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 = 16
sizeStates = 4
sizeConstants = 32
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 (ms)"
legend_constants[0] = "epi in component environment (dimensionless)"
legend_constants[1] = "endo in component environment (dimensionless)"
legend_constants[2] = "mcell in component environment (dimensionless)"
legend_states[0] = "u in component membrane (dimensionless)"
legend_algebraic[0] = "Vm in component membrane (mV)"
legend_constants[3] = "V_0 in component membrane (mV)"
legend_constants[4] = "V_fi in component membrane (mV)"
legend_algebraic[8] = "J_fi in component fast_inward_current (per_ms)"
legend_algebraic[14] = "J_so in component slow_outward_current (per_ms)"
legend_algebraic[15] = "J_si in component slow_inward_current (per_ms)"
legend_algebraic[1] = "J_stim in component membrane (per_ms)"
legend_algebraic[2] = "m in component m (dimensionless)"
legend_constants[5] = "u_m in component m (dimensionless)"
legend_algebraic[4] = "p in component p (dimensionless)"
legend_constants[6] = "u_p in component p (dimensionless)"
legend_algebraic[3] = "q in component q (dimensionless)"
legend_constants[13] = "u_q in component q (dimensionless)"
legend_algebraic[5] = "r in component r (dimensionless)"
legend_constants[15] = "u_r in component r (dimensionless)"
legend_constants[16] = "tau_fi in component fast_inward_current (ms)"
legend_constants[17] = "u_u in component fast_inward_current (dimensionless)"
legend_states[1] = "v in component fast_inward_current_v_gate (dimensionless)"
legend_algebraic[6] = "v_inf in component fast_inward_current_v_gate (dimensionless)"
legend_algebraic[9] = "tau_v_minus in component fast_inward_current_v_gate (ms)"
legend_constants[30] = "tau_v1_minus in component fast_inward_current_v_gate (ms)"
legend_constants[12] = "tau_v2_minus in component fast_inward_current_v_gate (ms)"
legend_constants[7] = "tau_v_plus in component fast_inward_current_v_gate (ms)"
legend_algebraic[11] = "tau_o in component slow_outward_current (ms)"
legend_constants[14] = "tau_o1 in component slow_outward_current (ms)"
legend_constants[31] = "tau_o2 in component slow_outward_current (ms)"
legend_algebraic[13] = "tau_so in component slow_outward_current (ms)"
legend_constants[18] = "tau_so1 in component slow_outward_current (ms)"
legend_constants[19] = "tau_so2 in component slow_outward_current (ms)"
legend_constants[20] = "k_so in component slow_outward_current (dimensionless)"
legend_constants[21] = "u_so in component slow_outward_current (dimensionless)"
legend_constants[22] = "tau_si in component slow_inward_current (ms)"
legend_states[2] = "w in component slow_inward_current_w_gate (dimensionless)"
legend_states[3] = "s in component slow_inward_current_s_gate (dimensionless)"
legend_algebraic[10] = "w_inf in component slow_inward_current_w_gate (dimensionless)"
legend_constants[23] = "tau_winf in component slow_inward_current_w_gate (ms)"
legend_constants[24] = "wstar_inf in component slow_inward_current_w_gate (dimensionless)"
legend_algebraic[12] = "tau_w_minus in component slow_inward_current_w_gate (ms)"
legend_constants[25] = "tau_w1_minus in component slow_inward_current_w_gate (ms)"
legend_constants[26] = "tau_w2_minus in component slow_inward_current_w_gate (ms)"
legend_constants[27] = "k_w_minus in component slow_inward_current_w_gate (dimensionless)"
legend_constants[28] = "u_w_minus in component slow_inward_current_w_gate (dimensionless)"
legend_constants[29] = "tau_w_plus in component slow_inward_current_w_gate (ms)"
legend_algebraic[7] = "tau_s in component slow_inward_current_s_gate (ms)"
