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 = 2
sizeStates = 34
sizeConstants = 55
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] = "v_c in component v_c (nanomolar)"
legend_algebraic[0] = "dv_c_dt in component dv_c_dt (flux)"
legend_constants[0] = "k_growth in component rate_constants (first_order_rate_constant)"
legend_states[1] = "v_n in component v_n (nanomolar)"
legend_algebraic[1] = "k_volume in component k_volume (dimensionless)"
legend_states[2] = "mcln2_c in component mcln2_c (nanomolar)"
legend_constants[1] = "k_50 in component rate_constants (first_order_rate_constant)"
legend_constants[2] = "k_10 in component rate_constants (first_order_rate_constant)"
legend_states[3] = "mcln2_n in component mcln2_n (nanomolar)"
legend_states[4] = "mclb5_c in component mclb5_c (nanomolar)"
legend_constants[3] = "k_51 in component rate_constants (first_order_rate_constant)"
legend_constants[4] = "k_11 in component rate_constants (first_order_rate_constant)"
legend_states[5] = "mclb5_n in component mclb5_n (nanomolar)"
legend_constants[5] = "k_1 in component rate_constants (first_order_rate_constant)"
legend_states[6] = "sbf_n in component sbf_n (nanomolar)"
legend_constants[6] = "k_2 in component rate_constants (first_order_rate_constant)"
legend_constants[7] = "k_39 in component rate_constants (first_order_rate_constant)"
legend_constants[8] = "k_34 in component rate_constants (second_order_rate_constant)"
legend_constants[9] = "k_35 in component rate_constants (first_order_rate_constant)"
legend_states[7] = "sbfwhi5p_n in component sbfwhi5p_n (nanomolar)"
legend_states[8] = "whi5_n in component whi5_n (nanomolar)"
legend_states[9] = "sbfwhi5_n in component sbfwhi5_n (nanomolar)"
legend_states[10] = "cln3_c in component cln3_c (nanomolar)"
legend_constants[10] = "k_6 in component rate_constants (flux)"
legend_constants[11] = "k_43 in component rate_constants (first_order_rate_constant)"
legend_constants[12] = "k_15 in component rate_constants (first_order_rate_constant)"
legend_states[11] = "cln2_c in component cln2_c (nanomolar)"
legend_constants[13] = "k_3 in component rate_constants (first_order_rate_constant)"
legend_constants[14] = "k_26 in component rate_constants (second_order_rate_constant)"
legend_constants[15] = "k_27 in component rate_constants (first_order_rate_constant)"
legend_constants[16] = "k_12 in component rate_constants (first_order_rate_constant)"
legend_states[12] = "cdk1_c in component cdk1_c (nanomolar)"
legend_states[13] = "cdk1cln2_c in component cdk1cln2_c (nanomolar)"
legend_states[14] = "clb5_c in component clb5_c (nanomolar)"
legend_constants[17] = "k_4 in component rate_constants (first_order_rate_constant)"
legend_constants[18] = "k_28 in component rate_constants (second_order_rate_constant)"
legend_constants[19] = "k_29 in component rate_constants (first_order_rate_constant)"
legend_constants[20] = "k_13 in component rate_constants (first_order_rate_constant)"
legend_states[15] = "cdk1clb5_c in component cdk1clb5_c (nanomolar)"
legend_constants[21] = "k_7 in component rate_constants (flux)"
legend_constants[22] = "k_44 in component rate_constants (first_order_rate_constant)"
legend_constants[23] = "k_49 in component rate_constants (first_order_rate_constant)"
legend_constants[24] = "k_16 in component rate_constants (first_order_rate_constant)"
legend_states[16] = "cdk1_n in component cdk1_n (nanomolar)"
legend_states[17] = "cln3_n in component cln3_n (nanomolar)"
legend_constants[25] = "k_24 in component rate_constants (second_order_rate_constant)"
legend_constants[26] = "k_25 in component rate_constants (first_order_rate_constant)"
legend_constants[27] = "k_20 in component rate_constants (first_order_rate_constant)"
legend_states[18] = "cdk1cln3_n in component cdk1cln3_n (nanomolar)"
