Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 16
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 (hour)"
legend_states[0] = "MP in component MP (nanomolar)"
legend_constants[46] = "vsP in component MP (flux)"
legend_constants[0] = "vmP in component MP (flux)"
legend_constants[1] = "kdmp in component MP (first_order_rate_constant)"
legend_constants[2] = "KAP in component MP (nanomolar)"
legend_constants[3] = "KmP in component MP (nanomolar)"
legend_constants[4] = "vstot in component model_parameters (flux)"
legend_constants[5] = "n in component model_parameters (dimensionless)"
legend_states[1] = "BN in component BN (nanomolar)"
legend_states[2] = "MC in component MC (nanomolar)"
legend_constants[47] = "vsC in component MC (flux)"
legend_constants[6] = "vmC in component MC (flux)"
legend_constants[7] = "kdmc in component MC (first_order_rate_constant)"
legend_constants[8] = "KAC in component MC (nanomolar)"
legend_constants[9] = "KmC in component MC (nanomolar)"
legend_states[3] = "MB in component MB (nanomolar)"
legend_constants[48] = "vsB in component MB (flux)"
legend_constants[10] = "vmB in component MB (flux)"
legend_constants[11] = "kdmb in component MB (first_order_rate_constant)"
legend_constants[12] = "KIB in component MB (nanomolar)"
legend_constants[13] = "KmB in component MB (nanomolar)"
legend_constants[14] = "m in component model_parameters (dimensionless)"
legend_states[4] = "PC in component PC (nanomolar)"
legend_constants[49] = "ksP in component model_parameters (first_order_rate_constant)"
legend_constants[15] = "Kp in component model_parameters (nanomolar)"
legend_constants[16] = "Kdp in component model_parameters (nanomolar)"
legend_constants[17] = "k3 in component model_parameters (second_order_rate_constant)"
legend_constants[18] = "k4 in component model_parameters (first_order_rate_constant)"
legend_constants[19] = "kdn in component model_parameters (first_order_rate_constant)"
legend_constants[50] = "V1P in component model_parameters (flux)"
legend_constants[20] = "V2P in component model_parameters (flux)"
legend_states[5] = "PCP in component PCP (nanomolar)"
legend_states[6] = "PCC in component PCC (nanomolar)"
legend_states[7] = "CC in component CC (nanomolar)"
legend_constants[51] = "ksC in component model_parameters (first_order_rate_constant)"
legend_constants[21] = "kdnc in component model_parameters (first_order_rate_constant)"
legend_constants[22] = "V1C in component model_parameters (flux)"
legend_constants[23] = "V2C in component model_parameters (flux)"
legend_states[8] = "CCP in component CCP (nanomolar)"
legend_constants[24] = "vdPC in component model_parameters (flux)"
legend_constants[25] = "Kd in component model_parameters (nanomolar)"
legend_constants[26] = "vdCC in component model_parameters (flux)"
legend_constants[27] = "k1 in component model_parameters (first_order_rate_constant)"
legend_constants[28] = "k2 in component model_parameters (first_order_rate_constant)"
legend_constants[52] = "V1PC in component model_parameters (flux)"
legend_constants[29] = "V2PC in component model_parameters (flux)"
legend_states[9] = "PCCP in component PCCP (nanomolar)"
legend_states[10] = "PCN in component PCN (nanomolar)"
legend_constants[30] = "k7 in component model_parameters (second_order_rate_constant)"
legend_constants[31] = "k8 in component model_parameters (first_order_rate_constant)"
legend_constants[53] = "V3PC in component model_parameters (flux)"
legend_constants[32] = "V4PC in component model_parameters (flux)"
legend_states[11] = "PCNP in component PCNP (nanomolar)"