legend_constants[8] = "tau_s1 in component slow_inward_current_s_gate (ms)"
legend_constants[11] = "tau_s2 in component slow_inward_current_s_gate (ms)"
legend_constants[9] = "k_s in component slow_inward_current_s_gate (dimensionless)"
legend_constants[10] = "u_s in component slow_inward_current_s_gate (dimensionless)"
legend_rates[0] = "d/dt u in component membrane (dimensionless)"
legend_rates[1] = "d/dt v in component fast_inward_current_v_gate (dimensionless)"
legend_rates[2] = "d/dt w in component slow_inward_current_w_gate (dimensionless)"
legend_rates[3] = "d/dt s in component slow_inward_current_s_gate (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1
constants[1] = 0
constants[2] = 0
states[0] = 0
constants[3] = -83
constants[4] = 2.7
constants[5] = 0.3
constants[6] = 0.13
states[1] = 1
constants[7] = 1.45
states[2] = 1
states[3] = 0
constants[8] = 2.7342
constants[9] = 2.0994
constants[10] = 0.9087
constants[11] = custom_piecewise([equal(constants[0] , 1.00000), 16.0000 , equal(constants[1] , 1.00000), 2.00000 , True, 4.00000])
constants[12] = custom_piecewise([equal(constants[0] , 1.00000), 1150.00 , equal(constants[1] , 1.00000), 10.0000 , True, 1.45000])
constants[13] = custom_piecewise([equal(constants[0] , 1.00000), 0.00600000 , equal(constants[1] , 1.00000), 0.0240000 , True, 0.100000])
constants[14] = custom_piecewise([equal(constants[0] , 1.00000), 400.000 , equal(constants[1] , 1.00000), 470.000 , True, 410.000])
constants[15] = custom_piecewise([equal(constants[0] , 1.00000), 0.00600000 , equal(constants[1] , 1.00000), 0.00600000 , True, 0.00500000])
constants[16] = custom_piecewise([equal(constants[0] , 1.00000), 0.110000 , equal(constants[1] , 1.00000), 0.104000 , True, 0.0780000])
constants[17] = custom_piecewise([equal(constants[0] , 1.00000), 1.55000 , equal(constants[1] , 1.00000), 1.56000 , True, 1.61000])
constants[18] = custom_piecewise([equal(constants[0] , 1.00000), 30.0200 , equal(constants[1] , 1.00000), 40.0000 , True, 91.0000])
constants[19] = custom_piecewise([equal(constants[0] , 1.00000), 0.996000 , equal(constants[1] , 1.00000), 1.20000 , True, 0.800000])
constants[20] = custom_piecewise([equal(constants[0] , 1.00000), 2.04600 , equal(constants[1] , 1.00000), 2.00000 , True, 2.10000])
constants[21] = custom_piecewise([equal(constants[0] , 1.00000), 0.650000 , equal(constants[1] , 1.00000), 0.650000 , True, 0.600000])
constants[22] = custom_piecewise([equal(constants[0] , 1.00000), 1.88750 , equal(constants[1] , 1.00000), 2.90130 , True, 3.38490])
constants[23] = custom_piecewise([equal(constants[0] , 1.00000), 0.0700000 , equal(constants[1] , 1.00000), 0.0273000 , True, 0.0100000])
constants[24] = custom_piecewise([equal(constants[0] , 1.00000), 0.940000 , equal(constants[1] , 1.00000), 0.780000 , True, 0.500000])
constants[25] = custom_piecewise([equal(constants[0] , 1.00000), 60.0000 , equal(constants[1] , 1.00000), 6.00000 , True, 70.0000])
constants[26] = custom_piecewise([equal(constants[0] , 1.00000), 15.0000 , equal(constants[1] , 1.00000), 140.000 , True, 8.00000])
constants[27] = custom_piecewise([equal(constants[0] , 1.00000), 65.0000 , equal(constants[1] , 1.00000), 200.000 , True, 200.000])
constants[28] = custom_piecewise([equal(constants[0] , 1.00000), 0.0300000 , equal(constants[1] , 1.00000), 0.0160000 , True, 0.0160000])
constants[29] = custom_piecewise([equal(constants[0] , 1.00000), 200.000 , equal(constants[1] , 1.00000), 280.000 , True, 280.000])
constants[30] = custom_piecewise([equal(constants[0] , 1.00000), 60.0000 , equal(constants[1] , 1.00000), 75.0000 , True, 80.0000])