legend_constants[28] = "k_21 in component rate_constants (first_order_rate_constant)"
legend_constants[29] = "k_46 in component rate_constants (first_order_rate_constant)"
legend_constants[30] = "k_53 in component rate_constants (first_order_rate_constant)"
legend_states[19] = "cdk1cln2_n in component cdk1cln2_n (nanomolar)"
legend_constants[31] = "k_33 in component rate_constants (first_order_rate_constant)"
legend_constants[32] = "k_32 in component rate_constants (second_order_rate_constant)"
legend_constants[33] = "k_48 in component rate_constants (first_order_rate_constant)"
legend_states[20] = "cdk1clb5sic1_c in component cdk1clb5sic1_c (nanomolar)"
legend_states[21] = "sic1_c in component sic1_c (nanomolar)"
legend_states[22] = "cdk1clb5_n in component cdk1clb5_n (nanomolar)"
legend_constants[34] = "k_41 in component rate_constants (first_order_rate_constant)"
legend_states[23] = "cdk1clb5sic1p_n in component cdk1clb5sic1p_n (nanomolar)"
legend_constants[35] = "k_31 in component rate_constants (first_order_rate_constant)"
legend_constants[36] = "k_30 in component rate_constants (second_order_rate_constant)"
legend_constants[37] = "k_40 in component rate_constants (first_order_rate_constant)"
legend_states[24] = "cdk1cln3far1_n in component cdk1cln3far1_n (nanomolar)"
legend_states[25] = "far1_n in component far1_n (nanomolar)"
legend_states[26] = "cdk1cln3far1p_n in component cdk1cln3far1p_n (nanomolar)"
legend_constants[38] = "k_36 in component rate_constants (second_order_rate_constant)"
legend_constants[39] = "k_37 in component rate_constants (second_order_rate_constant)"
legend_states[27] = "cdk1clb5sic1_n in component cdk1clb5sic1_n (nanomolar)"
legend_constants[40] = "k_47 in component rate_constants (first_order_rate_constant)"
legend_constants[41] = "k_38 in component rate_constants (second_order_rate_constant)"
legend_constants[42] = "k_9 in component rate_constants (flux)"
legend_constants[43] = "k_18 in component rate_constants (first_order_rate_constant)"
legend_states[28] = "whi5_c in component whi5_c (nanomolar)"
legend_constants[44] = "k_8 in component rate_constants (flux)"
legend_constants[45] = "k_45 in component rate_constants (first_order_rate_constant)"
legend_constants[46] = "k_17 in component rate_constants (first_order_rate_constant)"
legend_states[29] = "far1_c in component far1_c (nanomolar)"
legend_constants[47] = "k_5 in component rate_constants (flux)"
legend_constants[48] = "k_42 in component rate_constants (first_order_rate_constant)"
legend_constants[49] = "k_14 in component rate_constants (first_order_rate_constant)"
legend_states[30] = "whi5p_c in component whi5p_c (nanomolar)"
legend_constants[50] = "k_52 in component rate_constants (first_order_rate_constant)"
legend_states[31] = "whi5p_n in component whi5p_n (nanomolar)"
legend_states[32] = "sic1P_n in component sic1P_n (nanomolar)"
legend_states[33] = "far1P_n in component far1P_n (nanomolar)"
legend_constants[51] = "k_22 in component rate_constants (first_order_rate_constant)"
legend_constants[52] = "k_19 in component rate_constants (first_order_rate_constant)"
legend_constants[53] = "k_23 in component rate_constants (first_order_rate_constant)"
legend_rates[0] = "d/dt v_c in component v_c (nanomolar)"
legend_rates[1] = "d/dt v_n in component v_n (nanomolar)"
legend_rates[2] = "d/dt mcln2_c in component mcln2_c (nanomolar)"
legend_rates[4] = "d/dt mclb5_c in component mclb5_c (nanomolar)"
legend_rates[3] = "d/dt mcln2_n in component mcln2_n (nanomolar)"
legend_rates[5] = "d/dt mclb5_n in component mclb5_n (nanomolar)"
legend_rates[6] = "d/dt sbf_n in component sbf_n (nanomolar)"
legend_rates[10] = "d/dt cln3_c in component cln3_c (nanomolar)"
