Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 17
sizeStates = 7
sizeConstants = 40
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 (millisecond)"
legend_constants[0] = "V_cell in component environment (picoL)"
legend_constants[1] = "Ca_e in component environment (millimolar)"
legend_constants[2] = "K_e in component environment (millimolar)"
legend_constants[3] = "K_i in component environment (millimolar)"
legend_constants[4] = "V_tau in component environment (millivolt)"
legend_constants[5] = "k_tau in component environment (millivolt)"
legend_states[0] = "V in component membrane (millivolt)"
legend_constants[6] = "R in component membrane (joule_per_kilomole_kelvin)"
legend_constants[7] = "T in component membrane (kelvin)"
legend_constants[8] = "F in component membrane (coulomb_per_mole)"
legend_constants[9] = "Cm in component membrane (picoF)"
legend_algebraic[5] = "i_Ca_L in component L_type_calcium_current (picoA)"
legend_algebraic[8] = "i_Ca_T in component T_type_calcium_current (picoA)"
legend_algebraic[11] = "i_K_DR in component voltage_sensitive_K_current (picoA)"
legend_algebraic[13] = "i_K_Ca in component Ca_activated_K_current (picoA)"
legend_algebraic[15] = "i_leak in component leak_current (picoA)"
legend_algebraic[0] = "phi_Ca in component L_type_calcium_current (millivolt_millimolar)"
legend_constants[10] = "g_Ca_L in component L_type_calcium_current (nanoS_per_millimolar)"
legend_states[1] = "Ca_i in component cytosolic_calcium (millimolar)"
legend_states[2] = "m_L in component L_type_calcium_current_m_gate (dimensionless)"
legend_algebraic[1] = "m_L_infinity in component L_type_calcium_current_m_gate (dimensionless)"
legend_algebraic[6] = "tau_m_L in component L_type_calcium_current_m_gate (millisecond)"
legend_constants[11] = "tau_m_L_max in component L_type_calcium_current_m_gate (millisecond)"
legend_constants[12] = "V_m_L in component L_type_calcium_current_m_gate (millivolt)"
legend_constants[13] = "k_m_L in component L_type_calcium_current_m_gate (millivolt)"
legend_constants[14] = "g_Ca_T in component T_type_calcium_current (nanoS_per_millimolar)"
legend_states[3] = "m_T in component T_type_calcium_current_m_gate (dimensionless)"
legend_states[4] = "h_T in component T_type_calcium_current_h_gate (dimensionless)"
legend_algebraic[2] = "m_T_infinity in component T_type_calcium_current_m_gate (dimensionless)"
legend_algebraic[7] = "tau_m_T in component T_type_calcium_current_m_gate (millisecond)"
legend_constants[15] = "tau_m_T_max in component T_type_calcium_current_m_gate (millisecond)"
legend_constants[16] = "V_m_T in component T_type_calcium_current_m_gate (millivolt)"
legend_constants[17] = "k_m_T in component T_type_calcium_current_m_gate (millivolt)"
legend_algebraic[3] = "h_T_infinity in component T_type_calcium_current_h_gate (dimensionless)"
legend_constants[18] = "tau_h_T in component T_type_calcium_current_h_gate (millisecond)"
legend_constants[19] = "V_h_T in component T_type_calcium_current_h_gate (millivolt)"
legend_constants[20] = "k_h_T in component T_type_calcium_current_h_gate (millivolt)"
legend_algebraic[9] = "phi_K in component voltage_sensitive_K_current (millivolt_millimolar)"
legend_constants[21] = "g_K_DR in component voltage_sensitive_K_current (nanoS_per_millimolar)"
legend_states[5] = "n in component voltage_sensitive_K_current_n_gate (dimensionless)"
legend_algebraic[4] = "n_infinity in component voltage_sensitive_K_current_n_gate (dimensionless)"
legend_constants[22] = "tau_n in component voltage_sensitive_K_current_n_gate (millisecond)"
legend_constants[23] = "V_n in component voltage_sensitive_K_current_n_gate (millivolt)"
