epsilon_cdh_n3 in component model_parameters (dimensionless)"
legend_constants[120] = "epsilon_cdh_b5 in component model_parameters (dimensionless)"
legend_constants[121] = "epsilon_cdh_b2 in component model_parameters (dimensionless)"
legend_algebraic[11] = "Vpp_net in component Vpp_net (first_order_rate_constant)"
legend_constants[122] = "kpp_net_ in component model_parameters (first_order_rate_constant)"
legend_constants[123] = "kpp_net__ in component model_parameters (first_order_rate_constant)"
legend_states[35] = "PPX in component PPX (dimensionless)"
legend_algebraic[14] = "Vkp_net in component Vkp_net (first_order_rate_constant)"
legend_constants[124] = "kkp_net_ in component model_parameters (first_order_rate_constant)"
legend_constants[125] = "kkp_net__ in component model_parameters (first_order_rate_constant)"
legend_constants[126] = "ks_ppx in component model_parameters (first_order_rate_constant)"
legend_algebraic[6] = "Vd_ppx in component Vd_ppx (first_order_rate_constant)"
legend_constants[127] = "kd_ppx_ in component model_parameters (first_order_rate_constant)"
legend_constants[128] = "kd_ppx__ in component model_parameters (first_order_rate_constant)"
legend_constants[129] = "Jpds in component model_parameters (dimensionless)"
legend_constants[130] = "J20_ppx in component model_parameters (dimensionless)"
legend_constants[131] = "kd1_pds_ in component model_parameters (first_order_rate_constant)"
legend_constants[132] = "kd2_pds__ in component model_parameters (first_order_rate_constant)"
legend_constants[133] = "kd3_pds__ in component model_parameters (first_order_rate_constant)"
legend_constants[134] = "Kez in component model_parameters (dimensionless)"
legend_constants[135] = "Kez2 in component model_parameters (dimensionless)"
legend_rates[0] = "d/dt mass in component mass (dimensionless)"
legend_rates[1] = "d/dt Cln2 in component Cln2 (dimensionless)"
legend_rates[2] = "d/dt Clb5 in component Clb5 (dimensionless)"
legend_rates[9] = "d/dt Clb2 in component Clb2 (dimensionless)"
legend_rates[7] = "d/dt Sic1 in component Sic1 (dimensionless)"
legend_rates[16] = "d/dt Sic1P in component Sic1P (dimensionless)"
legend_rates[11] = "d/dt C2 in component C2 (dimensionless)"
legend_rates[4] = "d/dt C5 in component C5 (dimensionless)"
legend_rates[10] = "d/dt C2P in component C2P (dimensionless)"
legend_rates[3] = "d/dt C5P in component C5P (dimensionless)"
legend_rates[8] = "d/dt Cdc6 in component Cdc6 (dimensionless)"
legend_rates[17] = "d/dt Cdc6P in component Cdc6P (dimensionless)"
legend_rates[13] = "d/dt F2 in component F2 (dimensionless)"
legend_rates[18] = "d/dt Pds1 in component Pds1 (dimensionless)"
legend_rates[19] = "d/dt Esp1 in component Esp1 (dimensionless)"
legend_rates[20] = "d/dt ORI in component ORI (dimensionless)"
legend_rates[21] = "d/dt BUD in component BUD (dimensionless)"
legend_rates[22] = "d/dt SPN in component SPN (dimensionless)"
legend_rates[6] = "d/dt F5 in component F5 (dimensionless)"
legend_rates[12] = "d/dt F2P in component F2P (dimensionless)"
legend_rates[5] = "d/dt F5P in component F5P (dimensionless)"
legend_rates[23] = "d/dt Swi5_T in component Swi5_T (dimensionless)"
legend_rates[14] = "d/dt Swi5 in component Swi5 (dimensionless)"
legend_rates[24] = "d/dt APC_P in component APC_P (dimensionless)"
legend_rates[25] = "d/dt Cdc20_T in component Cdc20_T (dimensionless)"
legend_rates[26] = "d/dt Cdc20_A in component Cdc20_A (dimensionless)"
legend_rates[27] = "d/dt Cdh1_T in component Cdh1_T (dimensionless)"
legend_rates[28] = "d/dt Cdh1 in component Cdh1 (dimensionless)"
legend_rates[29] = "d/dt Tem1 in component Tem1 (dimensionless)"
legend_rates[30] = "d/dt Cdc15 in component Cdc15 (dimensionless)"
