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 = 31
sizeStates = 14
sizeConstants = 31
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] = "vol_myo in component environment (pL)"
legend_states[0] = "q_DAG in component environment (fmol)"
legend_states[1] = "q_PC in component environment (fmol)"
legend_states[2] = "q_IP3 in component environment (fmol)"
legend_states[3] = "q_Ino in component environment (fmol)"
legend_states[4] = "q_PLC in component environment (fmol)"
legend_states[5] = "q_Gq in component environment (fmol)"
legend_states[6] = "q_Ca in component environment (fmol)"
legend_states[7] = "q_Gq_PLC in component environment (fmol)"
legend_states[8] = "q_Ca_PLC in component environment (fmol)"
legend_states[9] = "q_Ca_Gq_PLC in component environment (fmol)"
legend_states[10] = "q_G_GDP in component environment (fmol)"
legend_states[11] = "q_PIP2 in component environment (fmol)"
legend_states[12] = "q_CaPLC_PIP2 in component environment (fmol)"
legend_states[13] = "q_CaGqPLC_PIP2 in component environment (fmol)"
legend_algebraic[20] = "v_R0_PLC in component PLC (fmol_per_sec)"
legend_algebraic[21] = "v_R1_PLC in component PLC (fmol_per_sec)"
legend_algebraic[22] = "v_R2a_PLC in component PLC (fmol_per_sec)"
legend_algebraic[23] = "v_R2b_PLC in component PLC (fmol_per_sec)"
legend_algebraic[24] = "v_R3a_PLC in component PLC (fmol_per_sec)"
legend_algebraic[25] = "v_R3b_PLC in component PLC (fmol_per_sec)"
legend_algebraic[26] = "v_R4_PLC in component PLC (fmol_per_sec)"
legend_algebraic[27] = "v_R5_PLC in component PLC (fmol_per_sec)"
legend_algebraic[28] = "v_R6_PLC in component PLC (fmol_per_sec)"
legend_algebraic[29] = "v_R7_PLC in component PLC (fmol_per_sec)"
legend_algebraic[30] = "v_R8_PLC in component PLC (fmol_per_sec)"
legend_algebraic[5] = "Gq_stim in component environment (fmol_per_sec)"
legend_constants[1] = "stimPeriod in component environment (second)"
legend_constants[2] = "stimDuration in component environment (second)"
legend_algebraic[0] = "tPeriod in component environment (second)"
legend_algebraic[1] = "cGq in component environment (mM)"
legend_algebraic[2] = "cCa in component environment (mM)"
legend_algebraic[3] = "cDAG in component environment (mM)"
legend_algebraic[4] = "cIP3 in component environment (mM)"
legend_constants[3] = "kappa_R0_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[4] = "kappa_R1_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[5] = "kappa_R2a_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[6] = "kappa_R2b_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[7] = "kappa_R3a_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[8] = "kappa_R3b_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[9] = "kappa_R4_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[10] = "kappa_R5_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[11] = "kappa_R6_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[12] = "kappa_R7_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[13] = "kappa_R8_PLC in component PLC_parameters (fmol_per_sec)"
legend_constants[14] = "K_DAG in component PLC_parameters (per_fmol)"
legend_constants[15] = "K_PC in component PLC_parameters (per_fmol)"
legend_constants[16] = "K_IP3 in component PLC_parameters (per_fmol)"
legend_constants[17] = "K_Ino in component PLC_parameters (per_fmol)"
legend_constants[18] = "K_PLC in component PLC_parameters (per_fmol)"
