Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 25
sizeStates = 8
sizeConstants = 49
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] = "V1 in component V1 (millivolt)"
legend_constants[0] = "C in component model_parameters (nanoF)"
legend_algebraic[3] = "i_NaP in component i_NaP (nanoA)"
legend_algebraic[5] = "i_K in component i_K (nanoA)"
legend_algebraic[9] = "i_L1 in component i_L1 (nanoA)"
legend_algebraic[13] = "i_synE1 in component i_synE1 (nanoA)"
legend_algebraic[22] = "i_synI1 in component i_synI1 (nanoA)"
legend_states[1] = "V2 in component V2 (millivolt)"
legend_algebraic[6] = "i_AD2 in component i_AD2 (nanoA)"
legend_algebraic[10] = "i_L2 in component i_L2 (nanoA)"
legend_algebraic[17] = "i_synE2 in component i_synE2 (nanoA)"
legend_algebraic[23] = "i_synI2 in component i_synI2 (nanoA)"
legend_states[2] = "V3 in component V3 (millivolt)"
legend_algebraic[7] = "i_AD3 in component i_AD3 (nanoA)"
legend_algebraic[11] = "i_L3 in component i_L3 (nanoA)"
legend_algebraic[14] = "i_synE3 in component i_synE3 (nanoA)"
legend_algebraic[24] = "i_synI3 in component i_synI3 (nanoA)"
legend_states[3] = "V4 in component V4 (millivolt)"
legend_algebraic[8] = "i_AD4 in component i_AD4 (nanoA)"
legend_algebraic[12] = "i_L4 in component i_L4 (nanoA)"
legend_algebraic[15] = "i_synE4 in component i_synE4 (nanoA)"
legend_algebraic[20] = "i_synI4 in component i_synI4 (nanoA)"
legend_constants[1] = "g_NaP in component model_parameters (nanoS)"
legend_constants[2] = "E_Na in component model_parameters (millivolt)"
legend_algebraic[1] = "m in component i_NaP_m_gate (dimensionless)"
legend_states[4] = "h in component i_NaP_h_gate (dimensionless)"
legend_algebraic[0] = "h_infinity in component i_NaP_h_gate (dimensionless)"
legend_algebraic[2] = "tau_h in component i_NaP_h_gate (millisecond)"
legend_constants[3] = "tau_h_max in component i_NaP_h_gate (millisecond)"
legend_constants[4] = "g_K in component model_parameters (nanoS)"
legend_constants[5] = "E_K in component model_parameters (millivolt)"
legend_algebraic[4] = "m in component i_K_m_gate (dimensionless)"
legend_constants[6] = "g_AD in component model_parameters (nanoS)"
legend_algebraic[18] = "f2_V2 in component model_parameters (dimensionless)"
legend_states[5] = "m in component i_AD2_m_gate (dimensionless)"
legend_constants[7] = "k_AD2 in component i_AD2_m_gate (dimensionless)"
legend_constants[8] = "tau_AD2 in component i_AD2_m_gate (millisecond)"
legend_algebraic[19] = "f3_V3 in component model_parameters (dimensionless)"
legend_states[6] = "m in component i_AD3_m_gate (dimensionless)"
legend_constants[9] = "k_AD3 in component i_AD3_m_gate (dimensionless)"
legend_constants[10] = "tau_AD3 in component i_AD3_m_gate (millisecond)"
legend_algebraic[21] = "f4_V4 in component model_parameters (dimensionless)"
legend_states[7] = "m in component i_AD4_m_gate (dimensionless)"
legend_constants[11] = "k_AD4 in component i_AD4_m_gate (dimensionless)"
legend_constants[12] = "tau_AD4 in component i_AD4_m_gate (millisecond)"
legend_constants[13] = "g_L in component model_parameters (nanoS)"
legend_constants[14] = "E_L in component model_parameters (millivolt)"
legend_constants[15] = "c11 in component i_synE1 (dimensionless)"