legend_states[12] = "IN in component IN (nanomolar)"
legend_constants[33] = "vdPCC in component model_parameters (flux)"
legend_constants[34] = "vdPCN in component model_parameters (flux)"
legend_states[13] = "BC in component BC (nanomolar)"
legend_constants[54] = "ksB in component model_parameters (first_order_rate_constant)"
legend_constants[35] = "k5 in component model_parameters (first_order_rate_constant)"
legend_constants[36] = "k6 in component model_parameters (first_order_rate_constant)"
legend_constants[37] = "V1B in component model_parameters (flux)"
legend_constants[38] = "V2B in component model_parameters (flux)"
legend_states[14] = "BCP in component BCP (nanomolar)"
legend_constants[39] = "vdBC in component model_parameters (flux)"
legend_constants[40] = "V3B in component model_parameters (flux)"
legend_constants[41] = "V4B in component model_parameters (flux)"
legend_states[15] = "BNP in component BNP (nanomolar)"
legend_constants[42] = "vdBN in component model_parameters (flux)"
legend_constants[43] = "vdIN in component model_parameters (flux)"
legend_constants[44] = "kstot in component model_parameters (first_order_rate_constant)"
legend_constants[45] = "Vphos in component model_parameters (flux)"
legend_rates[0] = "d/dt MP in component MP (nanomolar)"
legend_rates[2] = "d/dt MC in component MC (nanomolar)"
legend_rates[3] = "d/dt MB in component MB (nanomolar)"
legend_rates[4] = "d/dt PC in component PC (nanomolar)"
legend_rates[7] = "d/dt CC in component CC (nanomolar)"
legend_rates[5] = "d/dt PCP in component PCP (nanomolar)"
legend_rates[8] = "d/dt CCP in component CCP (nanomolar)"
legend_rates[6] = "d/dt PCC in component PCC (nanomolar)"
legend_rates[10] = "d/dt PCN in component PCN (nanomolar)"
legend_rates[9] = "d/dt PCCP in component PCCP (nanomolar)"
legend_rates[11] = "d/dt PCNP in component PCNP (nanomolar)"
legend_rates[13] = "d/dt BC in component BC (nanomolar)"
legend_rates[14] = "d/dt BCP in component BCP (nanomolar)"
legend_rates[1] = "d/dt BN in component BN (nanomolar)"
legend_rates[15] = "d/dt BNP in component BNP (nanomolar)"
legend_rates[12] = "d/dt IN in component IN (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] = 1.1
constants[1] = 0.01
constants[2] = 0.7
constants[3] = 0.3
constants[4] = 1.0
constants[5] = 4.0
states[1] = 0.1
states[2] = 0.3
constants[6] = 1.0
constants[7] = 0.01
constants[8] = 1.0
constants[9] = 0.4
states[3] = 3.1
constants[10] = 0.2
constants[11] = 0.01
constants[12] = 0.8
constants[13] = 0.4
constants[14] = 4.0
states[4] = 0.1
constants[15] = 0.1
constants[16] = 0.3
constants[17] = 0.8
constants[18] = 0.2
constants[19] = 0.01
constants[20] = 0.3
states[5] = 0.1
states[6] = 0.1
states[7] = 0.1
constants[21] = 0.01
constants[22] = 0.6
constants[23] = 0.1
states[8] = 0.1
constants[24] = 0.7
constants[25] = 0.3
constants[26] = 0.7
constants[27] = 0.8
constants[28] = 0.2
constants[29] = 0.1
states[9] = 0.1
states[10] = 0.1
constants[30] = 0.5
constants[31] = 0.1
constants[32] = 0.1
states[11] = 0.1
states[12] = 0.1
constants[33] = 1.0
constants[34] = 1.0
states[13] = 0.1
constants[35] = 0.4
constants[36] = 0.2
constants[37] = 1.0
constants[38] = 0.1
states[14] = 0.1
constants[39] = 1.0
constants[40] = 1.0
constants[41] = 0.2
states[15] = 0.1
constants[42] = 0.5
constants[43] = 0.8
constants[44] = 1.0
constants[45] = 0.6
constants[46] = constants[4]
constants[47] = 0.800000*constants[4]
constants[48] = 0.700000*constants[4]
constants[49] = 0.500000*constants[44]
constants[50] = constants[45]
constants[51] = constants[44]
constants[52] = constants[45]
