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 = 23
sizeStates = 14
sizeConstants = 90
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_constants[0] = "GLCo in component GLCo (millimolar)"
legend_states[0] = "GLCi in component GLCi (millimolar)"
legend_algebraic[9] = "v_GLT in component v_GLT (flux)"
legend_algebraic[8] = "v_GLK in component v_GLK (flux)"
legend_states[1] = "G6P in component G6P (millimolar)"
legend_algebraic[5] = "v_PGI in component v_PGI (flux)"
legend_constants[1] = "v_trehalose in component v_trehalose (flux)"
legend_constants[2] = "v_glycogen in component v_glycogen (flux)"
legend_states[2] = "F6P in component F6P (millimolar)"
legend_algebraic[20] = "v_PFK in component v_PFK (flux)"
legend_states[3] = "F16P in component F16P (millimolar)"
legend_algebraic[13] = "v_ALD in component v_ALD (flux)"
legend_constants[3] = "F26P in component F26P (millimolar)"
legend_states[4] = "TRIO in component TRIO (millimolar)"
legend_algebraic[10] = "v_GAPDH in component v_GAPDH (flux)"
legend_algebraic[21] = "v_G3PDH in component v_G3PDH (flux)"
legend_states[5] = "BPG in component BPG (millimolar)"
legend_algebraic[11] = "v_PGK in component v_PGK (flux)"
legend_states[6] = "P3G in component P3G (millimolar)"
legend_algebraic[6] = "v_PGM in component v_PGM (flux)"
legend_states[7] = "P2G in component P2G (millimolar)"
legend_algebraic[7] = "v_ENO in component v_ENO (flux)"
legend_states[8] = "PEP in component PEP (millimolar)"
legend_algebraic[12] = "v_PYK in component v_PYK (flux)"
legend_states[9] = "PYR in component PYR (millimolar)"
legend_algebraic[14] = "v_PDC in component v_PDC (flux)"
legend_states[10] = "ACE in component ACE (millimolar)"
legend_algebraic[15] = "v_ADH in component v_ADH (flux)"
legend_algebraic[22] = "v_succinate in component v_succinate (flux)"
legend_states[11] = "P in component P (millimolar)"
legend_algebraic[16] = "v_ATP in component v_ATP (flux)"
legend_states[12] = "NADH in component NADH (millimolar)"
legend_states[13] = "NAD in component NAD (millimolar)"
legend_algebraic[0] = "DHAP in component DHAP (millimolar)"
legend_constants[4] = "Keq_TPI in component DHAP (dimensionless)"
legend_algebraic[1] = "GAP in component GAP (millimolar)"
legend_algebraic[2] = "ADP in component ADP (millimolar)"
legend_constants[5] = "SUM_P in component ADP (millimolar)"
legend_constants[6] = "Keq_AK in component ADP (dimensionless)"
legend_algebraic[3] = "ATP in component ATP (millimolar)"
legend_algebraic[4] = "AMP in component AMP (millimolar)"
legend_constants[7] = "ETOH in component ETOH (millimolar)"
legend_constants[8] = "GLY in component GLY (millimolar)"
legend_constants[9] = "Km_G6P in component v_PGI (millimolar)"
legend_constants[10] = "Km_F6P in component v_PGI (millimolar)"
legend_constants[11] = "Keq_PGI in component v_PGI (dimensionless)"
legend_constants[12] = "v_max in component v_PGI (flux)"
legend_constants[13] = "Km_P3G in component v_PGM (millimolar)"
legend_constants[14] = "Km_P2G in component v_PGM (millimolar)"
legend_constants[15] = "Keq_PGM in component v_PGM (dimensionless)"
legend_constants[16] = "v_max in component v_PGM (flux)"
legend_constants[17] = "Km_P2G in component v_ENO (millimolar)"
legend_constants[18] = "Km_PEP in component v_ENO (millimolar)"
legend_constants[19] = "Keq_ENO in component v_ENO (dimensionless)"
legend_constants[20] = "v_max in component v_ENO (flux)"
legend_constants[21] = "Km_GLCi in component v_GLK (millimolar)"
legend_constants[22] = "Km_G6P in component v_GLK (millimolar)"
legend_constants[23] = "Km_ATP in component v_GLK (millimolar)"
