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 = 19
sizeStates = 11
sizeConstants = 72
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] = "G_o in component G_o (millimolar)"
legend_states[0] = "G in component G (millimolar)"
legend_algebraic[3] = "V_IN in component V_IN (flux)"
legend_algebraic[4] = "V_HK in component V_HK (flux)"
legend_states[1] = "G6P in component G6P (millimolar)"
legend_algebraic[5] = "V_PFK in component V_PFK (flux)"
legend_algebraic[8] = "V_G6PDH in component V_G6PDH (flux)"
legend_states[2] = "FDP in component FDP (millimolar)"
legend_algebraic[7] = "V_ALD in component V_ALD (flux)"
legend_states[3] = "G3P in component G3P (millimolar)"
legend_algebraic[9] = "V_GAPDH in component V_GAPDH (flux)"
legend_states[4] = "DPG in component DPG (millimolar)"
legend_algebraic[10] = "V_PGK in component V_PGK (flux)"
legend_states[5] = "PEP in component PEP (millimolar)"
legend_algebraic[15] = "V_PK in component V_PK (flux)"
legend_states[6] = "Py in component Py (millimolar)"
legend_algebraic[16] = "V_TCA in component V_TCA (flux)"
legend_algebraic[17] = "V_ADH in component V_ADH (flux)"
legend_states[7] = "ATP in component ATP (millimolar)"
legend_constants[1] = "PO in component ATP (dimensionless)"
legend_algebraic[18] = "V_ATPase in component V_ATPase (flux)"
legend_algebraic[0] = "ADP in component ADP (millimolar)"
legend_constants[2] = "Cn in component ADP (millimolar)"
legend_constants[3] = "AMP in component AMP (millimolar)"
legend_constants[4] = "GTP in component GTP (millimolar)"
legend_constants[5] = "GDP in component GDP (millimolar)"
legend_constants[6] = "H in component H (millimolar)"
legend_constants[7] = "NADP in component NADP (millimolar)"
legend_constants[8] = "NADH in component NADH (millimolar)"
legend_constants[9] = "NAD in component NAD (millimolar)"
legend_algebraic[2] = "CD in component CD (millimolar)"
legend_constants[10] = "CMTP in component CD (millimolar)"
legend_states[8] = "CT in component CT (millimolar)"
legend_states[9] = "CP in component CP (millimolar)"
legend_constants[11] = "kpol in component CT (third_order_rate_constant)"
legend_constants[12] = "kf in component CT (first_order_rate_constant)"
legend_constants[13] = "kb in component CT (second_order_rate_constant)"
legend_constants[14] = "kdp in component CP (first_order_rate_constant)"
legend_states[10] = "PKp in component PKp (millimolar)"
legend_constants[15] = "kp2 in component PKp (second_order_rate_constant)"
legend_constants[16] = "kp3 in component PKp (first_order_rate_constant)"
legend_constants[17] = "k4 in component PKp (second_order_rate_constant)"
legend_algebraic[1] = "PKt in component PKt (millimolar)"
legend_constants[18] = "C_PK in component PKt (millimolar)"
legend_constants[19] = "Ke_in in component V_IN (millimolar)"
legend_constants[20] = "KG_in in component V_IN (millimolar)"
legend_constants[21] = "V_IN_max in component V_IN (flux)"
legend_constants[22] = "KG_m in component V_HK (millimolar)"
legend_constants[23] = "KG_s in component V_HK (millimolar)"
legend_constants[24] = "KATP_m in component V_HK (millimolar)"
legend_constants[25] = "V_HK_max in component V_HK (flux)"
legend_constants[26] = "KG6P_r in component V_PFK (millimolar)"
legend_constants[27] = "KATP_r in component V_PFK (millimolar)"
legend_constants[28] = "KAMP_r in component V_PFK (millimolar)"
legend_constants[29] = "cATP in component V_PFK (dimensionless)"
