# 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 = 0 sizeStates = 9 sizeConstants = 20 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_voi = "t in component environment (s)" legend_constants[0] = "kf1 in component PKC (per_s)" legend_constants[1] = "kb1 in component PKC (per_s)" legend_constants[2] = "kf2 in component PKC (per_um_s)" legend_constants[3] = "kb2 in component PKC (per_s)" legend_constants[4] = "kf3 in component PKC (per_s)" legend_constants[5] = "kb3 in component PKC (per_s)" legend_constants[6] = "kf4 in component PKC (per_um_s)" legend_constants[7] = "kb4 in component PKC (per_s)" legend_constants[8] = "kf5 in component PKC (per_s)" legend_constants[9] = "kb5 in component PKC (per_s)" legend_constants[10] = "kf6 in component PKC (per_s)" legend_constants[11] = "kb6 in component PKC (per_s)" legend_constants[12] = "kf7 in component PKC (per_um_s)" legend_constants[13] = "kb7 in component PKC (per_s)" legend_constants[14] = "kf8 in component PKC (per_um_s)" legend_constants[15] = "kb8 in component PKC (per_s)" legend_constants[16] = "kf9 in component PKC (per_um_s)" legend_constants[17] = "kb9 in component PKC (per_s)" legend_constants[18] = "kf10 in component PKC (per_um_s)" legend_constants[19] = "kb10 in component PKC (per_s)" legend_states[0] = "PKC_i in component PKC (um)" legend_states[1] = "AA in component PKC (um)" legend_states[2] = "DAG in component PKC (um)" legend_states[3] = "Ca in component PKC (um)" legend_states[4] = "DAGPKC in component PKC (um)" legend_states[5] = "AADAGPKC in component PKC (um)" legend_states[6] = "DAGCaPKC in component PKC (um)" legend_states[7] = "CaPKC in component PKC (um)" legend_states[8] = "PKC_a in component PKC (um)" legend_rates[0] = "d/dt PKC_i in component PKC (um)" legend_rates[4] = "d/dt DAGPKC in component PKC (um)" legend_rates[5] = "d/dt AADAGPKC in component PKC (um)" legend_rates[7] = "d/dt CaPKC in component PKC (um)" legend_rates[6] = "d/dt DAGCaPKC in component PKC (um)" legend_rates[8] = "d/dt PKC_a in component PKC (um)" legend_rates[1] = "d/dt AA in component PKC (um)" legend_rates[2] = "d/dt DAG in component PKC (um)" legend_rates[3] = "d/dt Ca in component PKC (um)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 1 constants[1] = 50 constants[2] = 0.0000000002 constants[3] = 0.1 constants[4] = 1.2705 constants[5] = 3.5026 constants[6] = 0.000000002 constants[7] = 0.1 constants[8] = 1 constants[9] = 0.1 constants[10] = 2 constants[11] = 0.2 constants[12] = 0.000001 constants[13] = 0.5 constants[14] = 0.000000013333 constants[15] = 8.6348 constants[16] = 0.000000001 constants[17] = 0.1 constants[18] = 0.00000003 constants[19] = 2 states[0] = 1 states[1] = 1 states[2] = 0.1 states[3] = 0.1 states[4] = 0 states[5] = 0 states[6] = 0 states[7] = 0 states[8] = 0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = ((((((-states[0]*constants[0]+states[8]*constants[1])-states[0]*states[1]*constants[2])+states[8]*constants[3])-states[0]*states[2]*constants[16])+states[4]*constants[17])-states[0]*states[3]*constants[12])+states[7]*constants[13] rates[4] = ((states[0]*states[2]*constants[16]-states[4]*constants[17])-states[4]*states[1]*constants[18])+states[5]*constants[19] rates[5] = ((states[4]*states[1]*constants[18]-states[5]*constants[19])-states[5]*constants[10])+states[8]*constants[11] rates[7] = ((((((states[0]*states[3]*constants[12]-states[7]*constants[13])-states[7]*constants[4])+states[8]*constants[5])-states[7]*states[1]*constants[6])+states[8]*constants[7])-states[2]*states[7]*constants[14])+states[6]*constants[15] rates[6] = ((states[2]*states[7]*constants[14]-states[6]*constants[15])-states[6]*constants[8])+states[8]*constants[9] rates[8] = ((((((((((states[0]*constants[0]-states[8]*constants[1])+states[0]*states[1]*constants[2])-states[8]*constants[3])+states[7]*constants[4])-states[8]*constants[5])+states[7]*states[1]*constants[6])-states[8]*constants[7])+states[6]*constants[8])-states[8]*constants[9])+states[5]*constants[10])-states[8]*constants[11] rates[1] = ((((-states[0]*states[1]*constants[2]+states[8]*constants[3])-states[7]*states[1]*constants[6])+states[8]*constants[7])-states[4]*states[1]*constants[18])+states[5]*constants[19] rates[2] = ((-states[0]*states[2]*constants[16]+states[4]*constants[17])-states[2]*states[7]*constants[14])+states[6]*constants[15] rates[3] = -states[0]*states[3]*constants[12]+states[7]*constants[13] 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)