legend_rates[11] = "d/dt cln2_c in component cln2_c (nanomolar)"
legend_rates[14] = "d/dt clb5_c in component clb5_c (nanomolar)"
legend_rates[12] = "d/dt cdk1_c in component cdk1_c (nanomolar)"
legend_rates[17] = "d/dt cln3_n in component cln3_n (nanomolar)"
legend_rates[16] = "d/dt cdk1_n in component cdk1_n (nanomolar)"
legend_rates[13] = "d/dt cdk1cln2_c in component cdk1cln2_c (nanomolar)"
legend_rates[15] = "d/dt cdk1clb5_c in component cdk1clb5_c (nanomolar)"
legend_rates[19] = "d/dt cdk1cln2_n in component cdk1cln2_n (nanomolar)"
legend_rates[22] = "d/dt cdk1clb5_n in component cdk1clb5_n (nanomolar)"
legend_rates[18] = "d/dt cdk1cln3_n in component cdk1cln3_n (nanomolar)"
legend_rates[9] = "d/dt sbfwhi5_n in component sbfwhi5_n (nanomolar)"
legend_rates[7] = "d/dt sbfwhi5p_n in component sbfwhi5p_n (nanomolar)"
legend_rates[24] = "d/dt cdk1cln3far1_n in component cdk1cln3far1_n (nanomolar)"
legend_rates[27] = "d/dt cdk1clb5sic1_n in component cdk1clb5sic1_n (nanomolar)"
legend_rates[23] = "d/dt cdk1clb5sic1p_n in component cdk1clb5sic1p_n (nanomolar)"
legend_rates[26] = "d/dt cdk1cln3far1p_n in component cdk1cln3far1p_n (nanomolar)"
legend_rates[20] = "d/dt cdk1clb5sic1_c in component cdk1clb5sic1_c (nanomolar)"
legend_rates[21] = "d/dt sic1_c in component sic1_c (nanomolar)"
legend_rates[28] = "d/dt whi5_c in component whi5_c (nanomolar)"
legend_rates[29] = "d/dt far1_c in component far1_c (nanomolar)"
legend_rates[30] = "d/dt whi5p_c in component whi5p_c (nanomolar)"
legend_rates[32] = "d/dt sic1P_n in component sic1P_n (nanomolar)"
legend_rates[33] = "d/dt far1P_n in component far1P_n (nanomolar)"
legend_rates[8] = "d/dt whi5_n in component whi5_n (nanomolar)"
legend_rates[25] = "d/dt far1_n in component far1_n (nanomolar)"
legend_rates[31] = "d/dt whi5p_n in component whi5p_n (nanomolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.5
constants[0] = 0.0051
states[1] = 0.5
states[2] = 0
constants[1] = 0.6
constants[2] = 0.12
states[3] = 0
states[4] = 0
constants[3] = 0.6
constants[4] = 0.12
states[5] = 0
constants[5] = 0.03523
states[6] = 0
constants[6] = 0.03523
constants[7] = 1
constants[8] = 8.46
constants[9] = 0.0005
states[7] = 0
states[8] = 0
states[9] = 0.025544
states[10] = 0.000485
constants[10] = 0.00001
constants[11] = 0.005
constants[12] = 0.01
states[11] = 0
constants[13] = 0.32
constants[14] = 2.82
constants[15] = 0.55
constants[16] = 0.1
states[12] = 0.333333
states[13] = 0
states[14] = 0
constants[17] = 0.32
constants[18] = 2.82
constants[19] = 0.55
constants[20] = 0.35
states[15] = 0
constants[21] = 0.01
constants[22] = 0.005
constants[23] = 0.001
constants[24] = 0.03
states[16] = 0.0074127
states[17] = 0
constants[25] = 2.82
constants[26] = 0.55
constants[27] = 0.01
states[18] = 0
constants[28] = 0
constants[29] = 0.1
constants[30] = 0.001
states[19] = 0
constants[31] = 0.55
constants[32] = 84.6
constants[33] = 0.012
states[20] = 0
states[21] = 0.039234
states[22] = 0
constants[34] = 1
states[23] = 0
constants[35] = 0.55
constants[36] = 42300
constants[37] = 1
states[24] = 0
states[25] = 0
states[26] = 0
constants[38] = 4363.6
constants[39] = 4363.6
states[27] = 0
constants[40] = 1
constants[41] = 4363.6
constants[42] = 0.00005
constants[43] = 0.0008
states[28] = 0.073564
constants[44] = 0.00004
constants[45] = 0.005
constants[46] = 0.01
states[29] = 0.0037926
constants[47] = 0.000042
constants[48] = 0.005
constants[49] = 0.01
states[30] = 0
constants[50] = 0.005
states[31] = 0
states[32] = 0
states[33] = 0
constants[51] = 0.01
constants[52] = 0.01
constants[53] = 0.01
constants[54] = 0.00000
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[1] = constants[54]
rates[3] = constants[5]*states[6]-constants[1]*states[3]
rates[5] = constants[6]*states[6]-constants[3]*states[5]