constants[31] = custom_piecewise([equal(constants[0] , 1.00000), 6.00000 , equal(constants[1] , 1.00000), 6.00000 , True, 7.00000])
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[4] = custom_piecewise([less(states[0] , constants[6]), 0.00000 , True, 1.00000])
algebraic[7] = (1.00000-algebraic[4])*constants[8]+algebraic[4]*constants[11]
rates[3] = ((1.00000+tanh(constants[9]*(states[0]-constants[10])))/2.00000-states[3])/algebraic[7]
algebraic[2] = custom_piecewise([less(states[0] , constants[5]), 0.00000 , True, 1.00000])
algebraic[6] = custom_piecewise([less(states[0] , constants[13]), 1.00000 , True, 0.00000])
algebraic[3] = custom_piecewise([less(states[0] , constants[13]), 0.00000 , True, 1.00000])
algebraic[9] = algebraic[3]*constants[12]+(1.00000-algebraic[3])*constants[30]
rates[1] = ((1.00000-algebraic[2])*(algebraic[6]-states[1]))/algebraic[9]-(algebraic[2]*states[1])/constants[7]
algebraic[5] = custom_piecewise([less(states[0] , constants[15]), 0.00000 , True, 1.00000])
algebraic[10] = (1.00000-algebraic[5])*(1.00000-(states[0]*1.00000)/constants[23])+algebraic[5]*constants[24]
algebraic[12] = constants[25]+((constants[26]-constants[25])*(1.00000+tanh(constants[27]*(states[0]-constants[28]))))/2.00000
rates[2] = ((1.00000-algebraic[5])*(algebraic[10]-states[2]))/algebraic[12]-(algebraic[5]*states[2])/constants[29]
algebraic[8] = (-algebraic[2]*states[1]*(states[0]-constants[5])*(constants[17]-states[0]))/constants[16]
algebraic[11] = (1.00000-algebraic[5])*constants[14]+algebraic[5]*constants[31]
algebraic[13] = constants[18]+((constants[19]-constants[18])*(1.00000+tanh(constants[20]*(states[0]-constants[21]))))/2.00000
algebraic[14] = (states[0]*(1.00000-algebraic[4]))/algebraic[11]+algebraic[4]/algebraic[13]
algebraic[15] = (-algebraic[4]*states[2]*states[3])/constants[22]
algebraic[1] = custom_piecewise([greater_equal(voi , 100.000) & less_equal(voi , 101.000), -1.00000 , True, 0.00000])
rates[0] = -(algebraic[8]+algebraic[14]+algebraic[15]+algebraic[1])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[4] = custom_piecewise([less(states[0] , constants[6]), 0.00000 , True, 1.00000])
algebraic[7] = (1.00000-algebraic[4])*constants[8]+algebraic[4]*constants[11]
algebraic[2] = custom_piecewise([less(states[0] , constants[5]), 0.00000 , True, 1.00000])
algebraic[6] = custom_piecewise([less(states[0] , constants[13]), 1.00000 , True, 0.00000])
algebraic[3] = custom_piecewise([less(states[0] , constants[13]), 0.00000 , True, 1.00000])
algebraic[9] = algebraic[3]*constants[12]+(1.00000-algebraic[3])*constants[30]
algebraic[5] = custom_piecewise([less(states[0] , constants[15]), 0.00000 , True, 1.00000])
algebraic[10] = (1.00000-algebraic[5])*(1.00000-(states[0]*1.00000)/constants[23])+algebraic[5]*constants[24]
algebraic[12] = constants[25]+((constants[26]-constants[25])*(1.00000+tanh(constants[27]*(states[0]-constants[28]))))/2.00000
algebraic[8] = (-algebraic[2]*states[1]*(states[0]-constants[5])*(constants[17]-states[0]))/constants[16]
algebraic[11] = (1.00000-algebraic[5])*constants[14]+algebraic[5]*constants[31]
algebraic[13] = constants[18]+((constants[19]-constants[18])*(1.00000+tanh(constants[20]*(states[0]-constants[21]))))/2.00000
algebraic[14] = (states[0]*(1.00000-algebraic[4]))/algebraic[11]+algebraic[4]/algebraic[13]
algebraic[15] = (-algebraic[4]*states[2]*states[3])/constants[22]
algebraic[1] = custom_piecewise([greater_equal(voi , 100.000) & less_equal(voi , 101.000), -1.00000 , True, 0.00000])
algebraic[0] = constants[3]+states[0]*(constants[4]-constants[3])
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)