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 = 25
sizeStates = 8
sizeConstants = 24
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_states[0] = "V in component membrane (millivolt)"
legend_constants[0] = "R in component membrane (joule_per_kilomole_kelvin)"
legend_constants[1] = "T in component membrane (kelvin)"
legend_constants[2] = "F in component membrane (coulomb_per_mole)"
legend_constants[3] = "C in component membrane (microF_per_cm2)"
legend_algebraic[0] = "I_stim in component membrane (microA_per_cm2)"
legend_algebraic[7] = "i_Na in component fast_sodium_current (microA_per_cm2)"
legend_algebraic[15] = "i_si in component slow_inward_current (microA_per_cm2)"
legend_algebraic[17] = "i_K in component time_dependent_potassium_current (microA_per_cm2)"
legend_algebraic[21] = "i_K1 in component time_independent_potassium_current (microA_per_cm2)"
legend_algebraic[23] = "i_Kp in component plateau_potassium_current (microA_per_cm2)"
legend_algebraic[24] = "i_b in component background_current (microA_per_cm2)"
legend_constants[4] = "stim_start in component membrane (millisecond)"
legend_constants[5] = "stim_end in component membrane (millisecond)"
legend_constants[6] = "stim_period in component membrane (millisecond)"
legend_constants[7] = "stim_duration in component membrane (millisecond)"
legend_constants[8] = "stim_amplitude in component membrane (microA_per_cm2)"
legend_constants[9] = "g_Na in component fast_sodium_current (milliS_per_cm2)"
legend_constants[18] = "E_Na in component fast_sodium_current (millivolt)"
legend_constants[10] = "Nao in component ionic_concentrations (millimolar)"
legend_constants[11] = "Nai in component ionic_concentrations (millimolar)"
legend_states[1] = "m in component fast_sodium_current_m_gate (dimensionless)"
legend_states[2] = "h in component fast_sodium_current_h_gate (dimensionless)"
legend_states[3] = "j in component fast_sodium_current_j_gate (dimensionless)"
legend_algebraic[1] = "alpha_m in component fast_sodium_current_m_gate (per_millisecond)"
legend_algebraic[8] = "beta_m in component fast_sodium_current_m_gate (per_millisecond)"
legend_algebraic[2] = "alpha_h in component fast_sodium_current_h_gate (per_millisecond)"
legend_algebraic[9] = "beta_h in component fast_sodium_current_h_gate (per_millisecond)"
legend_algebraic[3] = "alpha_j in component fast_sodium_current_j_gate (per_millisecond)"
legend_algebraic[10] = "beta_j in component fast_sodium_current_j_gate (per_millisecond)"
legend_algebraic[14] = "E_si in component slow_inward_current (millivolt)"
legend_states[4] = "Cai in component intracellular_calcium_concentration (millimolar)"
legend_states[5] = "d in component slow_inward_current_d_gate (dimensionless)"
legend_states[6] = "f in component slow_inward_current_f_gate (dimensionless)"
legend_algebraic[4] = "alpha_d in component slow_inward_current_d_gate (per_millisecond)"
legend_algebraic[11] = "beta_d in component slow_inward_current_d_gate (per_millisecond)"
legend_algebraic[5] = "alpha_f in component slow_inward_current_f_gate (per_millisecond)"
legend_algebraic[12] = "beta_f in component slow_inward_current_f_gate (per_millisecond)"
legend_constants[19] = "g_K in component time_dependent_potassium_current (milliS_per_cm2)"
legend_constants[20] = "E_K in component time_dependent_potassium_current (millivolt)"
