# 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 = 11 sizeStates = 10 sizeConstants = 27 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 (second)" legend_algebraic[2] = "Rate_Ca_influx_across_the_SR in component Ca_influx_across_the_SR (flux)" legend_constants[0] = "Ca_e in component extracellular_calcium (molar)" legend_states[0] = "Ca_f in component fuzzy_space_calcium (molar)" legend_constants[1] = "k1 in component Ca_influx_across_the_SR (first_order_rate_constant)" legend_states[1] = "Ca_2_S1 in component Ca_bound_to_the_SRRC_fast_activating_binding_site (molar)" legend_states[2] = "Ca_S2 in component Ca_bound_to_the_SRRC_slow_inactivating_binding_site (molar)" legend_states[3] = "S1 in component SRRC_fast_activating_binding_site (molar)" legend_states[4] = "S2 in component SRRC_slow_inactivating_binding_site (molar)" legend_states[5] = "Ca_s in component SR_calcium (molar)" legend_algebraic[0] = "dCa2_S1_dt in component Ca_movement_through_the_SRRC (flux)" legend_algebraic[1] = "dCa_S2_dt in component Ca_movement_through_the_SRRC (flux)" legend_constants[2] = "k_on1 in component Ca_movement_through_the_SRRC (second_order_rate_constant)" legend_constants[3] = "k_off1 in component Ca_movement_through_the_SRRC (first_order_rate_constant)" legend_constants[4] = "k_on2 in component Ca_movement_through_the_SRRC (second_order_rate_constant)" legend_constants[5] = "k_off2 in component Ca_movement_through_the_SRRC (first_order_rate_constant)" legend_constants[6] = "k_s in component Ca_movement_through_the_SRRC (first_order_rate_constant)" legend_states[6] = "cas1 in component Ca_movement_through_the_SRRC (dimensionless)" legend_states[7] = "cas2 in component Ca_movement_through_the_SRRC (dimensionless)" legend_algebraic[4] = "dcas1_dt in component Ca_movement_through_the_SRRC (first_order_rate_constant)" legend_algebraic[5] = "dcas2_dt in component Ca_movement_through_the_SRRC (first_order_rate_constant)" legend_algebraic[3] = "r_o in component Ca_movement_through_the_SRRC (dimensionless)" legend_algebraic[6] = "Rate_Ca_movement_through_the_SRRC in component Ca_movement_through_the_SRRC (flux)" legend_constants[7] = "Km_NaCaX in component Ca_efflux_across_the_SR_by_NaCa_exchange (molar)" legend_constants[8] = "Vmax_NaCaX in component Ca_efflux_across_the_SR_by_NaCa_exchange (flux)" legend_algebraic[7] = "Rate_Ca_efflux_across_the_SR_by_NaCa_exchange in component Ca_efflux_across_the_SR_by_NaCa_exchange (flux)" legend_states[8] = "Ca_c in component cytosolic_calcium (molar)" legend_constants[9] = "kf in component Ca_movement_between_the_fuzzy_space_and_cytosol (first_order_rate_constant)" legend_algebraic[8] = "Rate_Ca_movement_between_the_fuzzy_space_and_cytosol in component Ca_movement_between_the_fuzzy_space_and_cytosol (flux)" legend_constants[10] = "Km_s in component Ca_uptake_by_SR_Ca_ATPase (molar)" legend_constants[11] = "Vmax_s in component Ca_uptake_by_SR_Ca_ATPase (flux)" legend_algebraic[9] = "Rate_Ca_uptake_by_SR_Ca_ATPase in component Ca_uptake_by_SR_Ca_ATPase (flux)" legend_states[9] = "Ca_CSQ in component calsequestrin_bound_calcium (molar)" legend_constants[12] = "K_ons in component Ca_buffering_in_the_SR (second_order_rate_constant)" legend_constants[13] = "K_offs in component Ca_buffering_in_the_SR (first_order_rate_constant)" legend_constants[14] = "Bmax_s in component Ca_buffering_in_the_SR (molar)" legend_algebraic[10] = "Rate_Ca_buffering_in_the_SR in component Ca_buffering_in_the_SR (flux)" legend_constants[15] = "Rt in component fuzzy_space_calcium (molar)" legend_constants[16] = "Bmax_f1 in component fuzzy_space_calcium (molar)" legend_constants[17] = "Bmax_f2 in component fuzzy_space_calcium (molar)" legend_constants[18] = "Kb_f1 in component fuzzy_space_calcium (molar)" legend_constants[19] = "Kb_f2 in component fuzzy_space_calcium (molar)" legend_constants[20] = "V_f in component fuzzy_space_calcium (dimensionless)" legend_constants[21] = "Bmax_c in component cytosolic_calcium (molar)" legend_constants[22] = "dye_c in component cytosolic_calcium (molar)" legend_constants[23] = "Kb_c in component cytosolic_calcium (molar)" legend_constants[24] = "Kb_dye in component cytosolic_calcium (molar)" legend_constants[25] = "V_c in component cytosolic_calcium (dimensionless)" legend_constants[26] = "V_s in component SR_calcium (dimensionless)" legend_rates[6] = "d/dt cas1 in component