legend_constants[16] = "c21 in component i_synE1 (dimensionless)"
legend_constants[17] = "c31 in component i_synE1 (dimensionless)"
legend_constants[18] = "d1 in component model_parameters (dimensionless)"
legend_constants[19] = "d2 in component model_parameters (dimensionless)"
legend_constants[20] = "d3 in component model_parameters (dimensionless)"
legend_constants[21] = "g_synE in component model_parameters (nanoS)"
legend_constants[22] = "E_synE in component model_parameters (millivolt)"
legend_constants[23] = "c12 in component i_synE2 (dimensionless)"
legend_constants[24] = "c22 in component i_synE2 (dimensionless)"
legend_constants[25] = "c32 in component i_synE2 (dimensionless)"
legend_constants[26] = "a12 in component i_synE2 (dimensionless)"
legend_algebraic[16] = "f1_V1 in component model_parameters (dimensionless)"
legend_constants[27] = "c13 in component i_synE3 (dimensionless)"
legend_constants[28] = "c23 in component i_synE3 (dimensionless)"
legend_constants[29] = "c33 in component i_synE3 (dimensionless)"
legend_constants[30] = "c14 in component i_synE4 (dimensionless)"
legend_constants[31] = "c24 in component i_synE4 (dimensionless)"
legend_constants[32] = "c34 in component i_synE4 (dimensionless)"
legend_constants[33] = "b21 in component i_synI1 (dimensionless)"
legend_constants[34] = "b31 in component i_synI1 (dimensionless)"
legend_constants[35] = "b41 in component i_synI1 (dimensionless)"
legend_constants[36] = "g_synI in component model_parameters (nanoS)"
legend_constants[37] = "E_synI in component model_parameters (millivolt)"
legend_constants[38] = "b32 in component i_synI2 (dimensionless)"
legend_constants[39] = "b42 in component i_synI2 (dimensionless)"
legend_constants[40] = "b23 in component i_synI3 (dimensionless)"
legend_constants[41] = "b43 in component i_synI3 (dimensionless)"
legend_constants[42] = "b24 in component i_synI4 (dimensionless)"
legend_constants[43] = "b34 in component i_synI4 (dimensionless)"
legend_constants[44] = "V_half in component model_parameters (millivolt)"
legend_constants[45] = "k_V1 in component model_parameters (millivolt)"
legend_constants[46] = "k_V2 in component model_parameters (millivolt)"
legend_constants[47] = "k_V3 in component model_parameters (millivolt)"
legend_constants[48] = "k_V4 in component model_parameters (millivolt)"
legend_rates[0] = "d/dt V1 in component V1 (millivolt)"
legend_rates[1] = "d/dt V2 in component V2 (millivolt)"
legend_rates[2] = "d/dt V3 in component V3 (millivolt)"
legend_rates[3] = "d/dt V4 in component V4 (millivolt)"
legend_rates[4] = "d/dt h in component i_NaP_h_gate (dimensionless)"
legend_rates[5] = "d/dt m in component i_AD2_m_gate (dimensionless)"
legend_rates[6] = "d/dt m in component i_AD3_m_gate (dimensionless)"
legend_rates[7] = "d/dt m in component i_AD4_m_gate (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = -50.0
constants[0] = 0.020
states[1] = -50.0
states[2] = -50.0
states[3] = -50.0
constants[1] = 5.0
constants[2] = 50.0
states[4] = 0.92
constants[3] = 6000
constants[4] = 5.0
constants[5] = -85.0
constants[6] = 10.0
states[5] = 0.92
constants[7] = 0.9
constants[8] = 2000
states[6] = 0.92
constants[9] = 1.3
constants[10] = 2000
states[7] = 0.92
constants[11] = 0.9
constants[12] = 1000
constants[13] = 2.8