legend_constants[30] = "cAMP in component V_PFK (dimensionless)"
legend_constants[31] = "cG6P in component V_PFK (dimensionless)"
legend_constants[32] = "Lo in component V_PFK (dimensionless)"
legend_constants[33] = "gr in component V_PFK (dimensionless)"
legend_constants[34] = "n1 in component V_PFK (dimensionless)"
legend_constants[35] = "V_PFK_max in component V_PFK (flux)"
legend_algebraic[6] = "TUB in component V_G6PDH (millimolar)"
legend_constants[36] = "KG6P in component V_G6PDH (millimolar)"
legend_constants[37] = "KNADP in component V_G6PDH (millimolar)"
legend_constants[38] = "KNADP_ in component V_G6PDH (millimolar)"
legend_constants[39] = "KTUB in component V_G6PDH (millimolar)"
legend_constants[40] = "V_G6PDH_max in component V_G6PDH (flux)"
legend_constants[41] = "V_G6PDH_max_II in component V_G6PDH (flux)"
legend_constants[42] = "KG3P_m in component V_ALD (millimolar)"
legend_constants[43] = "KFDP_m in component V_ALD (millimolar)"
legend_constants[44] = "V_ALD_max in component V_ALD (flux)"
legend_constants[45] = "V_ALD_max_r in component V_ALD (flux)"
legend_constants[46] = "K1 in component V_GAPDH (millimolar)"
legend_constants[47] = "K2 in component V_GAPDH (millimolar)"
legend_constants[48] = "K3 in component V_GAPDH (millimolar)"
legend_constants[49] = "KG3P in component V_GAPDH (millimolar)"
legend_constants[50] = "KNAD in component V_GAPDH (millimolar)"
legend_constants[51] = "KNADH_i in component V_GAPDH (millimolar)"
legend_constants[52] = "V_GAPDH_max in component V_GAPDH (flux)"
legend_constants[53] = "KDPG_m in component V_PGK (millimolar)"
legend_constants[54] = "V_PGK_max in component V_PGK (flux)"
legend_algebraic[11] = "R in component V_PK (dimensionless)"
legend_algebraic[12] = "T in component V_PK (dimensionless)"
legend_constants[55] = "KpH in component V_PK (millimolar)"
legend_constants[56] = "KPEP_r in component V_PK (millimolar)"
legend_constants[57] = "KADP_r in component V_PK (millimolar)"
legend_constants[58] = "KFDP_r in component V_PK (millimolar)"
legend_constants[59] = "cADP in component V_PK (dimensionless)"
legend_constants[60] = "cFDP in component V_PK (dimensionless)"
legend_constants[61] = "cPEP in component V_PK (dimensionless)"
legend_constants[62] = "Lo_PK in component V_PK (dimensionless)"
legend_constants[63] = "gr_PK in component V_PK (dimensionless)"
legend_constants[64] = "gt_PK in component V_PK (dimensionless)"
legend_algebraic[14] = "n in component V_PK (dimensionless)"
legend_algebraic[13] = "V_PK_max in component V_PK (flux)"
legend_constants[65] = "V_PKt_max in component V_PK (flux)"
legend_constants[66] = "V_PKp_max in component V_PK (flux)"
legend_constants[67] = "KPy_m in component V_TCA (millimolar)"
legend_constants[68] = "V_TCA_max in component V_TCA (flux)"
legend_constants[69] = "KPy__m in component V_ADH (millimolar)"
legend_constants[70] = "V_ADH_max in component V_ADH (flux)"
legend_constants[71] = "KATP in component V_ATPase (first_order_rate_constant)"
legend_rates[0] = "d/dt G in component G (millimolar)"
legend_rates[1] = "d/dt G6P in component G6P (millimolar)"
legend_rates[2] = "d/dt FDP in component FDP (millimolar)"
legend_rates[3] = "d/dt G3P in component G3P (millimolar)"
legend_rates[4] = "d/dt DPG in component DPG (millimolar)"
legend_rates[5] = "d/dt PEP in component PEP (millimolar)"
legend_rates[6] = "d/dt Py in component Py (millimolar)"
