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 = 9
sizeStates = 19
sizeConstants = 69
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 (minute)"
legend_states[0] = "Clb2 in component Clb2 (dimensionless)"
legend_constants[0] = "epsilon in component Clb2 (dimensionless)"
legend_constants[1] = "Jm in component Clb2 (dimensionless)"
legend_constants[2] = "ks_clb in component Clb2 (first_order_rate_constant)"
legend_constants[3] = "kd_clb_1 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[4] = "kd_clb_2 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[5] = "kd_clb_3 in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[8] = "kswe in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[7] = "kmih in component kinetic_parameters (first_order_rate_constant)"
legend_constants[6] = "kass in component kinetic_parameters (first_order_rate_constant)"
legend_constants[7] = "kdiss in component kinetic_parameters (first_order_rate_constant)"
legend_constants[8] = "kd_sic in component kinetic_parameters (first_order_rate_constant)"
legend_constants[9] = "kd_sic_1 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[10] = "kd_sic_2 in component kinetic_parameters (first_order_rate_constant)"
legend_states[1] = "M in component M (dimensionless)"
legend_states[2] = "Mcm_a in component Mcm_a (dimensionless)"
legend_states[3] = "Cdh1_a in component Cdh1_a (dimensionless)"
legend_states[4] = "Cdc20_a in component Cdc20_a (dimensionless)"
legend_states[5] = "Sic1 in component Sic1 (dimensionless)"
legend_states[6] = "PClb2 in component PClb2 (dimensionless)"
legend_states[7] = "Trim in component Trim (dimensionless)"
legend_states[8] = "Cln in component Cln (dimensionless)"
legend_states[9] = "PTrim in component PTrim (dimensionless)"
legend_constants[11] = "Ji_mcm in component Mcm_a (dimensionless)"
legend_constants[12] = "Ja_mcm in component Mcm_a (dimensionless)"
legend_constants[13] = "ki_mcm in component Mcm_a (first_order_rate_constant)"
legend_constants[14] = "ka_mcm in component Mcm_a (first_order_rate_constant)"
legend_algebraic[0] = "Mcm in component Mcm (dimensionless)"
legend_constants[15] = "ks_sic in component Sic1 (first_order_rate_constant)"
legend_states[10] = "Mih1_a in component Mih1_a (dimensionless)"
legend_constants[16] = "Ji_mih in component Mih1_a (dimensionless)"
legend_constants[17] = "Ja_mih in component Mih1_a (dimensionless)"
legend_constants[18] = "Vi_mih in component Mih1_a (first_order_rate_constant)"
legend_constants[19] = "Va_mih in component Mih1_a (first_order_rate_constant)"
legend_algebraic[1] = "Mih1 in component Mih1 (dimensionless)"
legend_states[11] = "IE_a in component IE_a (dimensionless)"
legend_constants[20] = "Ji_ie in component IE_a (dimensionless)"
legend_constants[21] = "Ja_ie in component IE_a (dimensionless)"
legend_constants[22] = "ki_ie in component IE_a (first_order_rate_constant)"
legend_constants[23] = "ka_ie in component IE_a (first_order_rate_constant)"
legend_algebraic[2] = "IE in component IE (dimensionless)"
legend_constants[24] = "Ji_cdc20 in component kinetic_parameters (dimensionless)"
legend_constants[25] = "Ja_cdc20 in component kinetic_parameters (dimensionless)"
legend_constants[26] = "ki_cdc20 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[27] = "kd_cdc20 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[28] = "ka_cdc20 in component kinetic_parameters (first_order_rate_constant)"
legend_states[12] = "Cdc20 in component Cdc20 (dimensionless)"
legend_constants[29] = "ks_cdc20_1 in component Cdc20 (first_order_rate_constant)"
legend_constants[30] = "ks_cdc20_2 in component Cdc20 (first_order_rate_constant)"
legend_constants[31] = "Js_cdc20 in component Cdc20 (dimensionless)"
