Generated Code
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# Size of variable arrays:
sizeAlgebraic = 17
sizeStates = 5
sizeConstants = 20
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_constants[0] = "C_m in component model_parameters (uF_per_cm2)"
legend_states[0] = "V_s in component soma_compartment (mV)"
legend_constants[1] = "V_Na in component soma_compartment (mV)"
legend_constants[2] = "V_K in component soma_compartment (mV)"
legend_states[1] = "V_D in component dendritic_compartment (mV)"
legend_algebraic[13] = "I_Na in component soma_compartment (uA_per_cm2)"
legend_algebraic[15] = "I_soma in component soma_compartment (uA_per_cm2)"
legend_algebraic[0] = "I_h in component soma_compartment (uA_per_cm2)"
legend_algebraic[6] = "I_K_DR in component soma_compartment (uA_per_cm2)"
legend_constants[3] = "g_K_DR in component soma_compartment (mS_per_cm2)"
legend_constants[4] = "g_Na in component soma_compartment (mS_per_cm2)"
legend_constants[5] = "g_c in component model_parameters (mS_per_cm2)"
legend_constants[6] = "g_h in component soma_compartment (mS_per_cm2)"
legend_constants[7] = "p in component model_parameters (dimensionless)"
legend_states[2] = "n in component gating_variables (dimensionless)"
legend_states[3] = "h in component gating_variables (dimensionless)"
legend_algebraic[10] = "m_infinity in component gating_variables (dimensionless)"
legend_constants[8] = "V_L in component dendritic_compartment (mV)"
legend_algebraic[16] = "I_D in component dendritic_compartment (uA_per_cm2)"
legend_algebraic[11] = "I_L in component dendritic_compartment (uA_per_cm2)"
legend_algebraic[7] = "I_pump in component dendritic_compartment (uA_per_cm2)"
legend_constants[19] = "I_pump_ss in component dendritic_compartment (uA_per_cm2)"
legend_algebraic[14] = "I_NMDA in component dendritic_compartment (uA_per_cm2)"
legend_algebraic[12] = "I_Na_NMDA in component dendritic_compartment (uA_per_cm2)"
legend_constants[14] = "R_pump in component dendritic_compartment (uA_per_cm2)"
legend_algebraic[1] = "f_NMDA in component dendritic_compartment (dimensionless)"
legend_constants[9] = "alpha in component dendritic_compartment (mMcm2_per_uAs)"
legend_constants[15] = "g_NMDA in component dendritic_compartment (mS_per_cm2)"
legend_constants[16] = "g_Na_NMDA in component dendritic_compartment (mS_per_cm2)"
legend_constants[17] = "g_L in component dendritic_compartment (mS_per_cm2)"
legend_states[4] = "Na in component dendritic_compartment (mM)"
legend_constants[10] = "Na_eq in component dendritic_compartment (mM)"
legend_constants[11] = "K_p in component dendritic_compartment (mM)"
legend_constants[12] = "K_Na in component dendritic_compartment (mM)"
legend_constants[13] = "q in component dendritic_compartment (mV)"
legend_algebraic[2] = "n_infinity in component gating_variables (dimensionless)"
legend_algebraic[3] = "h_infinity in component gating_variables (dimensionless)"
legend_algebraic[4] = "r_infinity in component gating_variables (dimensionless)"
legend_algebraic[8] = "tau_h in component gating_variables (second)"
legend_algebraic[9] = "tau_n in component gating_variables (second)"
legend_algebraic[5] = "tau_mL in component gating_variables (second)"
legend_constants[18] = "tau_r in component gating_variables (second)"
legend_rates[0] = "d/dt V_s in component soma_compartment (mV)"
legend_rates[1] = "d/dt V_D in component dendritic_compartment (mV)"
legend_rates[4] = "d/dt Na in component dendritic_compartment (mM)"
legend_rates[3] = "d/dt h in component gating_variables (dimensionless)"
legend_rates[2] = "d/dt n in component gating_variables (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1
states[0] = -64
constants[1] = 55
constants[2] = -85
states[1] = -77
constants[3] = 3.2