legend_rates[7] = "d/dt ATP in component ATP (millimolar)"
legend_rates[8] = "d/dt CT in component CT (millimolar)"
legend_rates[9] = "d/dt CP in component CP (millimolar)"
legend_rates[10] = "d/dt PKp in component PKp (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1
states[0] = 0.01
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] = 1.4
constants[1] = 4
constants[2] = 9
constants[3] = 0.5
constants[4] = 0.95
constants[5] = 0.05
constants[6] = 3.2e-8
constants[7] = 1
constants[8] = 0.01
constants[9] = 1
constants[10] = 0.9
states[8] = 0.2
states[9] = 1.2
constants[11] = 10
constants[12] = 3
constants[13] = 2.5
constants[14] = 0.0025
states[10] = 0.005
constants[15] = 10
constants[16] = 0.05
constants[17] = 0.02
constants[18] = 0.01
constants[19] = 12
constants[20] = 0.001
constants[21] = 10
constants[22] = 0.11
constants[23] = 0.0062
constants[24] = 0.1
constants[25] = 13
constants[26] = 1
constants[27] = 0.06
constants[28] = 0.025
constants[29] = 1
constants[30] = 0.019
constants[31] = 0.0005
constants[32] = 25000
constants[33] = 10
constants[34] = 2
constants[35] = 30
constants[36] = 0.05
constants[37] = 0.05
constants[38] = 0.05
constants[39] = 0.4
constants[40] = 1.6
constants[41] = 1
constants[42] = 20
constants[43] = 0.5
constants[44] = 2.5
constants[45] = 1
constants[46] = 1.1
constants[47] = 1.5
constants[48] = 2.5
constants[49] = 0.0025
constants[50] = 0.18
constants[51] = 0.0003
constants[52] = 10
constants[53] = 0.002
constants[54] = 3
constants[55] = 9.5e-9
constants[56] = 1
constants[57] = 0.06
constants[58] = 0.025
constants[59] = 1
constants[60] = 0.01
constants[61] = 0.02
constants[62] = 1000
constants[63] = 0.1
constants[64] = 1
constants[65] = 25
constants[66] = 50
constants[67] = 0.329
constants[68] = 10
constants[69] = 0.169
constants[70] = 0.5
constants[71] = 5
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[9] = constants[11]*states[8]*(power(states[9], 2.00000))-constants[14]*states[9]
algebraic[1] = constants[18]-states[10]
rates[10] = 0.100000*constants[15]*algebraic[1]*states[9]-(constants[16]*states[10]+constants[17]*states[10]*constants[4])
algebraic[2] = constants[10]-(states[8]+states[9])
rates[8] = -(constants[11]*states[8]*(power(states[9], 2.00000))+constants[12]*algebraic[2]+constants[13]*states[8]*constants[5])
algebraic[3] = constants[21]*(constants[0]/((constants[20]+constants[0])*(1.00000+states[1]/constants[19]))-states[0]/((constants[20]+states[0])*(1.00000+states[1]/constants[19])))
algebraic[4] = (constants[25]*1.00000)/(1.00000+(constants[23]*constants[24])/(states[0]*states[7])+constants[22]/states[0]+constants[24]/states[7])
rates[0] = algebraic[3]-algebraic[4]
algebraic[5] = (((((constants[35]*constants[33]*states[1])/constants[26])*states[7])/constants[27])*(power(1.00000+states[1]/constants[26]+states[7]/constants[27]+(((constants[33]*states[1])/constants[26])*states[7])/constants[27], constants[34]-1.00000)))/(power(1.00000+states[1]/constants[26]+states[7]/constants[27]+(((constants[33]*states[1])/constants[26])*states[7])/constants[27], constants[34])+constants[32]*(power((1.00000+(constants[30]*constants[3])/constants[28])/(1.00000+constants[3]/constants[28]), constants[34]))*(power(1.00000+(constants[31]*states[1])/constants[26]+(constants[29]*states[7])/constants[27]+(((constants[33]*constants[31]*states[1])/constants[26])*constants[29]*states[7])/constants[27], constants[34])))