legend_constants[32] = "Ji_cdh in component Cdh1_a (dimensionless)"
legend_constants[33] = "Ja_cdh in component Cdh1_a (dimensionless)"
legend_constants[34] = "ki_cdh in component Cdh1_a (first_order_rate_constant)"
legend_constants[35] = "ka_cdh_1 in component Cdh1_a (first_order_rate_constant)"
legend_constants[36] = "ki_cdh_1 in component Cdh1_a (first_order_rate_constant)"
legend_constants[37] = "ka_cdh_2 in component Cdh1_a (first_order_rate_constant)"
legend_algebraic[3] = "Cdh1 in component Cdh1 (dimensionless)"
legend_constants[38] = "ks_cln in component Cln (first_order_rate_constant)"
legend_constants[39] = "kd_cln in component Cln (first_order_rate_constant)"
legend_states[13] = "SBF_a in component SBF_a (dimensionless)"
legend_constants[40] = "Ji_sbf in component SBF_a (dimensionless)"
legend_constants[41] = "Ja_sbf in component SBF_a (dimensionless)"
legend_constants[42] = "ki_sbf_1 in component SBF_a (first_order_rate_constant)"
legend_constants[43] = "ka_sbf_1 in component SBF_a (first_order_rate_constant)"
legend_constants[44] = "ki_sbf_2 in component SBF_a (first_order_rate_constant)"
legend_constants[45] = "ka_sbf_2 in component SBF_a (first_order_rate_constant)"
legend_algebraic[4] = "SBF in component SBF (dimensionless)"
legend_states[14] = "Swe1 in component Swe1 (dimensionless)"
legend_constants[46] = "ks_swe in component Swe1 (first_order_rate_constant)"
legend_constants[47] = "ks_sweC in component Swe1 (first_order_rate_constant)"
legend_constants[48] = "khsl1 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[49] = "khsl1r in component kinetic_parameters (first_order_rate_constant)"
legend_constants[50] = "kd_swe_1 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[51] = "Ji_wee in component kinetic_parameters (dimensionless)"
legend_constants[52] = "Ja_wee in component kinetic_parameters (dimensionless)"
legend_constants[53] = "Vi_wee in component kinetic_parameters (first_order_rate_constant)"
legend_constants[54] = "Va_wee in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[5] = "BUD in component BUD (dimensionless)"
legend_states[15] = "PSwe1 in component PSwe1 (dimensionless)"
legend_states[16] = "Swe1M in component Swe1M (dimensionless)"
legend_states[17] = "PSwe1M in component PSwe1M (dimensionless)"
legend_constants[55] = "kd_swe_2 in component PSwe1M (first_order_rate_constant)"
legend_states[18] = "BE in component BE (dimensionless)"
legend_constants[56] = "ks_bud in component BE (first_order_rate_constant)"
legend_constants[57] = "kd_bud in component BE (first_order_rate_constant)"
legend_constants[58] = "mu in component M (first_order_rate_constant)"
legend_constants[59] = "IE_total in component IE (dimensionless)"
legend_constants[60] = "Cdh1_total in component Cdh1 (dimensionless)"
legend_constants[61] = "Mih1_total in component Mih1 (dimensionless)"
legend_constants[62] = "Mcm_total in component Mcm (dimensionless)"
legend_constants[63] = "SBF_total in component SBF (dimensionless)"
legend_algebraic[6] = "Swe1_total in component Swe1_total (dimensionless)"
legend_constants[64] = "kswe_1 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[65] = "kswe_2 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[66] = "kswe_3 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[67] = "kmih_1 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[68] = "kmih_2 in component kinetic_parameters (first_order_rate_constant)"
legend_rates[0] = "d/dt Clb2 in component Clb2 (dimensionless)"
legend_rates[6] = "d/dt PClb2 in component PClb2 (dimensionless)"
legend_rates[7] = "d/dt Trim in component Trim (dimensionless)"
legend_rates[9] = "d/dt PTrim in component PTrim (dimensionless)"
legend_rates[2] = "d/dt Mcm_a in component Mcm_a (dimensionless)"