constants[53] = constants[45]
constants[54] = constants[44]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = constants[46]*((power(states[1], constants[5]))/(power(constants[2], constants[5])+power(states[1], constants[5])))-(constants[0]*(states[0]/(constants[3]+states[0]))+constants[1]*states[0])
rates[2] = constants[47]*((power(states[1], constants[5]))/(power(constants[8], constants[5])+power(states[1], constants[5])))-(constants[6]*(states[2]/(constants[9]+states[2]))+constants[7]*states[2])
rates[3] = constants[48]*((power(constants[12], constants[14]))/(power(constants[12], constants[14])+power(states[1], constants[14])))-(constants[10]*(states[3]/(constants[13]+states[3]))+constants[11]*states[3])
rates[4] = (constants[49]*states[0]+constants[20]*(states[5]/(constants[16]+states[5]))+constants[18]*states[6])-(constants[50]*(states[4]/(constants[15]+states[4]))+constants[17]*states[4]*states[7]+constants[19]*states[4])
rates[7] = (constants[51]*states[2]+constants[23]*(states[8]/(constants[16]+states[8]))+constants[18]*states[6])-(constants[22]*(states[7]/(constants[15]+states[7]))+constants[17]*states[4]*states[7]+constants[21]*states[7])
rates[5] = constants[50]*(states[4]/(constants[15]+states[4]))-(constants[20]*(states[5]/(constants[16]+states[5]))+constants[24]*(states[5]/(constants[25]+states[5]))+constants[19]*states[5])
rates[8] = constants[22]*(states[7]/(constants[15]+states[7]))-(constants[23]*(states[8]/(constants[16]+states[8]))+constants[26]*(states[8]/(constants[25]+states[8]))+constants[19]*states[8])
rates[6] = (constants[29]*(states[9]/(constants[16]+states[9]))+constants[17]*states[4]*states[7]+constants[28]*states[10])-(constants[52]*(states[6]/(constants[15]+states[6]))+constants[18]*states[6]+constants[27]*states[6]+constants[19]*states[6])
rates[10] = (constants[32]*(states[11]/(constants[16]+states[11]))+constants[27]*states[6]+constants[31]*states[12])-(constants[53]*(states[10]/(constants[15]+states[10]))+constants[28]*states[10]+constants[30]*states[1]*states[10]+constants[19]*states[10])
rates[9] = constants[52]*(states[6]/(constants[15]+states[6]))-(constants[29]*(states[9]/(constants[16]+states[9]))+constants[33]*(states[9]/(constants[25]+states[9]))+constants[19]*states[9])
rates[11] = constants[53]*(states[10]/(constants[15]+states[10]))-(constants[32]*(states[11]/(constants[16]+states[11]))+constants[34]*(states[11]/(constants[25]+states[11]))+constants[19]*states[11])
rates[13] = (constants[38]*(states[14]/(constants[16]+states[14]))+constants[36]*states[1]+constants[54]*states[3])-(constants[37]*(states[13]/(constants[15]+states[13]))+constants[35]*states[13]+constants[19]*states[13])
rates[14] = constants[37]*(states[13]/(constants[15]+states[13]))-(constants[38]*(states[14]/(constants[16]+states[14]))+constants[39]*(states[14]/(constants[25]+states[14]))+constants[19]*states[14])
rates[1] = (constants[41]*(states[15]/(constants[16]+states[15]))+constants[35]*states[13]+constants[31]*states[12])-(constants[40]*(states[1]/(constants[15]+states[1]))+constants[36]*states[1]+constants[30]*states[1]*states[10]+constants[19]*states[1])
rates[15] = constants[40]*(states[1]/(constants[15]+states[1]))-(constants[41]*(states[15]/(constants[16]+states[15]))+constants[42]*(states[15]/(constants[25]+states[15]))+constants[19]*states[15])
rates[12] = constants[30]*states[1]*states[10]-(constants[31]*states[12]+constants[43]*(states[12]/(constants[25]+states[12]))+constants[19]*states[12])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
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)