constants[14] = -60.0
constants[15] = 0.115
constants[16] = 0.07
constants[17] = 0.025
constants[18] = 1.0
constants[19] = 1.0
constants[20] = 1.0
constants[21] = 10.0
constants[22] = 0.0
constants[23] = 0.3
constants[24] = 0.3
constants[25] = 0.0
constants[26] = 0.4
constants[27] = 0.63
constants[28] = 0.00
constants[29] = 0.00
constants[30] = 0.33
constants[31] = 0.40
constants[32] = 0.00
constants[33] = 0.00
constants[34] = 0.30
constants[35] = 0.20
constants[36] = 60.0
constants[37] = -75.0
constants[38] = 0.05
constants[39] = 0.35
constants[40] = 0.25
constants[41] = 0.10
constants[42] = 0.35
constants[43] = 0.35
constants[44] = 30.0
constants[45] = 8.0
constants[46] = 4.0
constants[47] = 4.0
constants[48] = 4.0
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = 1.00000/(1.00000+exp((states[0]+48.0000)/6.00000))
algebraic[2] = constants[3]/cosh((states[0]+48.0000)/12.0000)
rates[4] = (algebraic[0]-states[4])/algebraic[2]
algebraic[18] = 1.00000/(1.00000+exp(-(states[1]-constants[44])/constants[46]))
rates[5] = (constants[7]*algebraic[18]-states[5])/constants[8]
algebraic[19] = 1.00000/(1.00000+exp(-(states[2]-constants[44])/constants[47]))
rates[6] = (constants[9]*algebraic[19]-states[6])/constants[10]
algebraic[8] = constants[6]*states[7]*(1.00000/1000.00)*(states[3]-constants[5])
algebraic[12] = constants[13]*(1.00000/1000.00)*(states[3]-constants[14])
algebraic[15] = constants[21]*(1.00000/1000.00)*(states[3]-constants[22])*(constants[30]*constants[18]+constants[31]*constants[19]+constants[32]*constants[20])
algebraic[20] = constants[36]*(1.00000/1000.00)*(states[3]-constants[37])*(constants[42]*algebraic[18]+constants[43]*algebraic[19])
rates[3] = -(algebraic[8]+algebraic[12]+algebraic[15]+algebraic[20])/constants[0]
algebraic[21] = 1.00000/(1.00000+exp(-(states[3]-constants[44])/constants[48]))
rates[7] = (constants[11]*algebraic[21]-states[7])/constants[12]
algebraic[1] = 1.00000/(1.00000+exp(-(states[0]+40.0000)/6.00000))
algebraic[3] = constants[1]*algebraic[1]*states[4]*(1.00000/1000.00)*(states[0]-constants[2])
algebraic[4] = 1.00000/(1.00000+exp(-(states[0]+29.0000)/4.00000))
algebraic[5] = constants[4]*(power(algebraic[4], 4.00000))*(1.00000/1000.00)*(states[0]-constants[5])
algebraic[9] = constants[13]*(1.00000/1000.00)*(states[0]-constants[14])
algebraic[13] = constants[21]*(1.00000/1000.00)*(states[0]-constants[22])*(constants[15]*constants[18]+constants[16]*constants[19]+constants[17]*constants[20])
algebraic[22] = constants[36]*(1.00000/1000.00)*(states[0]-constants[37])*(constants[33]*algebraic[18]+constants[34]*algebraic[19]+constants[35]*algebraic[21])
rates[0] = -(algebraic[3]+algebraic[5]+algebraic[9]+algebraic[13]+algebraic[22])/constants[0]
algebraic[6] = constants[6]*states[5]*(1.00000/1000.00)*(states[1]-constants[5])
algebraic[10] = constants[13]*(1.00000/1000.00)*(states[1]-constants[14])
algebraic[16] = 1.00000/(1.00000+exp(-(states[0]-constants[44])/constants[45]))
algebraic[17] = constants[21]*(1.00000/1000.00)*(states[1]-constants[22])*(constants[26]*algebraic[16]+constants[23]*constants[18]+constants[24]*constants[19]+constants[25]*constants[20])
algebraic[23] = constants[36]*(1.00000/1000.00)*(states[1]-constants[37])*(constants[38]*algebraic[19]+constants[39]*algebraic[21])