legend_constants[24] = "k_n in component voltage_sensitive_K_current_n_gate (millivolt)"
legend_constants[25] = "g_K_Ca in component Ca_activated_K_current (nanoS_per_millimolar)"
legend_constants[26] = "Kc in component Ca_activated_K_current (millimolar)"
legend_constants[27] = "g_L in component leak_current (nanoS)"
legend_constants[28] = "V_L in component leak_current (millivolt)"
legend_states[6] = "Ca_er in component ER_calcium (millimolar)"
legend_algebraic[10] = "J_rel in component ER_calcium (millimolar_picoL_per_millisecond)"
legend_algebraic[12] = "J_up in component ER_calcium (millimolar_picoL_per_millisecond)"
legend_constants[38] = "V_er in component ER_calcium (picoL)"
legend_constants[29] = "K_er in component ER_calcium (millimolar)"
legend_constants[30] = "f_er in component ER_calcium (dimensionless)"
legend_constants[31] = "P in component ER_calcium (picoL_per_millisecond)"
legend_constants[32] = "v_er in component ER_calcium (millimolar_picoL_per_millisecond)"
legend_constants[39] = "V_c in component cytosolic_calcium (picoL)"
legend_constants[33] = "K_p in component cytosolic_calcium (millimolar)"
legend_constants[34] = "f_cyt in component cytosolic_calcium (dimensionless)"
legend_constants[35] = "v_p in component cytosolic_calcium (millimolar_micrometre_per_millisecond)"
legend_algebraic[14] = "J_in in component cytosolic_calcium (millimolar_micrometre_per_millisecond)"
legend_algebraic[16] = "J_eff in component cytosolic_calcium (millimolar_micrometre_per_millisecond)"
legend_constants[36] = "alpha in component cytosolic_calcium (millimolar_micrometre_per_millisecond_per_picoA)"
legend_constants[37] = "beta in component cytosolic_calcium (per_micrometre)"
legend_rates[0] = "d/dt V in component membrane (millivolt)"
legend_rates[2] = "d/dt m_L in component L_type_calcium_current_m_gate (dimensionless)"
legend_rates[3] = "d/dt m_T in component T_type_calcium_current_m_gate (dimensionless)"
legend_rates[4] = "d/dt h_T in component T_type_calcium_current_h_gate (dimensionless)"
legend_rates[5] = "d/dt n in component voltage_sensitive_K_current_n_gate (dimensionless)"
legend_rates[6] = "d/dt Ca_er in component ER_calcium (millimolar)"
legend_rates[1] = "d/dt Ca_i in component cytosolic_calcium (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1.77
constants[1] = 20
constants[2] = 5.6
constants[3] = 140
constants[4] = -60
constants[5] = 22
states[0] = -70
constants[6] = 8314
constants[7] = 310
constants[8] = 96845
constants[9] = 7
constants[10] = 9
states[1] = 0.00026
states[2] = 0
constants[11] = 27
constants[12] = -18
constants[13] = 12
constants[14] = 10
states[3] = 0
states[4] = 0
constants[15] = 10
constants[16] = -30
constants[17] = 10.5
constants[18] = 15
constants[19] = -57
constants[20] = 5
constants[21] = 0.1
states[5] = 0
constants[22] = 20
constants[23] = -20
constants[24] = 4.5
constants[25] = 0.09
constants[26] = 0.0004
constants[27] = 0.3
constants[28] = -67
states[6] = 0.0172
constants[29] = 0.0002
constants[30] = 0.0025
constants[31] = 0.0012
constants[32] = 0.00005
constants[33] = 0.00008
constants[34] = 0.01
constants[35] = 0.000045
constants[36] = 0.0000074
constants[37] = 0.47
constants[38] = constants[0]*0.150000
constants[39] = constants[0]*0.850000
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[3] = 1.00000/(1.00000+exp((states[0]-constants[19])/constants[20]))
rates[4] = (algebraic[3]-states[4])/constants[18]
algebraic[4] = 1.00000/(1.00000+exp((constants[23]-states[0])/constants[24]))
rates[5] = (algebraic[4]-states[5])/constants[22]
algebraic[1] = 1.00000/(1.00000+exp((constants[12]-states[0])/constants[13]))
