Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 21
sizeStates = 8
sizeConstants = 55
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] = "Vm in component membrane (millivolt)"
legend_algebraic[8] = "I_iCa in component membrane (picoampere)"
legend_algebraic[11] = "I_iNa in component membrane (picoampere)"
legend_constants[0] = "Cm in component membrane (picofarad)"
legend_algebraic[2] = "I_Ca in component I_Ca (picoampere)"
legend_algebraic[9] = "I_Na in component I_Na (picoampere)"
legend_algebraic[4] = "I_NSCC_Ca in component I_NSCC_Ca (picoampere)"
legend_algebraic[7] = "I_PM in component I_PM (picoampere)"
legend_algebraic[6] = "I_NSCC_Na in component I_NSCC_Na (picoampere)"
legend_constants[1] = "gCa in component I_Ca (picosiemens)"
legend_algebraic[0] = "ECa in component I_Ca (millivolt)"
legend_constants[2] = "T in component model_parameters (kelvin)"
legend_constants[3] = "R in component model_parameters (attojoule_per_zeptomole_kelvin)"
legend_constants[4] = "F in component model_parameters (femtocoulomb_per_zeptomole)"
legend_constants[5] = "CO in component model_parameters (micromolar)"
legend_states[1] = "CS1 in component CS1 (micromolar)"
legend_constants[6] = "gNSCC_Ca_ in component I_NSCC_Ca (picosiemens)"
legend_algebraic[3] = "gNSCC_Ca in component I_NSCC_Ca (picosiemens)"
legend_constants[7] = "hNSCC in component model_parameters (dimensionless)"
legend_constants[8] = "ENSCC in component model_parameters (millivolt)"
legend_constants[9] = "KNSCC in component model_parameters (micromolar)"
legend_constants[10] = "gNSCC_Na_ in component I_NSCC_Na (picosiemens)"
legend_algebraic[5] = "gNSCC_Na in component I_NSCC_Na (picosiemens)"
legend_constants[11] = "gPM in component I_PM (femtoampere)"
legend_constants[12] = "KPM in component I_PM (micromolar)"
legend_constants[13] = "gNa in component I_Na (femtoampere)"
legend_constants[14] = "KNa in component I_Na (micromolar)"
legend_constants[15] = "hNa in component I_Na (dimensionless)"
legend_states[2] = "NS1 in component NS1 (micromolar)"
legend_algebraic[10] = "JSERCA in component JSERCA (flux)"
legend_constants[16] = "VSERCA in component JSERCA (first_order_rate_constant)"
legend_constants[17] = "A2 in component JSERCA (dimensionless)"
legend_constants[18] = "A4 in component JSERCA (per_micromolar)"
legend_constants[19] = "A5 in component JSERCA (per_micromolar)"
legend_constants[20] = "A6 in component JSERCA (per_micromolar2)"
legend_states[3] = "CER in component CER (micromolar)"
legend_algebraic[13] = "JMCU in component JMCU (flux)"
legend_constants[21] = "VMCU in component JMCU (flux)"
legend_constants[22] = "KMCU in component JMCU (micromolar)"
legend_algebraic[12] = "epsilon_INH in component JMCU (dimensionless)"
legend_constants[23] = "KINH in component JMCU (micromolar)"
legend_constants[24] = "hINH in component JMCU (dimensionless)"
legend_states[4] = "CS2 in component CS2 (micromolar)"
legend_states[5] = "CMT in component CMT (micromolar)"
legend_algebraic[14] = "JNCX in component JNCX (flux)"
legend_constants[25] = "VNCX in component JNCX (flux)"
legend_constants[26] = "KNCX in component JNCX (micromolar)"
legend_algebraic[15] = "JS1S2 in component JS1S2 (flux)"
legend_constants[27] = "mu_S1S2 in component JS1S2 (first_order_rate_constant)"
legend_algebraic[19] = "JIPR in component JIPR (flux)"
legend_constants[28] = "kIPR in component JIPR (first_order_rate_constant)"
legend_constants[29] = "k_1 in component JIPR (flux)"
legend_constants[30] = "k1 in component JIPR (first_order_rate_constant)"
legend_constants[31] = "k2 in component JIPR (first_order_rate_constant)"
legend_constants[32] = "r2 in component JIPR (first_order_rate_constant)"
legend_constants[33] = "r_2 in component JIPR (flux)"
legend_constants[34] = "r4 in component JIPR (first_order_rate_constant)"
legend_constants[35] = "R1 in component JIPR (micromolar)"
legend_constants[36] = "R3 in component JIPR (micromolar)"
legend_algebraic[17] = "phi1 in component JIPR (first_order_rate_constant)"
legend_algebraic[18] = "phi_1 in component JIPR (flux)"
legend_algebraic[20] = "phi2 in component JIPR (first_order_rate_constant)"
legend_states[6] = "phi3 in component JIPR (first_order_rate_constant)"