legend_constants[12] = "PR_NaK in component time_dependent_potassium_current (dimensionless)"
legend_constants[13] = "Ko in component ionic_concentrations (millimolar)"
legend_constants[14] = "Ki in component ionic_concentrations (millimolar)"
legend_states[7] = "X in component time_dependent_potassium_current_X_gate (dimensionless)"
legend_algebraic[16] = "Xi in component time_dependent_potassium_current_Xi_gate (dimensionless)"
legend_algebraic[6] = "alpha_X in component time_dependent_potassium_current_X_gate (per_millisecond)"
legend_algebraic[13] = "beta_X in component time_dependent_potassium_current_X_gate (per_millisecond)"
legend_constants[21] = "E_K1 in component time_independent_potassium_current (millivolt)"
legend_constants[22] = "g_K1 in component time_independent_potassium_current (milliS_per_cm2)"
legend_algebraic[20] = "K1_infinity in component time_independent_potassium_current_K1_gate (dimensionless)"
legend_algebraic[18] = "alpha_K1 in component time_independent_potassium_current_K1_gate (per_millisecond)"
legend_algebraic[19] = "beta_K1 in component time_independent_potassium_current_K1_gate (per_millisecond)"
legend_constants[23] = "E_Kp in component plateau_potassium_current (millivolt)"
legend_constants[15] = "g_Kp in component plateau_potassium_current (milliS_per_cm2)"
legend_algebraic[22] = "Kp in component plateau_potassium_current (dimensionless)"
legend_constants[16] = "E_b in component background_current (millivolt)"
legend_constants[17] = "g_b in component background_current (milliS_per_cm2)"
legend_rates[0] = "d/dt V in component membrane (millivolt)"
legend_rates[1] = "d/dt m in component fast_sodium_current_m_gate (dimensionless)"
legend_rates[2] = "d/dt h in component fast_sodium_current_h_gate (dimensionless)"
legend_rates[3] = "d/dt j in component fast_sodium_current_j_gate (dimensionless)"
legend_rates[5] = "d/dt d in component slow_inward_current_d_gate (dimensionless)"
legend_rates[6] = "d/dt f in component slow_inward_current_f_gate (dimensionless)"
legend_rates[7] = "d/dt X in component time_dependent_potassium_current_X_gate (dimensionless)"
legend_rates[4] = "d/dt Cai in component intracellular_calcium_concentration (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = -84.3801107371
constants[0] = 8314
constants[1] = 310
constants[2] = 96484.6
constants[3] = 1
constants[4] = 100
constants[5] = 9000
constants[6] = 1000
constants[7] = 2
constants[8] = -25.5
constants[9] = 23
constants[10] = 140
constants[11] = 18
states[1] = 0.00171338077730188
states[2] = 0.982660523699656
states[3] = 0.989108212766685
states[4] = 0.00017948816388306
states[5] = 0.00302126301779861
states[6] = 0.999967936476325
constants[12] = 0.01833
constants[13] = 5.4
constants[14] = 145
states[7] = 0.0417603108167287
constants[15] = 0.0183
constants[16] = -59.87
constants[17] = 0.03921
constants[18] = ((constants[0]*constants[1])/constants[2])*log(constants[10]/constants[11])
constants[19] = 0.282000*(power(constants[13]/5.40000, 1.0/2))
constants[20] = ((constants[0]*constants[1])/constants[2])*log((constants[13]+constants[12]*constants[10])/(constants[14]+constants[12]*constants[11]))
constants[21] = ((constants[0]*constants[1])/constants[2])*log(constants[13]/constants[14])
constants[22] = 0.604700*(power(constants[13]/5.40000, 1.0/2))