legend_constants[24] = "Km_ADP in component v_GLK (millimolar)"
legend_constants[25] = "Keq_GLK in component v_GLK (dimensionless)"
legend_constants[26] = "v_max in component v_GLK (flux)"
legend_constants[27] = "Km_GAP in component v_GAPDH (millimolar)"
legend_constants[28] = "Km_BPG in component v_GAPDH (millimolar)"
legend_constants[29] = "Km_NAD in component v_GAPDH (millimolar)"
legend_constants[30] = "Km_NADH in component v_GAPDH (millimolar)"
legend_constants[31] = "v_max_f in component v_GAPDH (flux)"
legend_constants[32] = "v_max_r in component v_GAPDH (flux)"
legend_constants[33] = "Km_BPG in component v_PGK (millimolar)"
legend_constants[34] = "Km_P3G in component v_PGK (millimolar)"
legend_constants[35] = "Km_ADP in component v_PGK (millimolar)"
legend_constants[36] = "Km_ATP in component v_PGK (millimolar)"
legend_constants[37] = "Keq_PGK in component v_PGK (dimensionless)"
legend_constants[38] = "v_max in component v_PGK (flux)"
legend_constants[39] = "Km_PEP in component v_PYK (millimolar)"
legend_constants[40] = "Km_PYR in component v_PYK (millimolar)"
legend_constants[41] = "Km_ADP in component v_PYK (millimolar)"
legend_constants[42] = "Km_ATP in component v_PYK (millimolar)"
legend_constants[43] = "Keq_PYK in component v_PYK (dimensionless)"
legend_constants[44] = "v_max in component v_PYK (flux)"
legend_constants[45] = "Km_Glco in component v_GLT (millimolar)"
legend_constants[46] = "Km_Glci in component v_GLT (millimolar)"
legend_constants[47] = "Keq_Glc in component v_GLT (dimensionless)"
legend_constants[48] = "v_max in component v_GLT (flux)"
legend_constants[49] = "Km_F16P in component v_ALD (millimolar)"
legend_constants[50] = "Km_GAP in component v_ALD (millimolar)"
legend_constants[51] = "Km_GAPi in component v_ALD (millimolar)"
legend_constants[52] = "Km_DHAP in component v_ALD (millimolar)"
legend_constants[53] = "Keq_ALD in component v_ALD (millimolar)"
legend_constants[54] = "v_max in component v_ALD (flux)"
legend_constants[55] = "nPDC in component v_PDC (dimensionless)"
legend_constants[56] = "Km_PYR in component v_PDC (millimolar)"
legend_constants[57] = "v_max in component v_PDC (flux)"
legend_constants[58] = "Km_NAD in component v_ADH (millimolar)"
legend_constants[59] = "Km_NADH in component v_ADH (millimolar)"
legend_constants[60] = "Km_ACE in component v_ADH (millimolar)"
legend_constants[61] = "Km_ETOH in component v_ADH (millimolar)"
legend_constants[62] = "Ki_NADH in component v_ADH (millimolar)"
legend_constants[63] = "Ki_NAD in component v_ADH (millimolar)"
legend_constants[64] = "Ki_ACE in component v_ADH (millimolar)"
legend_constants[65] = "Ki_ETOH in component v_ADH (millimolar)"
legend_constants[66] = "v_max in component v_ADH (flux)"
legend_constants[67] = "Keq_ADH in component v_ADH (dimensionless)"
legend_constants[68] = "Km_ATPase in component v_ATP (first_order_rate_constant)"
legend_constants[69] = "v_max in component v_PFK (flux)"
legend_constants[70] = "gR in component v_PFK (dimensionless)"
legend_constants[71] = "L0 in component v_PFK (per_millimolar2)"
legend_constants[72] = "Km_F6P in component v_PFK (millimolar)"
legend_constants[73] = "Km_ATP in component v_PFK (millimolar)"
legend_constants[74] = "CATP in component v_PFK (millimolar)"
legend_constants[75] = "Km_AMP in component v_PFK (millimolar)"
legend_constants[76] = "CAMP in component v_PFK (dimensionless)"
legend_constants[77] = "Ki_ATP in component v_PFK (millimolar)"
legend_constants[78] = "Ci_ATP in component v_PFK (dimensionless)"
legend_constants[79] = "Km_F26BP in component v_PFK (millimolar)"
legend_constants[80] = "CF26BP in component v_PFK (dimensionless)"
