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 5 entries in each of the rate and state variable arrays.
% There are a total of 35 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_STATES(:,1) = strpad('GH in component GH (ng_ml)');
LEGEND_CONSTANTS(:,1) = strpad('GHS in component GH (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('k1 in component GH (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('kr1 in component GH (ng_ml_hr)');
LEGEND_CONSTANTS(:,4) = strpad('t1 in component GH (pg_ml)');
LEGEND_CONSTANTS(:,5) = strpad('n1 in component GH (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('n2 in component GH (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('g0 in component GH (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('ng0 in component GH (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('tg0 in component GH (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('t2 in component GH (pg_ml)');
LEGEND_STATES(:,2) = strpad('SRIF_PeV in component SRIF_PeV (pg_ml)');
LEGEND_CONSTANTS(:,34) = strpad('F1_GHS in component F (dimensionless)');
LEGEND_STATES(:,3) = strpad('GHRH in component GHRH (pg_ml)');
LEGEND_STATES(:,4) = strpad('ghr_GHRH in component ghr_GHRH (pg_ml)');
LEGEND_CONSTANTS(:,11) = strpad('k4 in component SRIF_PeV (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('kr4 in component SRIF_PeV (pg_ml_hr)');
LEGEND_CONSTANTS(:,13) = strpad('t5 in component SRIF_PeV (ng_ml)');
LEGEND_CONSTANTS(:,14) = strpad('n5 in component SRIF_PeV (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('S_basal in component SRIF_PeV (pg_ml_hr)');
LEGEND_STATES(:,5) = strpad('SRIF_ArC in component SRIF_ArC (pg_ml)');
LEGEND_CONSTANTS(:,16) = strpad('k2 in component SRIF_ArC (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('kr2 in component SRIF_ArC (pg_ml_hr)');
LEGEND_CONSTANTS(:,18) = strpad('t3 in component SRIF_ArC (pg_ml)');
LEGEND_CONSTANTS(:,19) = strpad('n3 in component SRIF_ArC (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('k3 in component GHRH (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('kr3 in component GHRH (pg_ml_hr)');
LEGEND_CONSTANTS(:,22) = strpad('t4 in component GHRH (pg_ml)');
LEGEND_CONSTANTS(:,23) = strpad('n4 in component GHRH (dimensionless)');
LEGEND_CONSTANTS(:,35) = strpad('F2_GHS in component F (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('g1 in component F (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('g2 in component F (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('tg1 in component F (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('tg2 in component F (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('ng1 in component F (dimensionless)');
LEGEND_CONSTANTS(:,29) = strpad('ng2 in component F (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('dghr_GHRH_dt in component ghr_GHRH (pg_ml_hr)');
LEGEND_ALGEBRAIC(:,1) = strpad('inject in component ghr_GHRH (pg_ml_hr)');
LEGEND_CONSTANTS(:,30) = strpad('kghr in component ghr_GHRH (first_order_rate_constant)');
LEGEND_CONSTANTS(:,31) = strpad('C in component ghr_GHRH (pg_ml_hr)');
LEGEND_CONSTANTS(:,32) = strpad('onset in component ghr_GHRH (hour)');
LEGEND_CONSTANTS(:,33) = strpad('duration in component ghr_GHRH (hour)');
