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 = 25
sizeStates = 7
sizeConstants = 30
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_constants[0] = "concentration in component Subtilin (nM)"
legend_constants[1] = "RNA1 in component SpeciesInitialConcentrations (nM)"
legend_constants[2] = "RNA2 in component SpeciesInitialConcentrations (nM)"
legend_constants[3] = "spaK in component SpeciesInitialConcentrations (nM)"
legend_constants[4] = "spaR in component SpeciesInitialConcentrations (nM)"
legend_constants[5] = "spaKactive in component SpeciesInitialConcentrations (nM)"
legend_constants[6] = "spaRactive in component SpeciesInitialConcentrations (nM)"
legend_constants[7] = "GFP in component SpeciesInitialConcentrations (nM)"
legend_constants[29] = "JRNA in component Template_Promoter_Constitutive (nM_per_s)"
legend_algebraic[4] = "JGain in component RNA1_interface (nM_per_s)"
legend_algebraic[0] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[11] = "J in component Template_ProteinCDS (nM_per_s)"
legend_algebraic[18] = "J in component Template_RxR2P1 (nM_per_s)"
legend_algebraic[15] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[13] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[14] = "J in component Template_RxR2P1 (nM_per_s)"
legend_algebraic[19] = "JGain in component spaK_interface (nM_per_s)"
legend_algebraic[16] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[20] = "JGain in component spaKactive_interface (nM_per_s)"
legend_algebraic[5] = "J in component Template_ProteinCDS (nM_per_s)"
legend_algebraic[17] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[21] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[22] = "JGain in component spaR_interface (nM_per_s)"
legend_algebraic[23] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[24] = "JGain in component spaRactive_interface (nM_per_s)"
legend_algebraic[2] = "JRNA in component Template_Promoter_Inductive (nM_per_s)"
legend_algebraic[9] = "JGain in component RNA2_interface (nM_per_s)"
legend_algebraic[6] = "J in component Template_RxR1P1 (nM_per_s)"
legend_algebraic[7] = "J in component Template_ProteinCDS (nM_per_s)"
legend_algebraic[12] = "JGain in component GFP_interface (nM_per_s)"
legend_algebraic[10] = "J in component Template_RxR1P1 (nM_per_s)"
legend_constants[8] = "cellVolume in component Chassis_Bacillus (femtoliter)"
legend_voi = "time in component Time (second)"
legend_constants[9] = "k in component Bugbuster_Promoter1 (PoPs)"
legend_states[0] = "concentration in component Template_Species (nM)"
legend_constants[10] = "kDecay in component Bioenvironment_Degradation_BugbusterRNA1 (per_s)"
legend_algebraic[1] = "RNARiPs in component Template_RBS (RiPsInAttoMoles)"
legend_constants[11] = "k in component Bugbuster_RBS_spaR (RiPs)"
legend_algebraic[8] = "RNARiPs in component Template_RBS (RiPsInAttoMoles)"
legend_constants[12] = "k in component Bugbuster_RBS_spaK (RiPs)"
legend_states[1] = "concentration in component Template_Species (nM)"
legend_constants[13] = "kDecay in component Bioenvironment_Degradation_spaK (per_s)"
legend_constants[14] = "k in component Bioenvironment_RxR2P1_spaKActivation (per_nM_per_s)"
legend_states[2] = "concentration in component Template_Species (nM)"
legend_constants[15] = "k in component Bioenvironment_Dephosphorylation_spaKactive (per_s)"
legend_constants[16] = "kDecay in component Bioenvironment_Degradation_spaKactive (per_s)"
legend_states[3] = "concentration in component Template_Species (nM)"
legend_constants[17] = "kDecay in component Bioenvironment_Degradation_spaR (per_s)"
legend_constants[18] = "k in component Bioenvironment_RxR2P1_spaRActivation (per_nM_per_s)"
legend_states[4] = "concentration in component Template_Species (nM)"
legend_constants[19] = "k in component Bioenvironment_Dephosphorylation_spaRactive (per_s)"
legend_constants[20] = "kDecay in component Bioenvironment_Degradation_spaRactive (per_s)"
legend_constants[21] = "k in component Bugbuster_Promoter2 (PoPs)"
legend_constants[22] = "n in component Bugbuster_Promoter2 (dimensionless)"
legend_constants[23] = "Km in component Bugbuster_Promoter2 (nM)"
legend_states[5] = "concentration in component Template_Species (nM)"
legend_constants[24] = "kDecay in component Bioenvironment_Degradation_BugbusterRNA2 (per_s)"
legend_algebraic[3] = "RNARiPs in component Template_RBS (RiPsInAttoMoles)"
legend_constants[25] = "k in component Bugbuster_RBS_GFP (RiPs)"
legend_states[6] = "concentration in component Template_Species (nM)"
legend_constants[26] = "kDecay in component Bioenvironment_Degradation_GFP (per_s)"
legend_constants[27] = "avogadrosConstant in component Template_Promoter_Constitutive (per_mole)"