algebraic[7] = ((constants[44]*states[2])/constants[43]-(constants[45]*states[3])/constants[42])/(1.00000+states[2]/constants[43]+states[3]/constants[42])
rates[2] = algebraic[5]-algebraic[7]
algebraic[6] = states[8]+algebraic[2]
algebraic[8] = constants[40]/((constants[36]*constants[37])/(states[1]*constants[7])+constants[36]/states[1]+constants[37]/constants[7]+1.00000)+constants[41]/((constants[36]*constants[38]*constants[39])/(states[1]*constants[7]*algebraic[6])+(constants[36]*constants[38])/(states[1]*constants[7])+(constants[38]*constants[39])/(constants[7]*algebraic[6])+(constants[36]*constants[39])/(states[1]*algebraic[6])+constants[39]/algebraic[6]+constants[36]/states[1]+constants[38]/constants[7]+1.00000)
rates[1] = algebraic[4]-(algebraic[5]+algebraic[8])
algebraic[0] = constants[2]-(states[7]+constants[3])
algebraic[9] = constants[52]/(1.00000+constants[49]/states[3]+(constants[50]/constants[9])*(1.00000+constants[3]/constants[46]+algebraic[0]/constants[47]+states[7]/constants[48])+((constants[49]*constants[50])/(states[3]*constants[9]))*(1.00000+constants[8]/constants[51])+1.00000+constants[3]/constants[46]+algebraic[0]/constants[47]+states[7]/constants[48])
rates[3] = 2.00000*algebraic[7]-algebraic[9]
algebraic[10] = (constants[54]*states[4])/(constants[53]+states[4])
rates[4] = algebraic[9]-algebraic[10]
algebraic[11] = 1.00000+states[5]/constants[56]+algebraic[0]/constants[57]+(((constants[63]*states[5])/constants[56])*algebraic[0])/constants[57]
algebraic[12] = 1.00000+(constants[61]*states[5])/constants[56]+(constants[59]*algebraic[0])/constants[57]+(((constants[64]*constants[61]*states[5])/constants[56])*constants[59]*algebraic[0])/constants[57]
algebraic[14] = 4.00000+states[10]/constants[18]
algebraic[13] = constants[65]+((constants[66]-constants[65])*states[10])/constants[18]
algebraic[15] = ((algebraic[13]/(1.00000+constants[55]/constants[6]))*(constants[63]*(states[5]/constants[56])*(algebraic[0]/constants[57])*(power(algebraic[11], algebraic[14]-1.00000))+constants[62]*(power((1.00000+(constants[60]*states[2])/constants[58])/(1.00000+states[2]/constants[58]), algebraic[14]))*(states[2]/constants[58])*constants[64]*((constants[61]*states[5])/constants[56])*((constants[59]*algebraic[0])/constants[57])*(power(algebraic[12], algebraic[14]-1.00000))))/(power(algebraic[11], algebraic[14])+constants[62]*(power((1.00000+(constants[60]*states[2])/constants[58])/(1.00000+states[2]/constants[58]), algebraic[14]))*(power(algebraic[12], algebraic[14])))
rates[5] = algebraic[10]-algebraic[15]
algebraic[16] = (constants[68]*(power(states[6], 2.00000)))/(power(constants[67], 2.00000)+power(states[6], 2.00000))
algebraic[17] = (constants[70]*states[6])/(constants[69]+states[6])
rates[6] = algebraic[15]-(algebraic[16]+algebraic[17])
algebraic[18] = constants[71]*states[7]
rates[7] = (algebraic[10]+algebraic[15]+constants[1]*algebraic[16])-(algebraic[4]+algebraic[5]+algebraic[18])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[1] = constants[18]-states[10]
algebraic[2] = constants[10]-(states[8]+states[9])
algebraic[3] = constants[21]*(constants[0]/((constants[20]+constants[0])*(1.00000+states[1]/constants[19]))-states[0]/((constants[20]+states[0])*(1.00000+states[1]/constants[19])))
algebraic[4] = (constants[25]*1.00000)/(1.00000+(constants[23]*constants[24])/(states[0]*states[7])+constants[22]/states[0]+constants[24]/states[7])