constants[23] = constants[21]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[1] = (0.320000*(states[0]+47.1300))/(1.00000-exp(-0.100000*(states[0]+47.1300)))
algebraic[8] = 0.0800000*exp(-states[0]/11.0000)
rates[1] = algebraic[1]*(1.00000-states[1])-algebraic[8]*states[1]
algebraic[2] = custom_piecewise([less(states[0] , -40.0000), 0.135000*exp((80.0000+states[0])/-6.80000) , True, 0.00000])
algebraic[9] = custom_piecewise([less(states[0] , -40.0000), 3.56000*exp(0.0790000*states[0])+310000.*exp(0.350000*states[0]) , True, 1.00000/(0.130000*(1.00000+exp((states[0]+10.6600)/-11.1000)))])
rates[2] = algebraic[2]*(1.00000-states[2])-algebraic[9]*states[2]
algebraic[3] = custom_piecewise([less(states[0] , -40.0000), ((-127140.*exp(0.244400*states[0])-3.47400e-05*exp(-0.0439100*states[0]))*(states[0]+37.7800))/(1.00000+exp(0.311000*(states[0]+79.2300))) , True, 0.00000])
algebraic[10] = custom_piecewise([less(states[0] , -40.0000), (0.121200*exp(-0.0105200*states[0]))/(1.00000+exp(-0.137800*(states[0]+40.1400))) , True, (0.300000*exp(-2.53500e-07*states[0]))/(1.00000+exp(-0.100000*(states[0]+32.0000)))])
rates[3] = algebraic[3]*(1.00000-states[3])-algebraic[10]*states[3]
algebraic[4] = (0.0950000*exp(-0.0100000*(states[0]-5.00000)))/(1.00000+exp(-0.0720000*(states[0]-5.00000)))
algebraic[11] = (0.0700000*exp(-0.0170000*(states[0]+44.0000)))/(1.00000+exp(0.0500000*(states[0]+44.0000)))
rates[5] = algebraic[4]*(1.00000-states[5])-algebraic[11]*states[5]
algebraic[5] = (0.0120000*exp(-0.00800000*(states[0]+28.0000)))/(1.00000+exp(0.150000*(states[0]+28.0000)))
algebraic[12] = (0.00650000*exp(-0.0200000*(states[0]+30.0000)))/(1.00000+exp(-0.200000*(states[0]+30.0000)))
rates[6] = algebraic[5]*(1.00000-states[6])-algebraic[12]*states[6]
algebraic[6] = (0.000500000*exp(0.0830000*(states[0]+50.0000)))/(1.00000+exp(0.0570000*(states[0]+50.0000)))
algebraic[13] = (0.00130000*exp(-0.0600000*(states[0]+20.0000)))/(1.00000+exp(-0.0400000*(states[0]+20.0000)))
rates[7] = algebraic[6]*(1.00000-states[7])-algebraic[13]*states[7]
algebraic[14] = 7.70000-13.0287*log(states[4]/1.00000)
algebraic[15] = 0.0900000*states[5]*states[6]*(states[0]-algebraic[14])
rates[4] = (-0.000100000/1.00000)*algebraic[15]+0.0700000*(0.000100000-states[4])
algebraic[0] = custom_piecewise([greater_equal(voi , constants[4]) & less_equal(voi , constants[5]) & less_equal((voi-constants[4])-floor((voi-constants[4])/constants[6])*constants[6] , constants[7]), constants[8] , True, 0.00000])
algebraic[7] = constants[9]*(power(states[1], 3.00000))*states[2]*states[3]*(states[0]-constants[18])
algebraic[16] = custom_piecewise([greater(states[0] , -100.000), (2.83700*(exp(0.0400000*(states[0]+77.0000))-1.00000))/((states[0]+77.0000)*exp(0.0400000*(states[0]+35.0000))) , True, 1.00000])
algebraic[17] = constants[19]*states[7]*algebraic[16]*(states[0]-constants[20])
algebraic[18] = 1.02000/(1.00000+exp(0.238500*((states[0]-constants[21])-59.2150)))
algebraic[19] = (0.491240*exp(0.0803200*((states[0]+5.47600)-constants[21]))+1.00000*exp(0.0617500*(states[0]-(constants[21]+594.310))))/(1.00000+exp(-0.514300*((states[0]-constants[21])+4.75300)))
algebraic[20] = algebraic[18]/(algebraic[18]+algebraic[19])
algebraic[21] = constants[22]*algebraic[20]*(states[0]-constants[21])