legend_constants[28] = "avogadrosConstant in component Template_Promoter_Inductive (per_mole)"
legend_rates[0] = "d/dt concentration in component Template_Species (nM)"
legend_rates[1] = "d/dt concentration in component Template_Species (nM)"
legend_rates[2] = "d/dt concentration in component Template_Species (nM)"
legend_rates[3] = "d/dt concentration in component Template_Species (nM)"
legend_rates[4] = "d/dt concentration in component Template_Species (nM)"
legend_rates[5] = "d/dt concentration in component Template_Species (nM)"
legend_rates[6] = "d/dt concentration in component Template_Species (nM)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 1000
constants[1] = 0
constants[2] = 0
constants[3] = 0
constants[4] = 0
constants[5] = 0
constants[6] = 0
constants[7] = 0
constants[8] = 1
constants[9] = 0.04
constants[10] = 0.0058
constants[11] = 0.1
constants[12] = 0.1818
constants[13] = 0.0012
constants[14] = 1e-4
constants[15] = 0.1
constants[16] = 0.0012
constants[17] = 0.0012
constants[18] = 1e-4
constants[19] = 0.1
constants[20] = 0.0012
constants[21] = 0.04
constants[22] = 2
constants[23] = 320
constants[24] = 0.0058
constants[25] = 0.145
constants[26] = 0.0012
constants[27] = 6.0221415e23
constants[28] = 6.0221415e23
constants[29] = constants[9]*1.00000e+09/(constants[8]*1.00000e-15*constants[27])
states[0] = constants[1]
states[1] = constants[3]
states[2] = constants[5]
states[3] = constants[4]
states[4] = constants[6]
states[5] = constants[2]
states[6] = constants[7]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = constants[10]*states[0]
algebraic[4] = constants[29]-algebraic[0]
rates[0] = algebraic[4]
algebraic[2] = constants[21]*states[4]**constants[22]/(constants[23]**constants[22]+states[4]**constants[22])*1.00000e+09/(constants[8]*1.00000e-15*constants[28])
algebraic[6] = constants[24]*states[5]
algebraic[9] = algebraic[2]-algebraic[6]
rates[5] = algebraic[9]
algebraic[3] = 1.00000e+09*constants[25]*states[5]*constants[8]*1.00000e-15
algebraic[7] = 1.00000e+06*algebraic[3]/constants[8]
algebraic[10] = constants[26]*states[6]
algebraic[12] = algebraic[7]-algebraic[10]
rates[6] = algebraic[12]
algebraic[8] = 1.00000e+09*constants[12]*states[0]*constants[8]*1.00000e-15
algebraic[11] = 1.00000e+06*algebraic[8]/constants[8]
algebraic[18] = states[2]*states[3]*constants[18]
algebraic[15] = constants[15]*states[2]
algebraic[13] = constants[13]*states[1]
algebraic[14] = constants[0]*states[1]*constants[14]
algebraic[19] = algebraic[11]+algebraic[18]+algebraic[15]-(algebraic[14]+algebraic[13])
rates[1] = algebraic[19]
algebraic[16] = constants[16]*states[2]
algebraic[20] = algebraic[14]-algebraic[16]+algebraic[15]+algebraic[18]
rates[2] = algebraic[20]
algebraic[1] = 1.00000e+09*constants[11]*states[0]*constants[8]*1.00000e-15
algebraic[5] = 1.00000e+06*algebraic[1]/constants[8]
algebraic[17] = constants[17]*states[3]
algebraic[21] = constants[19]*states[4]
algebraic[22] = algebraic[5]+algebraic[21]-(algebraic[17]+algebraic[18])
rates[3] = algebraic[22]
algebraic[23] = constants[20]*states[4]
algebraic[24] = algebraic[18]-algebraic[23]+algebraic[21]
rates[4] = algebraic[24]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[10]*states[0]
algebraic[4] = constants[29]-algebraic[0]
algebraic[2] = constants[21]*states[4]**constants[22]/(constants[23]**constants[22]+states[4]**constants[22])*1.00000e+09/(constants[8]*1.00000e-15*constants[28])
algebraic[6] = constants[24]*states[5]
algebraic[9] = algebraic[2]-algebraic[6]
algebraic[3] = 1.00000e+09*constants[25]*states[5]*constants[8]*1.00000e-15
algebraic[7] = 1.00000e+06*algebraic[3]/constants[8]
algebraic[10] = constants[26]*states[6]
algebraic[12] = algebraic[7]-algebraic[10]
algebraic[8] = 1.00000e+09*constants[12]*states[0]*constants[8]*1.00000e-15
algebraic[11] = 1.00000e+06*algebraic[8]/constants[8]
algebraic[18] = states[2]*states[3]*constants[18]
algebraic[15] = constants[15]*states[2]
algebraic[13] = constants[13]*states[1]
algebraic[14] = constants[0]*states[1]*constants[14]
algebraic[19] = algebraic[11]+algebraic[18]+algebraic[15]-(algebraic[14]+algebraic[13])
algebraic[16] = constants[16]*states[2]
algebraic[20] = algebraic[14]-algebraic[16]+algebraic[15]+algebraic[18]
algebraic[1] = 1.00000e+09*constants[11]*states[0]*constants[8]*1.00000e-15
algebraic[5] = 1.00000e+06*algebraic[1]/constants[8]
algebraic[17] = constants[17]*states[3]
algebraic[21] = constants[19]*states[4]
algebraic[22] = algebraic[5]+algebraic[21]-(algebraic[17]+algebraic[18])
algebraic[23] = constants[20]*states[4]
algebraic[24] = algebraic[18]-algebraic[23]+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)