legend_constants[19] = "K_Gq in component PLC_parameters (per_fmol)"
legend_constants[20] = "K_Ca in component PLC_parameters (per_fmol)"
legend_constants[21] = "K_Gq_PLC in component PLC_parameters (per_fmol)"
legend_constants[22] = "K_Ca_PLC in component PLC_parameters (per_fmol)"
legend_constants[23] = "K_Ca_Gq_PLC in component PLC_parameters (per_fmol)"
legend_constants[24] = "K_G_GDP in component PLC_parameters (per_fmol)"
legend_constants[25] = "K_PIP2 in component PLC_parameters (per_fmol)"
legend_constants[26] = "K_CaPLC_PIP2 in component PLC_parameters (per_fmol)"
legend_constants[27] = "K_CaGqPLC_PIP2 in component PLC_parameters (per_fmol)"
legend_constants[28] = "R in component constants (J_per_K_per_mol)"
legend_constants[29] = "T in component constants (kelvin)"
legend_algebraic[6] = "mu_DAG in component PLC (J_per_mol)"
legend_algebraic[7] = "mu_PC in component PLC (J_per_mol)"
legend_algebraic[8] = "mu_IP3 in component PLC (J_per_mol)"
legend_algebraic[9] = "mu_Ino in component PLC (J_per_mol)"
legend_algebraic[10] = "mu_PLC in component PLC (J_per_mol)"
legend_algebraic[11] = "mu_Gq in component PLC (J_per_mol)"
legend_algebraic[12] = "mu_Ca in component PLC (J_per_mol)"
legend_algebraic[13] = "mu_Gq_PLC in component PLC (J_per_mol)"
legend_algebraic[14] = "mu_Ca_PLC in component PLC (J_per_mol)"
legend_algebraic[15] = "mu_Ca_Gq_PLC in component PLC (J_per_mol)"
legend_algebraic[16] = "mu_G_GDP in component PLC (J_per_mol)"
legend_algebraic[17] = "mu_PIP2 in component PLC (J_per_mol)"
legend_algebraic[18] = "mu_CaPLC_PIP2 in component PLC (J_per_mol)"
legend_algebraic[19] = "mu_CaGqPLC_PIP2 in component PLC (J_per_mol)"
legend_constants[30] = "F in component constants (C_per_mol)"
legend_rates[0] = "d/dt q_DAG in component environment (fmol)"
legend_rates[1] = "d/dt q_PC in component environment (fmol)"
legend_rates[2] = "d/dt q_IP3 in component environment (fmol)"
legend_rates[3] = "d/dt q_Ino in component environment (fmol)"
legend_rates[4] = "d/dt q_PLC in component environment (fmol)"
legend_rates[5] = "d/dt q_Gq in component environment (fmol)"
legend_rates[6] = "d/dt q_Ca in component environment (fmol)"
legend_rates[7] = "d/dt q_Gq_PLC in component environment (fmol)"
legend_rates[8] = "d/dt q_Ca_PLC in component environment (fmol)"
legend_rates[9] = "d/dt q_Ca_Gq_PLC in component environment (fmol)"
legend_rates[10] = "d/dt q_G_GDP in component environment (fmol)"
legend_rates[11] = "d/dt q_PIP2 in component environment (fmol)"
legend_rates[12] = "d/dt q_CaPLC_PIP2 in component environment (fmol)"
legend_rates[13] = "d/dt q_CaGqPLC_PIP2 in component environment (fmol)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 38
states[0] = 0
states[1] = 0
states[2] = 0
states[3] = 0
states[4] = 30.4
states[5] = 38
states[6] = 38
states[7] = 0
states[8] = 0
states[9] = 38
states[10] = 0
states[11] = 380
states[12] = 0
states[13] = 0
constants[1] = 1
constants[2] = 0.01
constants[3] = 0.0700317
constants[4] = 0.178887
constants[5] = 71285.5
constants[6] = 2.73747
constants[7] = 5697.81
constants[8] = 0.00287164
constants[9] = 2.13383
constants[10] = 2.28508
constants[11] = 0.170556
constants[12] = 0.170556
constants[13] = 0.00226839
constants[14] = 0.577328
constants[15] = 0.00384885
constants[16] = 3.76694
constants[17] = 0.00150678
constants[18] = 0.000942826
constants[19] = 0.000141635
constants[20] = 0.000180564