algebraic[22] = 1.00000/(1.00000+exp((7.48800-states[0])/5.98000))
algebraic[23] = constants[15]*algebraic[22]*(states[0]-constants[23])
algebraic[24] = constants[17]*(states[0]-constants[16])
rates[0] = (-1.00000/constants[3])*(algebraic[0]+algebraic[7]+algebraic[15]+algebraic[17]+algebraic[21]+algebraic[23]+algebraic[24])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[1] = (0.320000*(states[0]+47.1300))/(1.00000-exp(-0.100000*(states[0]+47.1300)))
algebraic[8] = 0.0800000*exp(-states[0]/11.0000)
algebraic[2] = custom_piecewise([less(states[0] , -40.0000), 0.135000*exp((80.0000+states[0])/-6.80000) , True, 0.00000])
algebraic[9] = custom_piecewise([less(states[0] , -40.0000), 3.56000*exp(0.0790000*states[0])+310000.*exp(0.350000*states[0]) , True, 1.00000/(0.130000*(1.00000+exp((states[0]+10.6600)/-11.1000)))])
algebraic[3] = custom_piecewise([less(states[0] , -40.0000), ((-127140.*exp(0.244400*states[0])-3.47400e-05*exp(-0.0439100*states[0]))*(states[0]+37.7800))/(1.00000+exp(0.311000*(states[0]+79.2300))) , True, 0.00000])
algebraic[10] = custom_piecewise([less(states[0] , -40.0000), (0.121200*exp(-0.0105200*states[0]))/(1.00000+exp(-0.137800*(states[0]+40.1400))) , True, (0.300000*exp(-2.53500e-07*states[0]))/(1.00000+exp(-0.100000*(states[0]+32.0000)))])
algebraic[4] = (0.0950000*exp(-0.0100000*(states[0]-5.00000)))/(1.00000+exp(-0.0720000*(states[0]-5.00000)))
algebraic[11] = (0.0700000*exp(-0.0170000*(states[0]+44.0000)))/(1.00000+exp(0.0500000*(states[0]+44.0000)))
algebraic[5] = (0.0120000*exp(-0.00800000*(states[0]+28.0000)))/(1.00000+exp(0.150000*(states[0]+28.0000)))
algebraic[12] = (0.00650000*exp(-0.0200000*(states[0]+30.0000)))/(1.00000+exp(-0.200000*(states[0]+30.0000)))
algebraic[6] = (0.000500000*exp(0.0830000*(states[0]+50.0000)))/(1.00000+exp(0.0570000*(states[0]+50.0000)))
algebraic[13] = (0.00130000*exp(-0.0600000*(states[0]+20.0000)))/(1.00000+exp(-0.0400000*(states[0]+20.0000)))
algebraic[14] = 7.70000-13.0287*log(states[4]/1.00000)
algebraic[15] = 0.0900000*states[5]*states[6]*(states[0]-algebraic[14])
algebraic[0] = custom_piecewise([greater_equal(voi , constants[4]) & less_equal(voi , constants[5]) & less_equal((voi-constants[4])-floor((voi-constants[4])/constants[6])*constants[6] , constants[7]), constants[8] , True, 0.00000])
algebraic[7] = constants[9]*(power(states[1], 3.00000))*states[2]*states[3]*(states[0]-constants[18])
algebraic[16] = custom_piecewise([greater(states[0] , -100.000), (2.83700*(exp(0.0400000*(states[0]+77.0000))-1.00000))/((states[0]+77.0000)*exp(0.0400000*(states[0]+35.0000))) , True, 1.00000])
algebraic[17] = constants[19]*states[7]*algebraic[16]*(states[0]-constants[20])
algebraic[18] = 1.02000/(1.00000+exp(0.238500*((states[0]-constants[21])-59.2150)))
algebraic[19] = (0.491240*exp(0.0803200*((states[0]+5.47600)-constants[21]))+1.00000*exp(0.0617500*(states[0]-(constants[21]+594.310))))/(1.00000+exp(-0.514300*((states[0]-constants[21])+4.75300)))
algebraic[20] = algebraic[18]/(algebraic[18]+algebraic[19])
algebraic[21] = constants[22]*algebraic[20]*(states[0]-constants[21])
algebraic[22] = 1.00000/(1.00000+exp((7.48800-states[0])/5.98000))
algebraic[23] = constants[15]*algebraic[22]*(states[0]-constants[23])
algebraic[24] = constants[17]*(states[0]-constants[16])
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)