algebraic[6] = constants[11]/(exp((states[0]-constants[4])/constants[5])+2.00000*exp((2.00000*(constants[4]-states[0]))/constants[5]))
rates[2] = (algebraic[1]-states[2])/algebraic[6]
algebraic[2] = 1.00000/(1.00000+exp((constants[16]-states[0])/constants[17]))
algebraic[7] = constants[15]/(exp((states[0]-constants[4])/constants[5])+2.00000*exp((2.00000*(constants[4]-states[0]))/constants[5]))
rates[3] = (algebraic[2]-states[3])/algebraic[7]
algebraic[10] = constants[31]*(states[6]-states[1])
algebraic[12] = (constants[32]*(power(states[1], 2.00000)))/(power(states[1], 2.00000)+power(constants[29], 2.00000))
rates[6] = (-constants[30]/constants[38])*(algebraic[10]-algebraic[12])
algebraic[0] = (states[0]*(states[1]-constants[1])*exp((-2.00000*constants[8]*states[0])/(constants[6]*constants[7])))/(1.00000-exp((-2.00000*constants[8]*states[0])/(constants[6]*constants[7])))
algebraic[5] = constants[10]*(power(states[2], 2.00000))*algebraic[0]
algebraic[8] = constants[14]*(power(states[3], 2.00000))*states[4]*algebraic[0]
algebraic[9] = (states[0]*(constants[3]-constants[2])*exp((-1.00000*constants[8]*states[0])/(constants[6]*constants[7])))/(1.00000-exp((-1.00000*constants[8]*states[0])/(constants[6]*constants[7])))
algebraic[11] = constants[21]*states[5]*algebraic[9]
algebraic[13] = ((constants[25]*(power(states[1], 4.00000)))/(power(states[1], 4.00000)+power(constants[26], 4.00000)))*algebraic[9]
algebraic[15] = constants[27]*(states[0]-constants[28])
rates[0] = -(algebraic[5]+algebraic[8]+algebraic[11]+algebraic[13]+algebraic[15])/constants[9]
algebraic[14] = -constants[36]*(algebraic[5]+algebraic[8])
algebraic[16] = (constants[35]*(power(states[1], 2.00000)))/(power(states[1], 2.00000)+power(constants[33], 2.00000))
rates[1] = (constants[34]/constants[39])*(algebraic[10]-algebraic[12])+constants[34]*constants[37]*(algebraic[14]-algebraic[16])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[3] = 1.00000/(1.00000+exp((states[0]-constants[19])/constants[20]))
algebraic[4] = 1.00000/(1.00000+exp((constants[23]-states[0])/constants[24]))
algebraic[1] = 1.00000/(1.00000+exp((constants[12]-states[0])/constants[13]))
algebraic[6] = constants[11]/(exp((states[0]-constants[4])/constants[5])+2.00000*exp((2.00000*(constants[4]-states[0]))/constants[5]))
algebraic[2] = 1.00000/(1.00000+exp((constants[16]-states[0])/constants[17]))
algebraic[7] = constants[15]/(exp((states[0]-constants[4])/constants[5])+2.00000*exp((2.00000*(constants[4]-states[0]))/constants[5]))
algebraic[10] = constants[31]*(states[6]-states[1])
algebraic[12] = (constants[32]*(power(states[1], 2.00000)))/(power(states[1], 2.00000)+power(constants[29], 2.00000))
algebraic[0] = (states[0]*(states[1]-constants[1])*exp((-2.00000*constants[8]*states[0])/(constants[6]*constants[7])))/(1.00000-exp((-2.00000*constants[8]*states[0])/(constants[6]*constants[7])))
algebraic[5] = constants[10]*(power(states[2], 2.00000))*algebraic[0]
algebraic[8] = constants[14]*(power(states[3], 2.00000))*states[4]*algebraic[0]
algebraic[9] = (states[0]*(constants[3]-constants[2])*exp((-1.00000*constants[8]*states[0])/(constants[6]*constants[7])))/(1.00000-exp((-1.00000*constants[8]*states[0])/(constants[6]*constants[7])))
algebraic[11] = constants[21]*states[5]*algebraic[9]
algebraic[13] = ((constants[25]*(power(states[1], 4.00000)))/(power(states[1], 4.00000)+power(constants[26], 4.00000)))*algebraic[9]
algebraic[15] = constants[27]*(states[0]-constants[28])
algebraic[14] = -constants[36]*(algebraic[5]+algebraic[8])
algebraic[16] = (constants[35]*(power(states[1], 2.00000)))/(power(states[1], 2.00000)+power(constants[33], 2.00000))
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)