Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =2;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 30 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_VOI = strpad('time in component environment (hour)');
LEGEND_CONSTANTS(:,30) = strpad('F_c in component gastrointestinal_compartment_L_dopa (dimensionless)');
LEGEND_STATES(:,1) = strpad('A_dopa_c in component gastrointestinal_compartment_L_dopa (umole)');
LEGEND_CONSTANTS(:,1) = strpad('ka_c in component gastrointestinal_compartment_L_dopa (per_hour)');
LEGEND_CONSTANTS(:,22) = strpad('F_G in component gastrointestinal_compartment_L_dopa (dimensionless)');
LEGEND_CONSTANTS(:,29) = strpad('F_H in component gastrointestinal_compartment_L_dopa (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('CL_H in component gastrointestinal_compartment_L_dopa (liter_per_hour)');
LEGEND_CONSTANTS(:,2) = strpad('Q in component gastrointestinal_compartment_L_dopa (liter_per_hour)');
LEGEND_CONSTANTS(:,3) = strpad('f_H in component gastrointestinal_compartment_L_dopa (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('CL_dopa_0 in component L_dopa_clearance (liter_per_hour)');
LEGEND_STATES(:,2) = strpad('C_dopa_c in component body_compartment_L_dopa (uM)');
LEGEND_CONSTANTS(:,5) = strpad('V_dopa in component body_compartment_L_dopa (liter)');
LEGEND_ALGEBRAIC(:,2) = strpad('CL_dopa in component L_dopa_clearance (liter_per_hour)');
LEGEND_STATES(:,3) = strpad('C_OMD_c in component body_compartment_3_OMD (uM)');
LEGEND_CONSTANTS(:,6) = strpad('CL_OMD_c in component body_compartment_3_OMD (liter_per_hour)');
LEGEND_CONSTANTS(:,7) = strpad('V_OMD_c in component body_compartment_3_OMD (liter)');
LEGEND_CONSTANTS(:,23) = strpad('CL_COMT in component L_dopa_clearance (liter_per_hour)');
LEGEND_ALGEBRAIC(:,1) = strpad('CL_AADC in component L_dopa_clearance (liter_per_hour)');
LEGEND_CONSTANTS(:,24) = strpad('CL_AADC0 in component L_dopa_clearance (liter_per_hour)');
LEGEND_STATES(:,4) = strpad('C_Ro_central in component central_compartment_Ro (uM)');
LEGEND_CONSTANTS(:,27) = strpad('CL_REST in component L_dopa_clearance (liter_per_hour)');
LEGEND_CONSTANTS(:,8) = strpad('ki in component L_dopa_clearance (uM)');
LEGEND_STATES(:,5) = strpad('A_bens in component gastrointestinal_compartment_benserazide (umole)');
LEGEND_CONSTANTS(:,9) = strpad('ka_B in component gastrointestinal_compartment_benserazide (per_hour)');
LEGEND_CONSTANTS(:,10) = strpad('F_B in component gastrointestinal_compartment_benserazide (dimensionless)');
LEGEND_STATES(:,6) = strpad('C_bens_central in component central_compartment_benserazide (uM)');
LEGEND_CONSTANTS(:,11) = strpad('V1_B in component central_compartment_benserazide (liter)');
LEGEND_CONSTANTS(:,12) = strpad('CLd_B in component central_compartment_benserazide (liter_per_hour)');
LEGEND_STATES(:,7) = strpad('C_bens_peripheral in component peripheral_compartment_benserazide (uM)');
LEGEND_CONSTANTS(:,25) = strpad('CL_bens_total in component benserazide_clearance (liter_per_hour)');
LEGEND_CONSTANTS(:,13) = strpad('V2_B in component peripheral_compartment_benserazide (liter)');
LEGEND_CONSTANTS(:,28) = strpad('CL_Ro in component benserazide_clearance (liter_per_hour)');
LEGEND_CONSTANTS(:,14) = strpad('CL_B in component benserazide_clearance (liter_per_hour)');
LEGEND_CONSTANTS(:,15) = strpad('fm in component benserazide_clearance (dimensionless)');
LEGEND_STATES(:,8) = strpad('A_Ro in component gastrointestinal_compartment_Ro (umole)');
LEGEND_CONSTANTS(:,16) = strpad('ka_M in component gastrointestinal_compartment_Ro (per_hour)');
LEGEND_CONSTANTS(:,17) = strpad('F_Ro in component gastrointestinal_compartment_Ro (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('V1_M in component central_compartment_Ro (liter)');