algebraic[5] = (((((constants[35]*constants[33]*states[1])/constants[26])*states[7])/constants[27])*(power(1.00000+states[1]/constants[26]+states[7]/constants[27]+(((constants[33]*states[1])/constants[26])*states[7])/constants[27], constants[34]-1.00000)))/(power(1.00000+states[1]/constants[26]+states[7]/constants[27]+(((constants[33]*states[1])/constants[26])*states[7])/constants[27], constants[34])+constants[32]*(power((1.00000+(constants[30]*constants[3])/constants[28])/(1.00000+constants[3]/constants[28]), constants[34]))*(power(1.00000+(constants[31]*states[1])/constants[26]+(constants[29]*states[7])/constants[27]+(((constants[33]*constants[31]*states[1])/constants[26])*constants[29]*states[7])/constants[27], constants[34])))
algebraic[7] = ((constants[44]*states[2])/constants[43]-(constants[45]*states[3])/constants[42])/(1.00000+states[2]/constants[43]+states[3]/constants[42])
algebraic[6] = states[8]+algebraic[2]
algebraic[8] = constants[40]/((constants[36]*constants[37])/(states[1]*constants[7])+constants[36]/states[1]+constants[37]/constants[7]+1.00000)+constants[41]/((constants[36]*constants[38]*constants[39])/(states[1]*constants[7]*algebraic[6])+(constants[36]*constants[38])/(states[1]*constants[7])+(constants[38]*constants[39])/(constants[7]*algebraic[6])+(constants[36]*constants[39])/(states[1]*algebraic[6])+constants[39]/algebraic[6]+constants[36]/states[1]+constants[38]/constants[7]+1.00000)
algebraic[0] = constants[2]-(states[7]+constants[3])
algebraic[9] = constants[52]/(1.00000+constants[49]/states[3]+(constants[50]/constants[9])*(1.00000+constants[3]/constants[46]+algebraic[0]/constants[47]+states[7]/constants[48])+((constants[49]*constants[50])/(states[3]*constants[9]))*(1.00000+constants[8]/constants[51])+1.00000+constants[3]/constants[46]+algebraic[0]/constants[47]+states[7]/constants[48])
algebraic[10] = (constants[54]*states[4])/(constants[53]+states[4])
algebraic[11] = 1.00000+states[5]/constants[56]+algebraic[0]/constants[57]+(((constants[63]*states[5])/constants[56])*algebraic[0])/constants[57]
algebraic[12] = 1.00000+(constants[61]*states[5])/constants[56]+(constants[59]*algebraic[0])/constants[57]+(((constants[64]*constants[61]*states[5])/constants[56])*constants[59]*algebraic[0])/constants[57]
algebraic[14] = 4.00000+states[10]/constants[18]
algebraic[13] = constants[65]+((constants[66]-constants[65])*states[10])/constants[18]
algebraic[15] = ((algebraic[13]/(1.00000+constants[55]/constants[6]))*(constants[63]*(states[5]/constants[56])*(algebraic[0]/constants[57])*(power(algebraic[11], algebraic[14]-1.00000))+constants[62]*(power((1.00000+(constants[60]*states[2])/constants[58])/(1.00000+states[2]/constants[58]), algebraic[14]))*(states[2]/constants[58])*constants[64]*((constants[61]*states[5])/constants[56])*((constants[59]*algebraic[0])/constants[57])*(power(algebraic[12], algebraic[14]-1.00000))))/(power(algebraic[11], algebraic[14])+constants[62]*(power((1.00000+(constants[60]*states[2])/constants[58])/(1.00000+states[2]/constants[58]), algebraic[14]))*(power(algebraic[12], algebraic[14])))
algebraic[16] = (constants[68]*(power(states[6], 2.00000)))/(power(constants[67], 2.00000)+power(states[6], 2.00000))
algebraic[17] = (constants[70]*states[6])/(constants[69]+states[6])
algebraic[18] = constants[71]*states[7]
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)