legend_states[7] = "H in component JIPR (dimensionless)"
legend_constants[37] = "g_beta in component JIPR (first_order_rate_constant)"
legend_constants[38] = "h_beta in component JIPR (dimensionless)"
legend_constants[39] = "g_alpha in component JIPR (per_second_squared)"
legend_constants[40] = "K_beta in component JIPR (micromolar)"
legend_constants[50] = "alpha_phi3 in component JIPR (per_second_squared)"
legend_algebraic[1] = "beta_phi3 in component JIPR (first_order_rate_constant)"
legend_constants[41] = "P in component model_parameters (micromolar)"
legend_constants[49] = "lambda_MT_S1 in component CS1 (dimensionless)"
legend_constants[51] = "lambda_ER_S1 in component CS1 (dimensionless)"
legend_constants[42] = "delta_s in component model_parameters (micromolar_coulomb)"
legend_constants[43] = "gamma_S1 in component model_parameters (dimensionless)"
legend_constants[44] = "gamma_MT in component model_parameters (dimensionless)"
legend_constants[45] = "gamma_ER in component model_parameters (dimensionless)"
legend_constants[52] = "lambda_MT_S2 in component CS2 (dimensionless)"
legend_constants[53] = "lambda_ER_S2 in component CS2 (dimensionless)"
legend_constants[54] = "lambda_S1_S2 in component CS2 (dimensionless)"
legend_constants[46] = "gamma_S2 in component model_parameters (dimensionless)"
legend_algebraic[16] = "fm in component CMT (dimensionless)"
legend_constants[47] = "Km in component CMT (micromolar)"
legend_constants[48] = "Bm in component CMT (micromolar)"
legend_rates[0] = "d/dt Vm in component membrane (millivolt)"
legend_rates[7] = "d/dt H in component JIPR (dimensionless)"
legend_rates[6] = "d/dt phi3 in component JIPR (first_order_rate_constant)"
legend_rates[1] = "d/dt CS1 in component CS1 (micromolar)"
legend_rates[4] = "d/dt CS2 in component CS2 (micromolar)"
legend_rates[3] = "d/dt CER in component CER (micromolar)"
legend_rates[5] = "d/dt CMT in component CMT (micromolar)"
legend_rates[2] = "d/dt NS1 in component NS1 (micromolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = -70.1
constants[0] = 20.0
constants[1] = 0.01
constants[2] = 310.16
constants[3] = 8.314E-3
constants[4] = 0.09649
constants[5] = 1.8E3
states[1] = 0.120
constants[6] = 0.12
constants[7] = 3.0
constants[8] = 0.0
constants[9] = 0.12
constants[10] = 220.0
constants[11] = 420.0
constants[12] = 1.0
constants[13] = 1.5E4
constants[14] = 1.0E4
constants[15] = 4.0
states[2] = 1.01E4
constants[16] = 1.0E5
constants[17] = 6E-4
constants[18] = 3.57
constants[19] = 2.7E-5
constants[20] = 2.31E-5
states[3] = 203.0
constants[21] = 800.0
constants[22] = 10.0
constants[23] = 10.0
constants[24] = 4.0
states[4] = 0.023
states[5] = 0.220
constants[25] = 0.5
constants[26] = 0.3
constants[27] = 0.04
constants[28] = 2000.0
constants[29] = 6.4
constants[30] = 0.0
constants[31] = 4.0
constants[32] = 200.0
constants[33] = 0.0
constants[34] = 750.0
constants[35] = 36.0
constants[36] = 300.0
states[6] = 0.306
states[7] = 0.787
constants[37] = 300.0
constants[38] = 2.0
constants[39] = 0.02
constants[40] = 2.0
constants[41] = 1.0
constants[42] = 26.0
constants[43] = 100.0
constants[44] = 200.0
constants[45] = 20.0
constants[46] = 1.0
constants[47] = 0.01
constants[48] = 100.0
constants[49] = constants[44]/constants[43]
constants[50] = constants[39]
constants[51] = constants[45]/constants[43]
constants[52] = constants[44]/constants[46]
constants[53] = constants[45]/constants[46]
constants[54] = constants[43]/constants[46]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[1] = constants[37]*((power(states[4], constants[38]))/(power(constants[40], constants[38])+power(states[4], constants[38])))
rates[6] = constants[50]-algebraic[1]*states[6]
algebraic[0] = ((constants[3]*constants[2])/(2.00000*constants[4]))*log(constants[5]/states[1])
algebraic[2] = constants[1]*(states[0]-algebraic[0])
algebraic[3] = constants[6]*((power(constants[9], constants[7]))/(power(constants[9], constants[7])+power(states[1], constants[7])))
algebraic[4] = algebraic[3]*(states[0]-constants[8])
algebraic[7] = constants[11]*((power(states[1], 2.00000))/(power(constants[12], 2.00000)+power(states[1], 2.00000)))
algebraic[8] = algebraic[2]+algebraic[4]+algebraic[7]