legend_rates[31] = "d/dt Cdc14_T in component Cdc14_T (dimensionless)"
legend_rates[15] = "d/dt Cdc14 in component Cdc14 (dimensionless)"
legend_rates[34] = "d/dt Net1_T in component Net1_T (dimensionless)"
legend_rates[33] = "d/dt Net1 in component Net1 (dimensionless)"
legend_rates[32] = "d/dt RENT in component RENT (dimensionless)"
legend_rates[35] = "d/dt PPX in component PPX (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 1.206
constants[0] = 0.007702
states[1] = 0.0652
constants[1] = 0
constants[2] = 0.15
constants[3] = 0.12
states[2] = 0.0518
constants[4] = 0.0008
constants[5] = 0.005
constants[6] = 0.01
constants[7] = 0.06
constants[8] = 50
constants[9] = 0.01
constants[10] = 1
constants[11] = 1
states[3] = 0.0069
states[4] = 0.0701
states[5] = 7.9e-6
states[6] = 7.2e-5
states[7] = 0.0229
states[8] = 0.1076
states[9] = 0.1469
constants[12] = 0.001
constants[13] = 0.04
constants[14] = 0.05
constants[15] = 0.5
constants[16] = 50
constants[17] = 15
states[10] = 0.024
states[11] = 0.2384
states[12] = 0.0274
states[13] = 0.2361
constants[18] = 0.012
constants[19] = 0.12
constants[20] = 4
states[14] = 0.9562
states[15] = 0.4683
states[16] = 0.0064
constants[21] = 0.024
constants[22] = 0.12
constants[23] = 0.004
constants[24] = 4
states[17] = 0.0155
states[18] = 0.0256
constants[25] = 0
constants[26] = 0.03
constants[27] = 0.055
constants[28] = 0.5
constants[29] = 50
states[19] = 0.3013
states[20] = 0.0009
constants[30] = 2
constants[31] = 0.06
constants[32] = 0.9
constants[33] = 0.45
states[21] = 0.0085
constants[34] = 0.2
constants[35] = 0.06
constants[36] = 0.25
constants[37] = 0.05
constants[38] = 1
states[22] = 0.0305
constants[39] = 0.1
constants[40] = 0.06
constants[41] = 0.14
constants[42] = 0.01
constants[43] = 0.01
constants[44] = 0.1
constants[45] = 0.1
constants[46] = 0.15
constants[47] = 1
constants[48] = 0.4
constants[49] = 1
constants[50] = 6
constants[51] = 0.054
states[23] = 0.9765
constants[52] = 0.005
constants[53] = 0.08
constants[54] = 0.08
constants[55] = 2
constants[56] = 0.05
states[24] = 0.1015
constants[57] = 0.1
constants[58] = 0.15
constants[59] = 0.1
constants[60] = 0.1
states[25] = 1.9163
constants[61] = 0.006
constants[62] = 0.6
constants[63] = 0.3
states[26] = 0.4443
constants[64] = 0.05
constants[65] = 0.2
states[27] = 1
constants[66] = 0.01
constants[67] = 0.01
states[28] = 0.9305
constants[68] = 0.03
constants[69] = 0.03
states[29] = 0.9039
constants[70] = 0.1
constants[71] = 0.1
constants[72] = 1
states[30] = 0.6565
constants[73] = 0.002
constants[74] = 1
constants[75] = 0.001
constants[76] = 0.5
constants[77] = 1
states[31] = 2
constants[78] = 0.2
constants[79] = 0.1
constants[80] = 0.03
constants[81] = 1
constants[82] = 2
constants[83] = 200
constants[84] = 1
states[32] = 1.0495
states[33] = 0.0186
states[34] = 2.8
constants[85] = 0.084
constants[86] = 1
constants[87] = 0.01
constants[88] = 0.16
constants[89] = 0.003
constants[90] = 0.4
constants[91] = 0.15
constants[92] = 0.38
constants[93] = 2
constants[94] = 10
constants[95] = 2
constants[96] = 0.6
constants[97] = 8
constants[98] = 0.01
constants[99] = 1
constants[100] = 0.05
constants[101] = 0.06
constants[102] = 0.3
constants[103] = 0.03
constants[104] = 0.1
constants[105] = 0.45
constants[106] = 0.05
constants[107] = 0.01
constants[108] = 1
constants[109] = 0.06
constants[110] = 0.3
constants[111] = 0.03
constants[112] = 0.1
constants[113] = 0.55
constants[114] = 0.01
constants[115] = 0.8
constants[116] = 0.001
constants[117] = 0.08
constants[118] = 0.4
constants[119] = 0.25
constants[120] = 8
constants[121] = 1.2
constants[122] = 0.05
constants[123] = 3
states[35] = 0.1232
constants[124] = 0.01
constants[125] = 0.6