Ca_movement_through_the_SRRC (dimensionless)" legend_rates[7] = "d/dt cas2 in component Ca_movement_through_the_SRRC (dimensionless)" legend_rates[0] = "d/dt Ca_f in component fuzzy_space_calcium (molar)" legend_rates[8] = "d/dt Ca_c in component cytosolic_calcium (molar)" legend_rates[5] = "d/dt Ca_s in component SR_calcium (molar)" legend_rates[9] = "d/dt Ca_CSQ in component calsequestrin_bound_calcium (molar)" legend_rates[3] = "d/dt S1 in component SRRC_fast_activating_binding_site (molar)" legend_rates[4] = "d/dt S2 in component SRRC_slow_inactivating_binding_site (molar)" legend_rates[1] = "d/dt Ca_2_S1 in component Ca_bound_to_the_SRRC_fast_activating_binding_site (molar)" legend_rates[2] = "d/dt Ca_S2 in component Ca_bound_to_the_SRRC_slow_inactivating_binding_site (molar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 0.002 states[0] = 0.12e-6 constants[1] = 0.2 states[1] = 0 states[2] = 0 states[3] = 0 states[4] = 0 states[5] = 201e-6 constants[2] = 2000000000 constants[3] = 1400 constants[4] = 13000000 constants[5] = 3.9 constants[6] = 9 states[6] = 0 states[7] = 0 constants[7] = 0.000036 constants[8] = 0.0012 states[8] = 1e-7 constants[9] = 2500 constants[10] = 0.00000025 constants[11] = 0.000525 states[9] = 0 constants[12] = 8772 constants[13] = 5.596536 constants[14] = 0.008 constants[15] = 0.00000015 constants[16] = 0.0002 constants[17] = 0.0011 constants[18] = 0.000017 constants[19] = 0.000013 constants[20] = 0.0013 constants[21] = 0.00012 constants[22] = 0 constants[23] = 0.00000096 constants[24] = 2e-7 constants[25] = 0.9287 constants[26] = 0.07 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = constants[2]*states[0]*states[3]-((power(constants[3], 2.00000))/(constants[2]*states[0]))*states[1] rates[3] = -algebraic[0] algebraic[1] = constants[4]*states[0]*states[4]-constants[5]*states[2] rates[4] = -algebraic[1] rates[1] = algebraic[0] rates[2] = algebraic[1] algebraic[4] = constants[2]*states[0]*(1.00000-states[6])-((power(constants[3], 2.00000))/(constants[2]*states[0]))*states[6] rates[6] = algebraic[4] algebraic[5] = constants[4]*states[0]*(1.00000-states[7])-constants[5]*states[7] rates[7] = algebraic[5] algebraic[2] = constants[1]*(constants[0]-states[0]) algebraic[3] = states[6]*(1.00000-states[7]) algebraic[6] = constants[6]*algebraic[3]*(states[5]-states[0]) algebraic[7] = (constants[8]*states[0])/(constants[7]+states[0]) algebraic[8] = constants[9]*(states[0]-states[8]) rates[0] = ((algebraic[6]-(constants[15]*(algebraic[4]+algebraic[5])+algebraic[8]+algebraic[7]))+algebraic[2])/((constants[16]*constants[18])/(power(states[0]+constants[18], 2.00000))+(constants[17]*constants[19])/(power(states[0]+constants[19], 2.00000))+constants[20]) algebraic[9] = (constants[11]*(power(states[8], 2.00000)-(power(states[5], 2.00000))/(power(7000.00, 2.00000))))/(power(constants[10], 2.00000)+power(states[8], 2.00000)+(power(states[5], 2.00000))/(power(7000.00, 2.00000))) rates[8] = (algebraic[8]-algebraic[9])/((constants[21]*constants[23])/(power(states[8]+constants[23], 2.00000))+(constants[22]*constants[24])/(power(states[8]+constants[24], 2.00000))+constants[25]) algebraic[10] = constants[12]*states[5]*(constants[14]-states[9])-constants[13]*states[9] rates[5] = (algebraic[9]-algebraic[6])/constants[26]-algebraic[10] rates[9] = algebraic[10] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = constants[2]*states[0]*states[3]-((power(constants[3], 2.00000))/(constants[2]*states[0]))*states[1] algebraic[1] = constants[4]*states[0]*states[4]-constants[5]*states[2] algebraic[4] = constants[2]*states[0]*(1.00000-states[6])-((power(constants[3], 2.00000))/(constants[2]*states[0]))*states[6] algebraic[5] = constants[4]*states[0]*(1.00000-states[7])-constants[5]*states[7] algebraic[2] = constants[1]*(constants[0]-states[0]) algebraic[3] = states[6]*(1.00000-states[7]) algebraic[6] = constants[6]*algebraic[3]*(states[5]-states[0]) algebraic[7] = (constants[8]*states[0])/(constants[7]+states[0]) algebraic[8] = constants[9]*(states[0]-states[8]) algebraic[9] = (constants[11]*(power(states[8], 2.00000)-(power(states[5], 2.00000))/(power(7000.00, 2.00000))))/(power(constants[10], 2.00000)+power(states[8], 2.00000)+(power(states[5], 2.00000))/(power(7000.00, 2.00000))) algebraic[10] = constants[12]*states[5]*(constants[14]-states[9])-constants[13]*states[9] 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)