rates[6] = (constants[7]*states[7]-constants[8]*states[6]*states[8])+constants[9]*states[9]
rates[18] = (((constants[25]*states[17]*states[16]-constants[26]*states[18])+constants[35]*states[24])-constants[36]*states[25]*states[18])+constants[37]*states[26]
rates[9] = (constants[8]*states[6]*states[8]-constants[9]*states[9])-constants[38]*states[9]*states[18]
rates[7] = constants[38]*states[9]*states[18]-constants[7]*states[7]
rates[24] = (constants[36]*states[25]*states[18]-constants[35]*states[24])-constants[39]*states[24]*states[19]
rates[23] = constants[41]*states[27]*states[19]-constants[34]*states[23]
rates[26] = constants[39]*states[24]*states[19]-constants[37]*states[26]
rates[32] = constants[34]*states[23]
rates[33] = constants[37]*states[26]
rates[31] = (constants[7]*states[7]-constants[50]*states[31])-constants[53]*states[31]
algebraic[0] = constants[0]*states[0]
rates[0] = algebraic[0]
rates[10] = ((constants[10]-constants[11]*states[10])-constants[12]*states[10])-(algebraic[0]/states[0])*states[10]
rates[11] = (((constants[13]*states[2]-constants[14]*states[12]*states[11])+constants[15]*states[13])-constants[16]*states[11])-(algebraic[0]/states[0])*states[11]
rates[14] = (((constants[17]*states[4]-constants[18]*states[14]*states[12])+constants[19]*states[15])-constants[20]*states[14])-(algebraic[0]/states[0])*states[14]
rates[12] = ((((((constants[21]-constants[22]*states[12])+constants[23]*states[16]+constants[15]*states[13])-constants[14]*states[12]*states[11])-constants[18]*states[12]*states[14])+constants[19]*states[15])-constants[24]*states[12])-(algebraic[0]/states[0])*states[12]
rates[15] = ((((constants[18]*states[12]*states[14]-constants[19]*states[15])+constants[31]*states[20])-constants[32]*states[21]*states[15])-constants[33]*states[15])-(algebraic[0]/states[0])*states[15]
rates[20] = ((constants[32]*states[21]*states[15]-constants[31]*states[20])-constants[40]*states[20])-(algebraic[0]/states[0])*states[20]
rates[21] = (((constants[42]-constants[32]*states[21]*states[15])+constants[31]*states[20])-constants[43]*states[21])-(algebraic[0]/states[0])*states[21]
rates[28] = ((constants[44]-constants[45]*states[28])-constants[46]*states[28])-(algebraic[0]/states[0])*states[28]
rates[29] = ((constants[47]-constants[48]*states[29])-constants[49]*states[29])-(algebraic[0]/states[0])*states[29]
algebraic[1] = states[1]/states[0]
rates[2] = (constants[1]*states[3]*algebraic[1]-constants[2]*states[2])-(algebraic[0]/states[0])*states[2]
rates[4] = (constants[3]*states[5]*algebraic[1]-constants[4]*states[4])-(algebraic[0]/states[0])*states[4]
rates[17] = (((constants[11]*states[10])/algebraic[1]-constants[25]*states[17]*states[16])+constants[26]*states[18])-constants[27]*states[17]
rates[16] = ((((constants[22]*states[12])/algebraic[1]-constants[23]*states[16])-constants[25]*states[17]*states[16])+constants[26]*states[18])-constants[28]*states[16]
rates[13] = (((constants[14]*states[12]*states[11]-constants[15]*states[13])-constants[29]*states[13])+constants[30]*states[19]*algebraic[1])-(algebraic[0]/states[0])*states[13]
rates[19] = (constants[29]*states[13])/algebraic[1]-constants[30]*states[19]
rates[22] = constants[34]*states[23]+(constants[33]*states[15])/algebraic[1]
rates[27] = (constants[40]*states[20])/algebraic[1]-constants[41]*states[27]*states[19]
rates[30] = constants[50]*states[31]*algebraic[1]
rates[8] = ((constants[45]*states[28])/algebraic[1]-constants[8]*states[8]*states[6])-constants[51]*states[8]
rates[25] = (((constants[48]*states[29])/algebraic[1]-constants[36]*states[25]*states[18])+constants[35]*states[24])-constants[52]*states[25]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[0]*states[0]
algebraic[1] = states[1]/states[0]
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)