constants[21] = 0.117957
constants[22] = 0.126318
constants[23] = 1.58037
constants[24] = 0.000141635
constants[25] = 8.06835
constants[26] = 18.9051
constants[27] = 938.634
constants[28] = 8.31
constants[29] = 310
constants[30] = 96485
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[6] = constants[28]*constants[29]*log(constants[14]*states[0])
algebraic[7] = constants[28]*constants[29]*log(constants[15]*states[1])
algebraic[20] = constants[3]*(exp(algebraic[6]/(constants[28]*constants[29]))-exp(algebraic[7]/(constants[28]*constants[29])))
rates[1] = algebraic[20]
algebraic[8] = constants[28]*constants[29]*log(constants[16]*states[2])
algebraic[9] = constants[28]*constants[29]*log(constants[17]*states[3])
algebraic[21] = constants[4]*(exp(algebraic[8]/(constants[28]*constants[29]))-exp(algebraic[9]/(constants[28]*constants[29])))
rates[3] = algebraic[21]
algebraic[14] = constants[28]*constants[29]*log(constants[22]*states[8])
algebraic[17] = constants[28]*constants[29]*log(constants[25]*states[11])
algebraic[18] = constants[28]*constants[29]*log(constants[26]*states[12])
algebraic[22] = constants[5]*(exp((algebraic[17]+algebraic[14])/(constants[28]*constants[29]))-exp(algebraic[18]/(constants[28]*constants[29])))
algebraic[23] = constants[6]*(exp(algebraic[18]/(constants[28]*constants[29]))-exp((algebraic[6]+algebraic[8]+algebraic[14])/(constants[28]*constants[29])))
rates[12] = algebraic[22]-algebraic[23]
algebraic[15] = constants[28]*constants[29]*log(constants[23]*states[9])
algebraic[19] = constants[28]*constants[29]*log(constants[27]*states[13])
algebraic[24] = constants[7]*(exp((algebraic[17]+algebraic[15])/(constants[28]*constants[29]))-exp(algebraic[19]/(constants[28]*constants[29])))
rates[11] = -algebraic[22]-algebraic[24]
algebraic[25] = constants[8]*(exp(algebraic[19]/(constants[28]*constants[29]))-exp((algebraic[6]+algebraic[8]+algebraic[15])/(constants[28]*constants[29])))
rates[0] = (algebraic[23]+algebraic[25])-algebraic[20]
rates[2] = (algebraic[23]+algebraic[25])-algebraic[21]
rates[13] = algebraic[24]-algebraic[25]
algebraic[10] = constants[28]*constants[29]*log(constants[18]*states[4])
algebraic[12] = constants[28]*constants[29]*log(constants[20]*states[6])
algebraic[26] = constants[9]*(exp((algebraic[10]+algebraic[12])/(constants[28]*constants[29]))-exp(algebraic[14]/(constants[28]*constants[29])))
algebraic[11] = constants[28]*constants[29]*log(constants[19]*states[5])
algebraic[13] = constants[28]*constants[29]*log(constants[21]*states[7])
algebraic[27] = constants[10]*(exp((algebraic[10]+algebraic[11])/(constants[28]*constants[29]))-exp(algebraic[13]/(constants[28]*constants[29])))
rates[4] = -algebraic[26]-algebraic[27]
algebraic[28] = constants[11]*(exp((algebraic[13]+algebraic[12])/(constants[28]*constants[29]))-exp(algebraic[15]/(constants[28]*constants[29])))
rates[6] = -algebraic[26]-algebraic[28]
rates[7] = algebraic[27]-algebraic[28]
algebraic[29] = constants[12]*(exp(algebraic[15]/(constants[28]*constants[29]))-exp((algebraic[11]+algebraic[14])/(constants[28]*constants[29])))
algebraic[0] = voi-floor(voi/constants[1])*constants[1]
algebraic[5] = custom_piecewise([greater_equal(algebraic[0] , 0.300000) & less_equal(algebraic[0] , 0.300000+constants[2]), 0.00000*100.000 , True, 0.00000])
rates[5] = -algebraic[27]+algebraic[29]+algebraic[5]
algebraic[16] = constants[28]*constants[29]*log(constants[24]*states[10])