LEGEND_CONSTANTS(:,19) = strpad('CLd_M in component central_compartment_Ro (liter_per_hour)');
LEGEND_CONSTANTS(:,20) = strpad('CL_M in component central_compartment_Ro (liter_per_hour)');
LEGEND_STATES(:,9) = strpad('C_Ro_peripheral in component peripheral_compartment_Ro (uM)');
LEGEND_CONSTANTS(:,21) = strpad('V2_M in component peripheral_compartment_Ro (liter)');
LEGEND_RATES(:,1) = strpad('d/dt A_dopa_c in component gastrointestinal_compartment_L_dopa (umole)');
LEGEND_RATES(:,2) = strpad('d/dt C_dopa_c in component body_compartment_L_dopa (uM)');
LEGEND_RATES(:,3) = strpad('d/dt C_OMD_c in component body_compartment_3_OMD (uM)');
LEGEND_RATES(:,5) = strpad('d/dt A_bens in component gastrointestinal_compartment_benserazide (umole)');
LEGEND_RATES(:,6) = strpad('d/dt C_bens_central in component central_compartment_benserazide (uM)');
LEGEND_RATES(:,7) = strpad('d/dt C_bens_peripheral in component peripheral_compartment_benserazide (uM)');
LEGEND_RATES(:,8) = strpad('d/dt A_Ro in component gastrointestinal_compartment_Ro (umole)');
LEGEND_RATES(:,4) = strpad('d/dt C_Ro_central in component central_compartment_Ro (uM)');
LEGEND_RATES(:,9) = strpad('d/dt C_Ro_peripheral in component peripheral_compartment_Ro (uM)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
STATES(:,1) = 101;
CONSTANTS(:,1) = 1.29;
CONSTANTS(:,2) = 0.828;
CONSTANTS(:,3) = 0.13;
CONSTANTS(:,4) = 0.823;
STATES(:,2) = 0;
CONSTANTS(:,5) = 0.496;
STATES(:,3) = 0;
CONSTANTS(:,6) = 0.00895;
CONSTANTS(:,7) = 0.128;
STATES(:,4) = 0;
CONSTANTS(:,8) = 0.00246;
STATES(:,5) = 19.51;
CONSTANTS(:,9) = 0.94;
CONSTANTS(:,10) = 0.022;
STATES(:,6) = 0;
CONSTANTS(:,11) = 0.202;
CONSTANTS(:,12) = 0.072;
STATES(:,7) = 0;
CONSTANTS(:,13) = 0.127;
CONSTANTS(:,14) = 1.67;
CONSTANTS(:,15) = 0.15;
STATES(:,8) = 1.3658;
CONSTANTS(:,16) = 2.47;
CONSTANTS(:,17) = 1;
CONSTANTS(:,18) = 0.0691;
CONSTANTS(:,19) = 1.06;
CONSTANTS(:,20) = 4.29;
STATES(:,9) = 0;
CONSTANTS(:,21) = 3.2;
CONSTANTS(:,22) = 1.00000;
CONSTANTS(:,23) = CONSTANTS(:,4).*0.100000;
CONSTANTS(:,24) = CONSTANTS(:,4).*0.690000;
CONSTANTS(:,25) = CONSTANTS(:,14)./(1.00000 - CONSTANTS(:,15));
CONSTANTS(:,26) = CONSTANTS(:,3).*CONSTANTS(:,4);
CONSTANTS(:,27) = CONSTANTS(:,4).*0.210000;
CONSTANTS(:,28) = CONSTANTS(:,25).*CONSTANTS(:,15);
CONSTANTS(:,29) = 1.00000 - CONSTANTS(:,26)./CONSTANTS(:,2);
CONSTANTS(:,30) = CONSTANTS(:,29).*CONSTANTS(:,22);
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
RATES(:,1) = - CONSTANTS(:,1).*STATES(:,1);
RATES(:,3) = (1.00000./CONSTANTS(:,7)).*( CONSTANTS(:,23).*STATES(:,2) - CONSTANTS(:,6).*STATES(:,3));
RATES(:,5) = - CONSTANTS(:,9).*STATES(:,5);
RATES(:,6) = (1.00000./CONSTANTS(:,11)).*(( CONSTANTS(:,9).*STATES(:,5).*CONSTANTS(:,10) - CONSTANTS(:,25).*STATES(:,6))+ CONSTANTS(:,12).*(STATES(:,7) - STATES(:,6)));
RATES(:,7) = (1.00000./CONSTANTS(:,13)).*( CONSTANTS(:,12).*(STATES(:,6) - STATES(:,7)));
RATES(:,8) = - CONSTANTS(:,16).*STATES(:,8);
RATES(:,4) = (1.00000./CONSTANTS(:,18)).*(( CONSTANTS(:,16).*STATES(:,8).*CONSTANTS(:,17) - CONSTANTS(:,20).*STATES(:,4))+ CONSTANTS(:,28).*STATES(:,6)+ CONSTANTS(:,19).*(STATES(:,9) - STATES(:,4)));
RATES(:,9) = (1.00000./CONSTANTS(:,21)).*( CONSTANTS(:,19).*(STATES(:,4) - STATES(:,9)));
ALGEBRAIC(:,1) = CONSTANTS(:,24)./(1.00000+STATES(:,4)./CONSTANTS(:,8));
ALGEBRAIC(:,2) = ALGEBRAIC(:,1)+CONSTANTS(:,23)+CONSTANTS(:,27);
RATES(:,2) = (1.00000./CONSTANTS(:,5)).*( CONSTANTS(:,1).*STATES(:,1).*CONSTANTS(:,30) - ALGEBRAIC(:,2).*STATES(:,2));
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,1) = CONSTANTS(:,24)./(1.00000+STATES(:,4)./CONSTANTS(:,8));
ALGEBRAIC(:,2) = ALGEBRAIC(:,1)+CONSTANTS(:,23)+CONSTANTS(:,27);
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end