rates[1] = -(algebraic[6]+algebraic[10]+algebraic[17]+algebraic[23])/constants[0]
algebraic[7] = constants[6]*states[6]*(1.00000/1000.00)*(states[2]-constants[5])
algebraic[11] = constants[13]*(1.00000/1000.00)*(states[2]-constants[14])
algebraic[14] = constants[21]*(1.00000/1000.00)*(states[2]-constants[22])*(constants[27]*constants[18]+constants[28]*constants[19]+constants[29]*constants[20])
algebraic[24] = constants[36]*(1.00000/1000.00)*(states[2]-constants[37])*(constants[40]*algebraic[18]+constants[41]*algebraic[21])
rates[2] = -(algebraic[7]+algebraic[11]+algebraic[14]+algebraic[24])/constants[0]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = 1.00000/(1.00000+exp((states[0]+48.0000)/6.00000))
algebraic[2] = constants[3]/cosh((states[0]+48.0000)/12.0000)
algebraic[18] = 1.00000/(1.00000+exp(-(states[1]-constants[44])/constants[46]))
algebraic[19] = 1.00000/(1.00000+exp(-(states[2]-constants[44])/constants[47]))
algebraic[8] = constants[6]*states[7]*(1.00000/1000.00)*(states[3]-constants[5])
algebraic[12] = constants[13]*(1.00000/1000.00)*(states[3]-constants[14])
algebraic[15] = constants[21]*(1.00000/1000.00)*(states[3]-constants[22])*(constants[30]*constants[18]+constants[31]*constants[19]+constants[32]*constants[20])
algebraic[20] = constants[36]*(1.00000/1000.00)*(states[3]-constants[37])*(constants[42]*algebraic[18]+constants[43]*algebraic[19])
algebraic[21] = 1.00000/(1.00000+exp(-(states[3]-constants[44])/constants[48]))
algebraic[1] = 1.00000/(1.00000+exp(-(states[0]+40.0000)/6.00000))
algebraic[3] = constants[1]*algebraic[1]*states[4]*(1.00000/1000.00)*(states[0]-constants[2])
algebraic[4] = 1.00000/(1.00000+exp(-(states[0]+29.0000)/4.00000))
algebraic[5] = constants[4]*(power(algebraic[4], 4.00000))*(1.00000/1000.00)*(states[0]-constants[5])
algebraic[9] = constants[13]*(1.00000/1000.00)*(states[0]-constants[14])
algebraic[13] = constants[21]*(1.00000/1000.00)*(states[0]-constants[22])*(constants[15]*constants[18]+constants[16]*constants[19]+constants[17]*constants[20])
algebraic[22] = constants[36]*(1.00000/1000.00)*(states[0]-constants[37])*(constants[33]*algebraic[18]+constants[34]*algebraic[19]+constants[35]*algebraic[21])
algebraic[6] = constants[6]*states[5]*(1.00000/1000.00)*(states[1]-constants[5])
algebraic[10] = constants[13]*(1.00000/1000.00)*(states[1]-constants[14])
algebraic[16] = 1.00000/(1.00000+exp(-(states[0]-constants[44])/constants[45]))
algebraic[17] = constants[21]*(1.00000/1000.00)*(states[1]-constants[22])*(constants[26]*algebraic[16]+constants[23]*constants[18]+constants[24]*constants[19]+constants[25]*constants[20])
algebraic[23] = constants[36]*(1.00000/1000.00)*(states[1]-constants[37])*(constants[38]*algebraic[19]+constants[39]*algebraic[21])
algebraic[7] = constants[6]*states[6]*(1.00000/1000.00)*(states[2]-constants[5])
algebraic[11] = constants[13]*(1.00000/1000.00)*(states[2]-constants[14])
algebraic[14] = constants[21]*(1.00000/1000.00)*(states[2]-constants[22])*(constants[27]*constants[18]+constants[28]*constants[19]+constants[29]*constants[20])
algebraic[24] = constants[36]*(1.00000/1000.00)*(states[2]-constants[37])*(constants[40]*algebraic[18]+constants[41]*algebraic[21])
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)