constants[126] = 0.1
constants[127] = 0.17
constants[128] = 2
constants[129] = 0.04
constants[130] = 0.15
constants[131] = 0.01
constants[132] = 0.2
constants[133] = 0.04
constants[134] = 0.3
constants[135] = 0.2
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = states[0]*constants[0]
rates[20] = constants[30]*(constants[32]*states[2]+constants[33]*states[9])-constants[31]*states[20]
rates[22] = (constants[39]*states[9])/(constants[41]+states[9])-constants[40]*states[22]
rates[24] = (constants[57]*states[9]*(1.00000-states[24]))/((constants[59]+1.00000)-states[24])-(constants[58]*states[24])/(constants[60]+states[24])
rates[27] = constants[66]-constants[67]*states[27]
rates[30] = (constants[73]*(constants[72]-states[29])+constants[74]*states[29]+constants[75]*states[15])*(constants[77]-states[30])-constants[76]*states[30]
rates[31] = constants[78]-constants[79]*states[31]
rates[34] = constants[85]-constants[80]*states[34]
algebraic[3] = custom_piecewise([greater(states[20] , 1.00000) & less(states[22] , 1.00000), 8.00000 , True, 0.0100000])
rates[26] = (constants[64]+constants[65]*states[24])*(states[25]-states[26])-(algebraic[3]+constants[63])*states[26]
algebraic[6] = constants[127]+(constants[128]*(constants[130]+states[26])*constants[129])/(constants[129]+states[18])
rates[35] = constants[126]-algebraic[6]*states[35]
algebraic[0] = (2.00000*constants[44]*constants[47]*states[9])/((constants[46]+constants[45]*constants[46]+constants[44]*constants[47]*states[9]+power(power((constants[46]+constants[45]*constants[46]+constants[44]*constants[47]*states[9])-constants[47]*states[9], 2.00000)-4.00000*(constants[46]-constants[47]*states[9])*constants[44]*constants[47]*states[9], 1.0/2))-constants[47]*states[9])
algebraic[7] = algebraic[0]
rates[23] = (constants[52]+constants[53]*algebraic[7])-constants[54]*states[23]
rates[14] = (constants[52]+constants[53]*algebraic[7]+constants[55]*states[15]*(states[23]-states[14]))-(constants[54]+constants[56]*states[9])*states[14]
rates[25] = (constants[61]+constants[62]*algebraic[7])-constants[63]*states[25]
algebraic[4] = custom_piecewise([greater(states[20] , 1.00000) & less(states[22] , 1.00000), 1.00000 , True, 0.200000])
algebraic[8] = custom_piecewise([greater(states[22] , 1.00000) & greater(states[9] , constants[134]), 1.00000 , True, 0.100000])
rates[29] = (algebraic[8]*(constants[72]-states[29]))/((constants[70]+constants[72])-states[29])-(algebraic[4]*states[29])/(constants[71]+states[29])
algebraic[5] = states[31]-(states[32]+states[15])
algebraic[9] = (states[34]+states[15])-(states[33]+states[31])
rates[15] = (constants[78]+constants[80]*(states[32]+algebraic[5])+constants[81]*states[32]+constants[82]*algebraic[5])-(constants[79]*states[15]+(constants[83]*states[33]+constants[84]*algebraic[9])*states[15])
algebraic[10] = (constants[48]*constants[49]*states[0])/(constants[50]+constants[49]*states[0])
rates[21] = constants[34]*(constants[36]*states[1]+constants[37]*algebraic[10]+constants[38]*states[2])-constants[35]*states[21]
algebraic[11] = constants[122]+constants[123]*states[35]
algebraic[14] = (constants[124]+constants[125]*states[30])*states[0]
rates[33] = (constants[85]+constants[79]*states[32]+constants[81]*states[32]+algebraic[11]*algebraic[9])-(constants[80]*states[33]+constants[83]*states[15]*states[33]+algebraic[14]*states[33])
rates[32] = (constants[83]*states[15]*states[33]+algebraic[11]*algebraic[5])-((constants[79]+constants[80])*states[32]+constants[81]*states[32]+algebraic[14]*states[32])
algebraic[13] = constants[114]+constants[115]*states[15]
algebraic[16] = constants[116]+constants[117]*(constants[119]*algebraic[10]+constants[118]*states[1]+constants[120]*states[2]+constants[121]*states[9])