algebraic[9] = constants[13]*((power(states[2], constants[15]))/(power(constants[14], constants[15])+power(states[2], constants[15])))
algebraic[5] = constants[10]*((power(constants[9], constants[7]))/(power(constants[9], constants[7])+power(states[1], constants[7])))
algebraic[6] = algebraic[5]*(states[0]-constants[8])
algebraic[11] = algebraic[6]+algebraic[9]
rates[0] = -((algebraic[8]+algebraic[11])/constants[0])
rates[2] = -(constants[42]/1.00000)*algebraic[11]
algebraic[10] = (constants[16]*(states[1]-constants[17]*states[3]))/(1.00000+constants[18]*states[1]+constants[19]*states[3]+constants[20]*states[1]*states[3])
algebraic[14] = constants[25]*(states[5]/(states[5]+constants[26]))
algebraic[15] = constants[27]*(states[4]-states[1])
rates[1] = (algebraic[15]+constants[49]*algebraic[14])-((constants[42]/2.00000)*algebraic[8]+constants[51]*algebraic[10])
algebraic[12] = (power(constants[23], constants[24]))/(power(constants[23], constants[24])+power(states[5], constants[24]))
algebraic[13] = constants[21]*((power(states[4], 2.00000))/(power(constants[22], 2.00000)+power(states[4], 2.00000)))*algebraic[12]
algebraic[16] = 1.00000/(1.00000+(constants[47]*constants[48])/(power(constants[47]+states[5], 2.00000)))
rates[5] = algebraic[16]*(algebraic[13]-algebraic[14])
algebraic[17] = (constants[30]*constants[35]+constants[32]*states[4])/(constants[35]+states[4])
algebraic[18] = ((constants[29]+constants[33])*constants[36])/(constants[36]+states[4])
algebraic[20] = (constants[31]*constants[36]+constants[34]*states[4])/(constants[36]+states[4])
rates[7] = states[6]*(1.00000-states[7])-((constants[41]*algebraic[17]*algebraic[20])/(constants[41]*algebraic[17]+algebraic[18]))*states[7]
algebraic[19] = constants[28]*(power((constants[41]*algebraic[17]*states[7])/(constants[41]*algebraic[17]+algebraic[18]), 4.00000))*(states[3]-states[4])
rates[4] = constants[53]*algebraic[19]-(constants[54]*algebraic[15]+constants[52]*algebraic[13])
rates[3] = algebraic[10]-algebraic[19]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[1] = constants[37]*((power(states[4], constants[38]))/(power(constants[40], constants[38])+power(states[4], constants[38])))
algebraic[0] = ((constants[3]*constants[2])/(2.00000*constants[4]))*log(constants[5]/states[1])
algebraic[2] = constants[1]*(states[0]-algebraic[0])
algebraic[3] = constants[6]*((power(constants[9], constants[7]))/(power(constants[9], constants[7])+power(states[1], constants[7])))
algebraic[4] = algebraic[3]*(states[0]-constants[8])
algebraic[7] = constants[11]*((power(states[1], 2.00000))/(power(constants[12], 2.00000)+power(states[1], 2.00000)))
algebraic[8] = algebraic[2]+algebraic[4]+algebraic[7]
algebraic[9] = constants[13]*((power(states[2], constants[15]))/(power(constants[14], constants[15])+power(states[2], constants[15])))
algebraic[5] = constants[10]*((power(constants[9], constants[7]))/(power(constants[9], constants[7])+power(states[1], constants[7])))
algebraic[6] = algebraic[5]*(states[0]-constants[8])
algebraic[11] = algebraic[6]+algebraic[9]
algebraic[10] = (constants[16]*(states[1]-constants[17]*states[3]))/(1.00000+constants[18]*states[1]+constants[19]*states[3]+constants[20]*states[1]*states[3])
algebraic[14] = constants[25]*(states[5]/(states[5]+constants[26]))
algebraic[15] = constants[27]*(states[4]-states[1])
algebraic[12] = (power(constants[23], constants[24]))/(power(constants[23], constants[24])+power(states[5], constants[24]))
algebraic[13] = constants[21]*((power(states[4], 2.00000))/(power(constants[22], 2.00000)+power(states[4], 2.00000)))*algebraic[12]
algebraic[16] = 1.00000/(1.00000+(constants[47]*constants[48])/(power(constants[47]+states[5], 2.00000)))
algebraic[17] = (constants[30]*constants[35]+constants[32]*states[4])/(constants[35]+states[4])
algebraic[18] = ((constants[29]+constants[33])*constants[36])/(constants[36]+states[4])
algebraic[20] = (constants[31]*constants[36]+constants[34]*states[4])/(constants[36]+states[4])
algebraic[19] = constants[28]*(power((constants[41]*algebraic[17]*states[7])/(constants[41]*algebraic[17]+algebraic[18]), 4.00000))*(states[3]-states[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)