legend_constants[81] = "Km_F16BP in component v_PFK (millimolar)"
legend_constants[82] = "CF16BP in component v_PFK (dimensionless)"
legend_algebraic[18] = "L in component v_PFK (per_millimolar2)"
legend_algebraic[17] = "R in component v_PFK (dimensionless)"
legend_algebraic[19] = "T in component v_PFK (millimolar)"
legend_constants[83] = "Km_DHAP in component v_G3PDH (millimolar)"
legend_constants[84] = "Km_GLY in component v_G3PDH (millimolar)"
legend_constants[85] = "Km_NADH in component v_G3PDH (millimolar)"
legend_constants[86] = "Km_NAD in component v_G3PDH (millimolar)"
legend_constants[87] = "Keq_G3PDH in component v_G3PDH (dimensionless)"
legend_constants[88] = "v_max in component v_G3PDH (flux)"
legend_constants[89] = "Km_succinate in component v_succinate (first_order_rate_constant)"
legend_rates[0] = "d/dt GLCi in component GLCi (millimolar)"
legend_rates[1] = "d/dt G6P in component G6P (millimolar)"
legend_rates[2] = "d/dt F6P in component F6P (millimolar)"
legend_rates[3] = "d/dt F16P in component F16P (millimolar)"
legend_rates[4] = "d/dt TRIO in component TRIO (millimolar)"
legend_rates[5] = "d/dt BPG in component BPG (millimolar)"
legend_rates[6] = "d/dt P3G in component P3G (millimolar)"
legend_rates[7] = "d/dt P2G in component P2G (millimolar)"
legend_rates[8] = "d/dt PEP in component PEP (millimolar)"
legend_rates[9] = "d/dt PYR in component PYR (millimolar)"
legend_rates[10] = "d/dt ACE in component ACE (millimolar)"
legend_rates[11] = "d/dt P in component P (millimolar)"
legend_rates[12] = "d/dt NADH in component NADH (millimolar)"
legend_rates[13] = "d/dt NAD in component NAD (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 50.0
states[0] = 0.087
states[1] = 2.45
constants[1] = 2.4
constants[2] = 6.0
states[2] = 0.62
states[3] = 5.51
constants[3] = 0.02
states[4] = 0.96
states[5] = 0.0
states[6] = 0.9
states[7] = 0.12
states[8] = 0.07
states[9] = 1.85
states[10] = 0.17
states[11] = 6.31
states[12] = 0.39
states[13] = 1.20
constants[4] = 0.045
constants[5] = 4.1
constants[6] = 0.450
constants[7] = 50.0
constants[8] = 0.15
constants[9] = 1.4
constants[10] = 0.3
constants[11] = 0.314
constants[12] = 339.677
constants[13] = 1.2
constants[14] = 0.08
constants[15] = 0.19
constants[16] = 2525.81
constants[17] = 0.04
constants[18] = 0.5
constants[19] = 6.7
constants[20] = 365.806
constants[21] = 0.08
constants[22] = 30.0
constants[23] = 0.15
constants[24] = 0.23
constants[25] = 3800
constants[26] = 226.452
constants[27] = 0.21
constants[28] = 0.0098
constants[29] = 0.09
constants[30] = 0.06
constants[31] = 1184.52
constants[32] = 6549.68
constants[33] = 0.003
constants[34] = 0.53
constants[35] = 0.2
constants[36] = 0.3
constants[37] = 3200
constants[38] = 1306.45
constants[39] = 0.14
constants[40] = 21.0
constants[41] = 0.53
constants[42] = 1.5
constants[43] = 6500
constants[44] = 1088.71
constants[45] = 1.1918
constants[46] = 1.1918
constants[47] = 1
constants[48] = 97.264
constants[49] = 0.3
constants[50] = 2.0
constants[51] = 10.0
constants[52] = 2.4
constants[53] = 0.069
constants[54] = 322.258
constants[55] = 1.9
constants[56] = 4.33
constants[57] = 174.194
constants[58] = 0.17
constants[59] = 0.11
constants[60] = 1.11
constants[61] = 17.0
constants[62] = 0.031
constants[63] = 0.92
constants[64] = 1.1
constants[65] = 90.0
constants[66] = 810.0
constants[67] = 0.000069
constants[68] = 33.7
constants[69] = 182.903
constants[70] = 5.12
constants[71] = 0.66
constants[72] = 0.1
constants[73] = 0.71
constants[74] = 3.0
constants[75] = 0.0995
constants[76] = 0.0845
constants[77] = 0.65