legend_rates[5] = "d/dt Sic1 in component Sic1 (dimensionless)"
legend_rates[10] = "d/dt Mih1_a in component Mih1_a (dimensionless)"
legend_rates[11] = "d/dt IE_a in component IE_a (dimensionless)"
legend_rates[4] = "d/dt Cdc20_a in component Cdc20_a (dimensionless)"
legend_rates[12] = "d/dt Cdc20 in component Cdc20 (dimensionless)"
legend_rates[3] = "d/dt Cdh1_a in component Cdh1_a (dimensionless)"
legend_rates[8] = "d/dt Cln in component Cln (dimensionless)"
legend_rates[13] = "d/dt SBF_a in component SBF_a (dimensionless)"
legend_rates[14] = "d/dt Swe1 in component Swe1 (dimensionless)"
legend_rates[15] = "d/dt PSwe1 in component PSwe1 (dimensionless)"
legend_rates[16] = "d/dt Swe1M in component Swe1M (dimensionless)"
legend_rates[17] = "d/dt PSwe1M in component PSwe1M (dimensionless)"
legend_rates[18] = "d/dt BE in component BE (dimensionless)"
legend_rates[1] = "d/dt M in component M (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.184
constants[0] = 0.5
constants[1] = 10
constants[2] = 0.015
constants[3] = 0.015
constants[4] = 1
constants[5] = 0.1
constants[6] = 300
constants[7] = 0.1
constants[8] = 0.01
constants[9] = 1
constants[10] = 3
states[1] = 0.802
states[2] = 0.933
states[3] = 0.993
states[4] = 1.438
states[5] = 0.003
states[6] = 0
states[7] = 0.084
states[8] = 0.054
states[9] = 0
constants[11] = 0.1
constants[12] = 0.1
constants[13] = 0.15
constants[14] = 1
constants[15] = 0.1
states[10] = 0.808
constants[16] = 0.1
constants[17] = 0.1
constants[18] = 0.3
constants[19] = 1
states[11] = 0.522
constants[20] = 0.01
constants[21] = 0.01
constants[22] = 0.04
constants[23] = 0.1
constants[24] = 0.001
constants[25] = 0.001
constants[26] = 0.25
constants[27] = 0.1
constants[28] = 1
states[12] = 1.172
constants[29] = 0.005
constants[30] = 0.3
constants[31] = 0.3
constants[32] = 0.01
constants[33] = 0.01
constants[34] = 35
constants[35] = 1
constants[36] = 2
constants[37] = 10
constants[38] = 0.1
constants[39] = 0.1
states[13] = 0.124
constants[40] = 0.01
constants[41] = 0.01
constants[42] = 1
constants[43] = 1
constants[44] = 2
constants[45] = 0
states[14] = 0
constants[46] = 0.0025
constants[47] = 0
constants[48] = 1
constants[49] = 0.01
constants[50] = 0.007
constants[51] = 0.05
constants[52] = 0.05
constants[53] = 1
constants[54] = 0.3
states[15] = 0
states[16] = 0.018
states[17] = 0.013
constants[55] = 0.05
states[18] = 0
constants[56] = 0.1
constants[57] = 0.1
constants[58] = 0.005
constants[59] = 1
constants[60] = 1
constants[61] = 1
constants[62] = 1
constants[63] = 1
constants[64] = 2
constants[65] = 0.01
constants[66] = 0.2
constants[67] = 5
constants[68] = 0.5
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[5] = (constants[15]+constants[7]*(states[9]+states[7])+(constants[3]+constants[4]*states[3]+constants[5]*states[4])*(states[9]+states[7]))-((constants[8]+constants[9]*states[8]+constants[10]*states[0])*states[5]+constants[6]*states[5]*(states[0]+states[6]))
rates[4] = (constants[28]*states[11]*states[12])/(constants[25]+states[12])-((constants[26]*states[4])/(constants[24]+states[4])+constants[27]*states[4])
rates[12] = (constants[29]+(constants[30]*(power(states[0], 4.00000)))/(power(constants[31], 4.00000)+power(states[0], 4.00000))+(constants[26]*states[4])/(constants[24]+states[4]))-((constants[28]*states[11]*states[12])/(constants[25]+states[12])+constants[27]*states[12])
rates[8] = constants[38]*states[13]-constants[39]*states[8]
rates[18] = constants[56]*states[8]-constants[57]*states[18]
rates[1] = constants[58]*states[1]
algebraic[0] = constants[62]-states[2]
rates[2] = (-constants[13]*states[2])/(constants[11]+states[2])+(constants[14]*algebraic[0]*states[0])/(constants[12]+algebraic[0])