algebraic[30] = constants[13]*(exp(algebraic[15]/(constants[28]*constants[29]))-exp((algebraic[16]+algebraic[14])/(constants[28]*constants[29])))
rates[8] = -algebraic[22]+algebraic[23]+algebraic[26]+algebraic[29]+algebraic[30]
rates[9] = ((-algebraic[24]+algebraic[25]+algebraic[28])-algebraic[29])-algebraic[30]
rates[10] = algebraic[30]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[6] = constants[28]*constants[29]*log(constants[14]*states[0])
algebraic[7] = constants[28]*constants[29]*log(constants[15]*states[1])
algebraic[20] = constants[3]*(exp(algebraic[6]/(constants[28]*constants[29]))-exp(algebraic[7]/(constants[28]*constants[29])))
algebraic[8] = constants[28]*constants[29]*log(constants[16]*states[2])
algebraic[9] = constants[28]*constants[29]*log(constants[17]*states[3])
algebraic[21] = constants[4]*(exp(algebraic[8]/(constants[28]*constants[29]))-exp(algebraic[9]/(constants[28]*constants[29])))
algebraic[14] = constants[28]*constants[29]*log(constants[22]*states[8])
algebraic[17] = constants[28]*constants[29]*log(constants[25]*states[11])
algebraic[18] = constants[28]*constants[29]*log(constants[26]*states[12])
algebraic[22] = constants[5]*(exp((algebraic[17]+algebraic[14])/(constants[28]*constants[29]))-exp(algebraic[18]/(constants[28]*constants[29])))
algebraic[23] = constants[6]*(exp(algebraic[18]/(constants[28]*constants[29]))-exp((algebraic[6]+algebraic[8]+algebraic[14])/(constants[28]*constants[29])))
algebraic[15] = constants[28]*constants[29]*log(constants[23]*states[9])
algebraic[19] = constants[28]*constants[29]*log(constants[27]*states[13])
algebraic[24] = constants[7]*(exp((algebraic[17]+algebraic[15])/(constants[28]*constants[29]))-exp(algebraic[19]/(constants[28]*constants[29])))
algebraic[25] = constants[8]*(exp(algebraic[19]/(constants[28]*constants[29]))-exp((algebraic[6]+algebraic[8]+algebraic[15])/(constants[28]*constants[29])))
algebraic[10] = constants[28]*constants[29]*log(constants[18]*states[4])
algebraic[12] = constants[28]*constants[29]*log(constants[20]*states[6])
algebraic[26] = constants[9]*(exp((algebraic[10]+algebraic[12])/(constants[28]*constants[29]))-exp(algebraic[14]/(constants[28]*constants[29])))
algebraic[11] = constants[28]*constants[29]*log(constants[19]*states[5])
algebraic[13] = constants[28]*constants[29]*log(constants[21]*states[7])
algebraic[27] = constants[10]*(exp((algebraic[10]+algebraic[11])/(constants[28]*constants[29]))-exp(algebraic[13]/(constants[28]*constants[29])))
algebraic[28] = constants[11]*(exp((algebraic[13]+algebraic[12])/(constants[28]*constants[29]))-exp(algebraic[15]/(constants[28]*constants[29])))
algebraic[29] = constants[12]*(exp(algebraic[15]/(constants[28]*constants[29]))-exp((algebraic[11]+algebraic[14])/(constants[28]*constants[29])))
algebraic[0] = voi-floor(voi/constants[1])*constants[1]
algebraic[5] = custom_piecewise([greater_equal(algebraic[0] , 0.300000) & less_equal(algebraic[0] , 0.300000+constants[2]), 0.00000*100.000 , True, 0.00000])
algebraic[16] = constants[28]*constants[29]*log(constants[24]*states[10])
algebraic[30] = constants[13]*(exp(algebraic[15]/(constants[28]*constants[29]))-exp((algebraic[16]+algebraic[14])/(constants[28]*constants[29])))
algebraic[1] = states[5]/constants[0]
algebraic[2] = states[6]/constants[0]
algebraic[3] = states[0]/constants[0]
algebraic[4] = states[2]/constants[0]
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)