constants[78] = 100.0
constants[79] = 0.000682
constants[80] = 0.0174
constants[81] = 0.111
constants[82] = 0.397
constants[83] = 0.4
constants[84] = 1
constants[85] = 0.023
constants[86] = 0.93
constants[87] = 4300
constants[88] = 70.15
constants[89] = 21.4
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[6] = ((constants[16]/constants[13])*(states[6]-states[7]/constants[15]))/(1.00000+states[6]/constants[13]+states[7]/constants[14])
algebraic[7] = ((constants[20]/constants[17])*(states[7]-states[8]/constants[19]))/(1.00000+states[7]/constants[17]+states[8]/constants[18])
rates[7] = algebraic[6]-algebraic[7]
algebraic[2] = (constants[5]-power((power(states[11], 2.00000))*(1.00000-4.00000*constants[6])+2.00000*constants[5]*states[11]*(4.00000*constants[6]-1.00000)+power(constants[5], 2.00000), 1.0/2))/(1.00000-4.00000*constants[6])
algebraic[3] = (states[11]-algebraic[2])/2.00000
algebraic[8] = ((constants[26]/(constants[21]*constants[23]))*(states[0]*algebraic[3]-(states[1]*algebraic[2])/constants[25]))/((1.00000+states[0]/constants[21]+states[1]/constants[22])*(1.00000+algebraic[3]/constants[23]+algebraic[2]/constants[24]))
algebraic[5] = ((constants[12]/constants[9])*(states[1]-states[2]/constants[11]))/(1.00000+states[1]/constants[9]+states[2]/constants[10])
rates[1] = algebraic[8]-(algebraic[5]+2.00000*constants[1]+constants[2])
algebraic[9] = (constants[48]*(constants[0]-states[0]/constants[47]))/(constants[45]*(1.00000+constants[0]/constants[45]+states[0]/constants[46]+(0.910000*constants[0]*states[0])/(constants[46]*constants[45])))
rates[0] = algebraic[9]-algebraic[8]
algebraic[10] = ((constants[31]*(constants[4]/(1.00000+constants[4]))*states[4]*states[13])/(constants[27]*constants[29])-(constants[32]*states[5]*states[12])/(constants[28]*constants[30]))/((1.00000+((constants[4]/(1.00000+constants[4]))*states[4])/constants[27]+states[5]/constants[28])*(1.00000+states[13]/constants[29]+states[12]/constants[30]))
algebraic[11] = ((constants[38]/(constants[34]*constants[36]))*(constants[37]*states[5]*algebraic[2]-states[6]*algebraic[3]))/((1.00000+states[5]/constants[33]+states[6]/constants[34])*(1.00000+algebraic[3]/constants[36]+algebraic[2]/constants[35]))
rates[5] = algebraic[10]-algebraic[11]
rates[6] = algebraic[11]-algebraic[6]
algebraic[12] = ((constants[44]/(constants[39]*constants[41]))*(states[8]*algebraic[2]-(states[9]*algebraic[3])/constants[43]))/((1.00000+states[8]/constants[39]+states[9]/constants[40])*(1.00000+algebraic[3]/constants[42]+algebraic[2]/constants[41]))
rates[8] = algebraic[7]-algebraic[12]
algebraic[14] = (constants[57]*((power(states[9], constants[55]))/(power(constants[56], constants[55]))))/(1.00000+(power(states[9], constants[55]))/(power(constants[56], constants[55])))
rates[9] = algebraic[12]-algebraic[14]
algebraic[4] = constants[5]-(algebraic[3]+algebraic[2])
algebraic[18] = constants[71]*(power((1.00000+constants[78]*(algebraic[3]/constants[77]))/(1.00000+algebraic[3]/constants[77]), 2.00000))*(power((1.00000+constants[76]*(algebraic[4]/constants[75]))/(1.00000+algebraic[4]/constants[75]), 2.00000))*(power((1.00000+constants[80]*(constants[3]/constants[79])+constants[82]*(states[3]/constants[81]))/(1.00000+constants[3]/constants[79]+states[3]/constants[81]), 2.00000))
algebraic[17] = 1.00000+states[2]/constants[72]+algebraic[3]/constants[73]+constants[70]*(states[2]/constants[72])*(algebraic[3]/constants[73])
algebraic[19] = 1.00000+constants[74]*(algebraic[3]/constants[73])
algebraic[20] = constants[69]*constants[70]*(states[2]/constants[72])*(algebraic[3]/constants[73])*(algebraic[17]/(power(algebraic[17], 2.00000)+algebraic[18]*(power(algebraic[19], 2.00000))))