constants[4] = 3.2
constants[5] = 0.1
constants[6] = 0.1
constants[7] = 0.5
states[2] = 0.002
states[3] = 1
constants[8] = -50
constants[9] = 0.173
states[4] = 5.09
constants[10] = 8
constants[11] = 15
constants[12] = 15
constants[13] = 12.5
constants[14] = 18.0000*(constants[7]/(1.00000-constants[7]))
constants[15] = 1.25000*(constants[7]/(1.00000-constants[7]))
constants[16] = 1.00000*(constants[7]/(1.00000-constants[7]))
constants[17] = 0.180000*(constants[7]/(1.00000-constants[7]))
constants[18] = 190.000
constants[19] = (((constants[14]*constants[7])/(1.00000-constants[7]))*(power(constants[10], 3.00000)))/(power(constants[12], 3.00000)+power(constants[10], 3.00000))
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]+30.0000)/8.30000))
algebraic[8] = 0.430000+0.860000/(1.00000+exp((states[0]+25.0000)/5.00000))
rates[3] = (algebraic[3]-states[3])/algebraic[8]
algebraic[2] = 1.00000/(1.00000+exp(-(states[0]+31.0000)/5.30000))
algebraic[9] = (0.800000+1.60000/(1.00000+exp(0.100000*(states[0]+25.0000))))/(1.00000+exp(-0.100000*(states[0]+70.0000)))
rates[2] = (algebraic[2]-states[2])/algebraic[9]
algebraic[7] = (((constants[14]*constants[7])/(1.00000-constants[7]))*(power(states[1]*1.00000+states[4], 3.00000)))/(power(constants[11], 3.00000)+power(states[1]*1.00000+states[4], 3.00000))
algebraic[1] = 1.00000/(1.00000+0.141000*exp(-states[1]/constants[13]))
algebraic[12] = constants[16]*algebraic[1]*(states[1]-constants[1])
rates[4] = constants[9]*(-algebraic[12]-3.00000*(algebraic[7]-constants[19]))
algebraic[10] = 1.00000/(1.00000+exp(-(states[0]+35.0000)/6.20000))
algebraic[13] = constants[4]*states[3]*(states[0]-constants[1])*(power(algebraic[10], 3.00000))
algebraic[0] = constants[6]*states[3]*(states[0]+30.0000)
algebraic[6] = constants[3]*(states[0]-constants[2])*(power(states[2], 2.00000))
algebraic[15] = algebraic[13]+algebraic[6]+algebraic[0]
rates[0] = (-algebraic[15]-(constants[5]/constants[7])*(states[1]-states[0]))/constants[0]
algebraic[11] = constants[17]*(states[1]-constants[8])
algebraic[14] = constants[15]*algebraic[1]*states[1]
algebraic[16] = ((algebraic[14]+algebraic[7])-constants[19])+algebraic[11]
rates[1] = (-algebraic[16]+(constants[5]/(1.00000-constants[7]))*(states[0]-states[1]))/constants[0]
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]+30.0000)/8.30000))
algebraic[8] = 0.430000+0.860000/(1.00000+exp((states[0]+25.0000)/5.00000))
algebraic[2] = 1.00000/(1.00000+exp(-(states[0]+31.0000)/5.30000))
algebraic[9] = (0.800000+1.60000/(1.00000+exp(0.100000*(states[0]+25.0000))))/(1.00000+exp(-0.100000*(states[0]+70.0000)))
algebraic[7] = (((constants[14]*constants[7])/(1.00000-constants[7]))*(power(states[1]*1.00000+states[4], 3.00000)))/(power(constants[11], 3.00000)+power(states[1]*1.00000+states[4], 3.00000))
algebraic[1] = 1.00000/(1.00000+0.141000*exp(-states[1]/constants[13]))
algebraic[12] = constants[16]*algebraic[1]*(states[1]-constants[1])
algebraic[10] = 1.00000/(1.00000+exp(-(states[0]+35.0000)/6.20000))
algebraic[13] = constants[4]*states[3]*(states[0]-constants[1])*(power(algebraic[10], 3.00000))
algebraic[0] = constants[6]*states[3]*(states[0]+30.0000)
algebraic[6] = constants[3]*(states[0]-constants[2])*(power(states[2], 2.00000))
algebraic[15] = algebraic[13]+algebraic[6]+algebraic[0]
algebraic[11] = constants[17]*(states[1]-constants[8])
algebraic[14] = constants[15]*algebraic[1]*states[1]
algebraic[16] = ((algebraic[14]+algebraic[7])-constants[19])+algebraic[11]
algebraic[4] = 1.00000/(1.00000+exp((states[0]+80.0000)/8.00000))
algebraic[5] = 0.400000/(5.00000*exp(-(states[1]+11.0000)/8.30000)+(-(states[1]+11.0000)/8.30000)/(exp(-(states[1]+11.0000)/8.30000)-1.00000))
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)