algebraic[1] = constants[61]-states[10]
rates[10] = (-constants[18]*states[10])/(constants[16]+states[10])+(constants[19]*states[0]*algebraic[1])/(constants[17]+algebraic[1])
algebraic[2] = constants[59]-states[11]
rates[11] = (-constants[22]*states[11])/(constants[20]+states[11])+(constants[23]*states[0]*algebraic[2])/(constants[21]+algebraic[2])
algebraic[3] = constants[60]-states[3]
rates[3] = (-(constants[34]*states[0]+constants[36]*states[8])*states[3])/(constants[32]+states[3])+((constants[35]+constants[37]*states[4])*algebraic[3])/(constants[33]+algebraic[3])
algebraic[4] = constants[63]-states[13]
rates[13] = (-(constants[42]+constants[44]*states[0])*states[13])/(constants[40]+states[13])+((constants[43]*states[1]+constants[45]*states[8])*algebraic[4])/(constants[41]+algebraic[4])
algebraic[5] = custom_piecewise([less_equal(states[18] , 0.600000) & less(states[0] , 0.200000), 0.00000 , True, 1.00000])
rates[14] = (constants[46]*states[13]+constants[47]+constants[49]*states[16]+(constants[54]*states[15])/(constants[52]+states[15]))-(constants[48]*algebraic[5]*states[14]+(constants[53]*states[0]*states[14])/(constants[51]+states[14])+constants[50]*states[14])
rates[15] = (constants[49]*states[17]+(constants[53]*states[14]*states[0])/(constants[51]+states[14]))-(constants[48]*algebraic[5]*states[15]+(constants[54]*states[15])/(constants[52]+states[15])+constants[50]*states[15])
rates[16] = (constants[48]*algebraic[5]*states[14]+(constants[54]*states[17])/(constants[52]+states[17]))-(constants[49]*states[16]+(constants[53]*states[0]*states[16])/(constants[51]+states[16])+constants[50]*states[16])
rates[17] = (constants[48]*algebraic[5]*states[15]+(constants[53]*states[0]*states[16])/(constants[51]+states[16]))-(constants[49]*states[17]+(constants[54]*states[17])/(constants[52]+states[17])+constants[55]*states[17])
algebraic[8] = constants[64]*states[14]+constants[65]*states[16]+constants[66]*states[15]
algebraic[7] = constants[67]*states[10]+constants[68]*algebraic[1]
rates[0] = ((constants[2]*(constants[0]+states[2])*states[1])/(1.00000+states[1]/constants[1])+algebraic[7]*states[6]+constants[7]*states[7]+(constants[8]+constants[9]*states[8]+constants[10]*states[0])*states[7])-((constants[3]+constants[4]*states[3]+constants[5]*states[4])*states[0]+algebraic[8]*states[0]+constants[6]*states[5]*states[0])
rates[6] = (algebraic[8]*states[0]+constants[7]*states[9]+(constants[8]+constants[9]*states[8]+constants[10]*states[0])*states[9])-((constants[3]+constants[4]*states[3]+constants[5]*states[4])*states[6]+algebraic[7]*states[6]+constants[6]*states[5]*states[6])
rates[7] = (constants[6]*states[5]*states[0]+algebraic[7]*states[9])-(constants[7]*states[7]+(constants[8]+constants[9]*states[8]+constants[10]*states[0])*states[7]+(constants[3]+constants[4]*states[3]+constants[5]*states[4])*states[7]+algebraic[8]*states[7])
rates[9] = (algebraic[8]*states[7]+constants[6]*states[5]*states[6])-(constants[7]*states[9]+(constants[8]+constants[9]*states[8]+constants[10]*states[0])*states[9]+(constants[3]+constants[4]*states[3]+constants[5]*states[4])*states[9]+algebraic[7]*states[9])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[62]-states[2]
algebraic[1] = constants[61]-states[10]
algebraic[2] = constants[59]-states[11]
algebraic[3] = constants[60]-states[3]
algebraic[4] = constants[63]-states[13]
algebraic[5] = custom_piecewise([less_equal(states[18] , 0.600000) & less(states[0] , 0.200000), 0.00000 , True, 1.00000])
algebraic[8] = constants[64]*states[14]+constants[65]*states[16]+constants[66]*states[15]
algebraic[7] = constants[67]*states[10]+constants[68]*algebraic[1]
algebraic[6] = states[14]+states[15]+states[16]+states[17]
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)