rates[2] = algebraic[5]-algebraic[20]
algebraic[13] = ((constants[54]/constants[49])*(states[3]-((constants[4]/(1.00000+constants[4]))*states[4]*(1.00000/(1.00000+constants[4]))*states[4])/constants[53]))/(1.00000+states[3]/constants[49]+((constants[4]/(1.00000+constants[4]))*states[4])/constants[50]+((1.00000/(1.00000+constants[4]))*states[4])/constants[52]+((constants[4]/(1.00000+constants[4]))*states[4]*(1.00000/(1.00000+constants[4]))*states[4])/(constants[50]*constants[52])+(states[3]*(constants[4]/(1.00000+constants[4]))*states[4])/(constants[51]*constants[49]))
rates[3] = algebraic[20]-algebraic[13]
algebraic[21] = ((constants[88]/(constants[83]*constants[85]))*((1.00000/(1.00000+constants[4]))*states[4]*states[12]-(constants[8]*states[13])/constants[87]))/((1.00000+((1.00000/(1.00000+constants[4]))*states[4])/constants[83]+constants[8]/constants[84])*(1.00000+states[12]/constants[85]+states[13]/constants[86]))
rates[4] = 2.00000*algebraic[13]-(algebraic[10]+algebraic[21])
algebraic[15] = -((constants[66]/(constants[63]*constants[61]))*((states[13]*constants[7]-(states[12]*states[10])/constants[67])/(1.00000+states[13]/constants[63]+(constants[58]*constants[7])/(constants[63]*constants[61])+(constants[59]*states[10])/(constants[62]*constants[60])+states[12]/constants[62]+(states[13]*constants[7])/(constants[63]*constants[61])+(constants[59]*states[13]*states[10])/(constants[63]*constants[62]*constants[60])+(constants[58]*constants[7]*states[12])/(constants[63]*constants[61]*constants[62])+(states[12]*states[10])/(constants[62]*constants[60])+(states[13]*constants[7]*states[10])/(constants[63]*constants[61]*constants[64])+(constants[7]*states[12]*states[10])/(constants[65]*constants[62]*constants[60]))))
algebraic[22] = constants[89]*states[10]
rates[10] = algebraic[14]-(algebraic[15]+2.00000*algebraic[22])
algebraic[16] = constants[68]*algebraic[3]
rates[11] = (algebraic[11]+algebraic[12])-(algebraic[8]+algebraic[20]+algebraic[16]+constants[1]+constants[2]+4.00000*algebraic[22])
rates[12] = (algebraic[10]+3.00000*algebraic[22])-(algebraic[15]+algebraic[21])
rates[13] = (algebraic[15]+algebraic[21])-(algebraic[10]+3.00000*algebraic[22])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[6] = ((constants[16]/constants[13])*(states[6]-states[7]/constants[15]))/(1.00000+states[6]/constants[13]+states[7]/constants[14])
algebraic[7] = ((constants[20]/constants[17])*(states[7]-states[8]/constants[19]))/(1.00000+states[7]/constants[17]+states[8]/constants[18])
algebraic[2] = (constants[5]-power((power(states[11], 2.00000))*(1.00000-4.00000*constants[6])+2.00000*constants[5]*states[11]*(4.00000*constants[6]-1.00000)+power(constants[5], 2.00000), 1.0/2))/(1.00000-4.00000*constants[6])
algebraic[3] = (states[11]-algebraic[2])/2.00000
algebraic[8] = ((constants[26]/(constants[21]*constants[23]))*(states[0]*algebraic[3]-(states[1]*algebraic[2])/constants[25]))/((1.00000+states[0]/constants[21]+states[1]/constants[22])*(1.00000+algebraic[3]/constants[23]+algebraic[2]/constants[24]))
algebraic[5] = ((constants[12]/constants[9])*(states[1]-states[2]/constants[11]))/(1.00000+states[1]/constants[9]+states[2]/constants[10])
algebraic[9] = (constants[48]*(constants[0]-states[0]/constants[47]))/(constants[45]*(1.00000+constants[0]/constants[45]+states[0]/constants[46]+(0.910000*constants[0]*states[0])/(constants[46]*constants[45])))