rates[28] = (constants[66]+(algebraic[13]*(states[27]-states[28]))/((constants[68]+states[27])-states[28]))-(constants[67]*states[28]+(algebraic[16]*states[28])/(constants[69]+states[28]))
algebraic[21] = constants[89]+constants[90]*states[28]+constants[91]*states[26]
rates[9] = ((constants[12]+constants[13]*algebraic[7])*states[0]+constants[11]*states[10]+constants[14]*states[11]+constants[10]*states[12]+constants[15]*states[13])-(algebraic[21]+constants[16]*states[7]+constants[17]*states[8])*states[9]
algebraic[20] = constants[87]+constants[88]*states[26]
algebraic[12] = constants[51]*states[0]
algebraic[15] = states[7]+states[16]+states[11]+states[10]+states[4]+states[3]
algebraic[23] = constants[98]+(constants[99]*(constants[102]*algebraic[10]+constants[103]*algebraic[12]+constants[101]*states[1]+constants[104]*states[2]+constants[105]*states[9]))/(constants[100]+algebraic[15])
rates[7] = (constants[18]+constants[19]*states[14]+(algebraic[21]+constants[14])*states[11]+(algebraic[20]+constants[7])*states[4]+constants[20]*states[15]*states[16])-(constants[16]*states[9]+constants[8]*states[2]+algebraic[23])*states[7]
rates[16] = (algebraic[23]*states[7]-(constants[20]*states[15]+constants[11])*states[16])+algebraic[21]*states[10]+algebraic[20]*states[3]
rates[11] = (constants[16]*states[9]*states[7]+constants[20]*states[15]*states[10])-(constants[14]+algebraic[21]+algebraic[23])*states[11]
rates[4] = (constants[8]*states[2]*states[7]+constants[20]*states[15]*states[3])-(constants[7]+algebraic[20]+algebraic[23])*states[4]
rates[10] = algebraic[23]*states[11]-(constants[20]*states[15]+constants[11]+algebraic[21])*states[10]
rates[3] = algebraic[23]*states[4]-(constants[20]*states[15]+constants[11]+algebraic[20])*states[3]
algebraic[24] = constants[96]+constants[97]*states[9]
algebraic[22] = constants[92]*(constants[93]*states[1]+constants[94]*(algebraic[10]+algebraic[12])+constants[95]*states[2])
algebraic[25] = (2.00000*constants[42]*algebraic[22])/((algebraic[24]+constants[43]*algebraic[24]+constants[42]*algebraic[22]+power(power((algebraic[24]+constants[43]*algebraic[24]+constants[42]*algebraic[22])-algebraic[22], 2.00000)-4.00000*(algebraic[24]-algebraic[22])*constants[42]*algebraic[22], 1.0/2))-algebraic[22])
algebraic[26] = algebraic[25]
rates[2] = ((constants[4]+constants[5]*algebraic[26])*states[0]+constants[11]*states[3]+constants[7]*states[4]+constants[10]*states[5]+constants[6]*states[6])-(algebraic[20]+constants[8]*states[7]+constants[9]*states[8])*states[2]
algebraic[27] = algebraic[26]
rates[1] = (constants[1]+constants[2]*algebraic[27])*states[0]-constants[3]*states[1]
algebraic[17] = states[8]+states[17]+states[13]+states[12]+states[6]+states[5]
algebraic[28] = constants[107]+(constants[108]*(constants[110]*algebraic[10]+constants[111]*algebraic[12]+constants[109]*states[1]+constants[112]*states[2]+constants[113]*states[9]))/(constants[106]+algebraic[17])
rates[8] = (constants[21]+constants[22]*states[14]+constants[23]*algebraic[27]+(algebraic[21]+constants[15])*states[13]+(algebraic[20]+constants[6])*states[6]+constants[24]*states[15]*states[17])-(constants[17]*states[9]+constants[9]*states[2]+algebraic[28])*states[8]
rates[17] = (algebraic[28]*states[8]-(constants[24]*states[15]+constants[10])*states[17])+algebraic[21]*states[12]+algebraic[20]*states[5]
rates[13] = (constants[17]*states[9]*states[8]+constants[24]*states[15]*states[12])-(constants[15]+algebraic[21]+algebraic[28])*states[13]
algebraic[29] = constants[131]+constants[132]*states[26]+constants[133]*states[28]
algebraic[18] = constants[86]-states[19]
