# 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 = 6 sizeStates = 4 sizeConstants = 17 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 temporalExistence (second)" legend_constants[0] = "alphaTF in component Device_TFgenerator (uM_per_second)" legend_constants[14] = "JTF in component Device_TFgenerator (uM_per_second)" legend_states[0] = "TFS in component BioEnv_TFSAssociation (uM)" legend_algebraic[5] = "Jgain_TF in component BioEnv_TFSAssociation_interface (uM_per_second)" legend_constants[15] = "Jgain_TFS in component BioEnv_TFSAssociation_interface (uM_per_second)" legend_algebraic[3] = "JTF in component Device_PhzMSgenerator (uM_per_second)" legend_states[1] = "TF in component BioEnv_TFSAssociation (uM)" legend_constants[1] = "s in component BioEnv_TFSAssociation (uM)" legend_constants[2] = "betaTFS in component BioEnv_TFSAssociation (per_uM_per_second)" legend_constants[3] = "kd in component BioEnv_TFSAssociation (per_second)" legend_constants[4] = "deltaTFS in component BioEnv_TFSAssociation (per_second)" legend_constants[5] = "deltaTF in component BioEnv_TFSAssociation (per_second)" legend_algebraic[0] = "Jassociation in component BioEnv_TFSAssociation (uM_per_second)" legend_constants[6] = "gammaPhzMS in component Device_PhzMSgenerator (uM)" legend_constants[7] = "betaPhzMS in component Device_PhzMSgenerator (uM_per_second)" legend_algebraic[1] = "JPhzMS in component Device_PhzMSgenerator (uM_per_second)" legend_constants[8] = "gammaTF in component Device_PhzMSgenerator (uM)" legend_constants[9] = "betaTF in component Device_PhzMSgenerator (uM_per_second)" legend_constants[10] = "feedbackOn in component Device_PhzMSgenerator (dimensionless)" legend_algebraic[4] = "Jgain_PhzMS in component BioEnv_PhzMStoPYO_interface (uM_per_second)" legend_constants[16] = "Jgain_PYO in component BioEnv_PhzMStoPYO_interface (uM_per_second)" legend_states[2] = "PhzMS in component BioEnv_PhzMStoPYO (uM)" legend_states[3] = "PYO in component BioEnv_PhzMStoPYO (uM)" legend_constants[11] = "deltaPhzMS in component BioEnv_PhzMStoPYO (per_second)" legend_constants[12] = "alphaPYO in component BioEnv_PhzMStoPYO (per_second)" legend_constants[13] = "deltaPYO in component BioEnv_PhzMStoPYO (per_second)" legend_algebraic[2] = "JPYOformation in component BioEnv_PhzMStoPYO (uM_per_second)" legend_rates[1] = "d/dt TF in component BioEnv_TFSAssociation (uM)" legend_rates[0] = "d/dt TFS in component BioEnv_TFSAssociation (uM)" legend_rates[2] = "d/dt PhzMS in component BioEnv_PhzMStoPYO (uM)" legend_rates[3] = "d/dt PYO in component BioEnv_PhzMStoPYO (uM)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 0.05 states[0] = 0 states[1] = 8.6207 constants[1] = 5 constants[2] = 1e6 constants[3] = 4e6 constants[4] = 3.851e-4 constants[5] = 5.8e-3 constants[6] = 5 constants[7] = 0.1 constants[8] = 4 constants[9] = 0.07 constants[10] = 1 states[2] = 0 states[3] = 0 constants[11] = 8.0225e-6 constants[12] = 1.3 constants[13] = 5.8e-1 constants[14] = constants[0] constants[15] = 0.00000 constants[16] = 0.00000 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = constants[2]*constants[1]*states[1]-constants[3]*states[0] rates[0] = (algebraic[0]-constants[4]*states[0])+constants[15] algebraic[2] = constants[12]*states[2] rates[3] = (constants[16]-constants[13]*states[3])+algebraic[2] algebraic[1] = (constants[7]*states[0])/(constants[6]+states[0]) algebraic[4] = algebraic[1] rates[2] = algebraic[4]-constants[11]*states[2] algebraic[3] = custom_piecewise([constants[10] != 0.00000, (constants[9]*states[0])/(constants[8]+states[0]) , True, 0.00000]) algebraic[5] = constants[14]+algebraic[3] rates[1] = (-algebraic[0]+algebraic[5])-constants[5]*states[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = constants[2]*constants[1]*states[1]-constants[3]*states[0] algebraic[2] = constants[12]*states[2] algebraic[1] = (constants[7]*states[0])/(constants[6]+states[0]) algebraic[4] = algebraic[1] algebraic[3] = custom_piecewise([constants[10] != 0.00000, (constants[9]*states[0])/(constants[8]+states[0]) , True, 0.00000]) algebraic[5] = constants[14]+algebraic[3] 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)