algebraic[10] = ((constants[31]*(constants[4]/(1.00000+constants[4]))*states[4]*states[13])/(constants[27]*constants[29])-(constants[32]*states[5]*states[12])/(constants[28]*constants[30]))/((1.00000+((constants[4]/(1.00000+constants[4]))*states[4])/constants[27]+states[5]/constants[28])*(1.00000+states[13]/constants[29]+states[12]/constants[30]))
algebraic[11] = ((constants[38]/(constants[34]*constants[36]))*(constants[37]*states[5]*algebraic[2]-states[6]*algebraic[3]))/((1.00000+states[5]/constants[33]+states[6]/constants[34])*(1.00000+algebraic[3]/constants[36]+algebraic[2]/constants[35]))
algebraic[12] = ((constants[44]/(constants[39]*constants[41]))*(states[8]*algebraic[2]-(states[9]*algebraic[3])/constants[43]))/((1.00000+states[8]/constants[39]+states[9]/constants[40])*(1.00000+algebraic[3]/constants[42]+algebraic[2]/constants[41]))
algebraic[14] = (constants[57]*((power(states[9], constants[55]))/(power(constants[56], constants[55]))))/(1.00000+(power(states[9], constants[55]))/(power(constants[56], constants[55])))
algebraic[4] = constants[5]-(algebraic[3]+algebraic[2])
algebraic[18] = constants[71]*(power((1.00000+constants[78]*(algebraic[3]/constants[77]))/(1.00000+algebraic[3]/constants[77]), 2.00000))*(power((1.00000+constants[76]*(algebraic[4]/constants[75]))/(1.00000+algebraic[4]/constants[75]), 2.00000))*(power((1.00000+constants[80]*(constants[3]/constants[79])+constants[82]*(states[3]/constants[81]))/(1.00000+constants[3]/constants[79]+states[3]/constants[81]), 2.00000))
algebraic[17] = 1.00000+states[2]/constants[72]+algebraic[3]/constants[73]+constants[70]*(states[2]/constants[72])*(algebraic[3]/constants[73])
algebraic[19] = 1.00000+constants[74]*(algebraic[3]/constants[73])
algebraic[20] = constants[69]*constants[70]*(states[2]/constants[72])*(algebraic[3]/constants[73])*(algebraic[17]/(power(algebraic[17], 2.00000)+algebraic[18]*(power(algebraic[19], 2.00000))))
algebraic[13] = ((constants[54]/constants[49])*(states[3]-((constants[4]/(1.00000+constants[4]))*states[4]*(1.00000/(1.00000+constants[4]))*states[4])/constants[53]))/(1.00000+states[3]/constants[49]+((constants[4]/(1.00000+constants[4]))*states[4])/constants[50]+((1.00000/(1.00000+constants[4]))*states[4])/constants[52]+((constants[4]/(1.00000+constants[4]))*states[4]*(1.00000/(1.00000+constants[4]))*states[4])/(constants[50]*constants[52])+(states[3]*(constants[4]/(1.00000+constants[4]))*states[4])/(constants[51]*constants[49]))
algebraic[21] = ((constants[88]/(constants[83]*constants[85]))*((1.00000/(1.00000+constants[4]))*states[4]*states[12]-(constants[8]*states[13])/constants[87]))/((1.00000+((1.00000/(1.00000+constants[4]))*states[4])/constants[83]+constants[8]/constants[84])*(1.00000+states[12]/constants[85]+states[13]/constants[86]))
algebraic[15] = -((constants[66]/(constants[63]*constants[61]))*((states[13]*constants[7]-(states[12]*states[10])/constants[67])/(1.00000+states[13]/constants[63]+(constants[58]*constants[7])/(constants[63]*constants[61])+(constants[59]*states[10])/(constants[62]*constants[60])+states[12]/constants[62]+(states[13]*constants[7])/(constants[63]*constants[61])+(constants[59]*states[13]*states[10])/(constants[63]*constants[62]*constants[60])+(constants[58]*constants[7]*states[12])/(constants[63]*constants[61]*constants[62])+(states[12]*states[10])/(constants[62]*constants[60])+(states[13]*constants[7]*states[10])/(constants[63]*constants[61]*constants[64])+(constants[7]*states[12]*states[10])/(constants[65]*constants[62]*constants[60]))))
algebraic[22] = constants[89]*states[10]
algebraic[16] = constants[68]*algebraic[3]
algebraic[0] = states[4]/(1.00000+constants[4])
algebraic[1] = (states[4]*constants[4])/(1.00000+constants[4])
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)