rates[18] = (constants[25]+constants[26]*algebraic[27]+constants[27]*algebraic[7]+constants[28]*algebraic[18])-(algebraic[29]+constants[29]*states[19])*states[18]
rates[19] = -constants[29]*states[18]*states[19]+(constants[28]+algebraic[29])*algebraic[18]
rates[6] = (constants[9]*states[2]*states[8]+constants[24]*states[15]*states[5])-(constants[6]+algebraic[20]+algebraic[28])*states[6]
rates[12] = algebraic[28]*states[13]-(constants[24]*states[15]+constants[10]+algebraic[21])*states[12]
rates[5] = algebraic[28]*states[6]-(constants[24]*states[15]+constants[10]+algebraic[20])*states[5]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[3] = custom_piecewise([greater(states[20] , 1.00000) & less(states[22] , 1.00000), 8.00000 , True, 0.0100000])
algebraic[6] = constants[127]+(constants[128]*(constants[130]+states[26])*constants[129])/(constants[129]+states[18])
algebraic[0] = (2.00000*constants[44]*constants[47]*states[9])/((constants[46]+constants[45]*constants[46]+constants[44]*constants[47]*states[9]+power(power((constants[46]+constants[45]*constants[46]+constants[44]*constants[47]*states[9])-constants[47]*states[9], 2.00000)-4.00000*(constants[46]-constants[47]*states[9])*constants[44]*constants[47]*states[9], 1.0/2))-constants[47]*states[9])
algebraic[7] = algebraic[0]
algebraic[4] = custom_piecewise([greater(states[20] , 1.00000) & less(states[22] , 1.00000), 1.00000 , True, 0.200000])
algebraic[8] = custom_piecewise([greater(states[22] , 1.00000) & greater(states[9] , constants[134]), 1.00000 , True, 0.100000])
algebraic[5] = states[31]-(states[32]+states[15])
algebraic[9] = (states[34]+states[15])-(states[33]+states[31])
algebraic[10] = (constants[48]*constants[49]*states[0])/(constants[50]+constants[49]*states[0])
algebraic[11] = constants[122]+constants[123]*states[35]
algebraic[14] = (constants[124]+constants[125]*states[30])*states[0]
algebraic[13] = constants[114]+constants[115]*states[15]
algebraic[16] = constants[116]+constants[117]*(constants[119]*algebraic[10]+constants[118]*states[1]+constants[120]*states[2]+constants[121]*states[9])
algebraic[21] = constants[89]+constants[90]*states[28]+constants[91]*states[26]
algebraic[20] = constants[87]+constants[88]*states[26]
algebraic[12] = constants[51]*states[0]
algebraic[15] = states[7]+states[16]+states[11]+states[10]+states[4]+states[3]
algebraic[23] = constants[98]+(constants[99]*(constants[102]*algebraic[10]+constants[103]*algebraic[12]+constants[101]*states[1]+constants[104]*states[2]+constants[105]*states[9]))/(constants[100]+algebraic[15])
algebraic[24] = constants[96]+constants[97]*states[9]
algebraic[22] = constants[92]*(constants[93]*states[1]+constants[94]*(algebraic[10]+algebraic[12])+constants[95]*states[2])
algebraic[25] = (2.00000*constants[42]*algebraic[22])/((algebraic[24]+constants[43]*algebraic[24]+constants[42]*algebraic[22]+power(power((algebraic[24]+constants[43]*algebraic[24]+constants[42]*algebraic[22])-algebraic[22], 2.00000)-4.00000*(algebraic[24]-algebraic[22])*constants[42]*algebraic[22], 1.0/2))-algebraic[22])
algebraic[26] = algebraic[25]
algebraic[27] = algebraic[26]
algebraic[17] = states[8]+states[17]+states[13]+states[12]+states[6]+states[5]
algebraic[28] = constants[107]+(constants[108]*(constants[110]*algebraic[10]+constants[111]*algebraic[12]+constants[109]*states[1]+constants[112]*states[2]+constants[113]*states[9]))/(constants[106]+algebraic[17])
algebraic[29] = constants[131]+constants[132]*states[26]+constants[133]*states[28]
algebraic[18] = constants[86]-states[19]
algebraic[1] = states[2]+states[4]+states[3]+states[6]+states[5]
algebraic[2] = states[9]+states[11]+states[10]+states[13]+states[12]
algebraic[19] = algebraic[15]+algebraic[17]
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)