LEGEND_RATES(:,1) = strpad('d/dt GH in component GH (ng_ml)');
LEGEND_RATES(:,2) = strpad('d/dt SRIF_PeV in component SRIF_PeV (pg_ml)');
LEGEND_RATES(:,5) = strpad('d/dt SRIF_ArC in component SRIF_ArC (pg_ml)');
LEGEND_RATES(:,3) = strpad('d/dt GHRH in component GHRH (pg_ml)');
LEGEND_RATES(:,4) = strpad('d/dt ghr_GHRH in component ghr_GHRH (pg_ml)');
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) = 0.0;
CONSTANTS(:,1) = 20.0;
CONSTANTS(:,2) = 3.0;
CONSTANTS(:,3) = 600.0;
CONSTANTS(:,4) = 400.0;
CONSTANTS(:,5) = 5.0;
CONSTANTS(:,6) = 2.0;
CONSTANTS(:,7) = 1.0;
CONSTANTS(:,8) = 2.9;
CONSTANTS(:,9) = 200.0;
CONSTANTS(:,10) = 10.0;
STATES(:,2) = 0.0;
STATES(:,3) = 0.0;
STATES(:,4) = 0.0;
CONSTANTS(:,11) = 25.0;
CONSTANTS(:,12) = 20400.0;
CONSTANTS(:,13) = 10.0;
CONSTANTS(:,14) = 2.0;
CONSTANTS(:,15) = 900.0;
STATES(:,5) = 0.0;
CONSTANTS(:,16) = 25.0;
CONSTANTS(:,17) = 2200.0;
CONSTANTS(:,18) = 400.0;
CONSTANTS(:,19) = 2.0;
CONSTANTS(:,20) = 40.0;
CONSTANTS(:,21) = 63000.0;
CONSTANTS(:,22) = 28.0;
CONSTANTS(:,23) = 5.0;
CONSTANTS(:,24) = 45000.0;
CONSTANTS(:,25) = 100.0;
CONSTANTS(:,26) = 390.0;
CONSTANTS(:,27) = 10000.0;
CONSTANTS(:,28) = 3.0;
CONSTANTS(:,29) = 2.0;
CONSTANTS(:,30) = 15.0;
CONSTANTS(:,31) = 10000.0;
CONSTANTS(:,32) = 2.0;
CONSTANTS(:,33) = 0.2;
CONSTANTS(:,34) = CONSTANTS(:,24).*(power(CONSTANTS(:,1)./CONSTANTS(:,26), CONSTANTS(:,28))./(1.00000+power(CONSTANTS(:,1)./CONSTANTS(:,26), CONSTANTS(:,28))));
CONSTANTS(:,35) = CONSTANTS(:,25).*(power(CONSTANTS(:,1)./CONSTANTS(:,27), CONSTANTS(:,29))./(1.00000+power(CONSTANTS(:,1)./CONSTANTS(:,27), CONSTANTS(:,29))));
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(:,3).*(power((STATES(:,3)+STATES(:,4))./CONSTANTS(:,4), CONSTANTS(:,5))./(power((STATES(:,3)+STATES(:,4))./CONSTANTS(:,4), CONSTANTS(:,5))+1.00000)+ CONSTANTS(:,7).*(power(CONSTANTS(:,1)./CONSTANTS(:,9), CONSTANTS(:,8))./(1.00000+power(CONSTANTS(:,1)./CONSTANTS(:,9), CONSTANTS(:,8))))+(1.00000+CONSTANTS(:,34))./(1.00000+power(STATES(:,2)./CONSTANTS(:,10), CONSTANTS(:,6))+CONSTANTS(:,34))) - CONSTANTS(:,2).*STATES(:,1);
RATES(:,2) = - ( CONSTANTS(:,11).*STATES(:,2))+ CONSTANTS(:,12).*(power(STATES(:,1)./CONSTANTS(:,13), CONSTANTS(:,14))./(power(STATES(:,1)./CONSTANTS(:,13), CONSTANTS(:,14))+1.00000))+CONSTANTS(:,15);
RATES(:,5) = CONSTANTS(:,17).*(power((STATES(:,3)+STATES(:,4))./CONSTANTS(:,18), CONSTANTS(:,19))./(1.00000+power((STATES(:,3)+STATES(:,4))./CONSTANTS(:,18), CONSTANTS(:,19)))) - CONSTANTS(:,16).*STATES(:,5);
RATES(:,3) = ( CONSTANTS(:,21).*((1.00000+CONSTANTS(:,35))./(1.00000+power((STATES(:,2)+STATES(:,5))./CONSTANTS(:,22), CONSTANTS(:,23))+CONSTANTS(:,35)))+ STATES(:,4).*1.00000) - CONSTANTS(:,20).*STATES(:,3);
ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,32), 0.00000 , VOI>=CONSTANTS(:,32)&VOI<=CONSTANTS(:,32)+CONSTANTS(:,33), CONSTANTS(:,31) , VOI>CONSTANTS(:,32)+CONSTANTS(:,33), 0.00000 }, NaN);
RATES(:,4) = ALGEBRAIC(:,1) - CONSTANTS(:,30).*STATES(:,4);
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) = piecewise({VOI<CONSTANTS(:,32), 0.00000 , VOI>=CONSTANTS(:,32)&VOI<=CONSTANTS(:,32)+CONSTANTS(:,33), CONSTANTS(:,31) , VOI>CONSTANTS(:,32)+CONSTANTS(:,33), 0.00000 }, NaN);
ALGEBRAIC(:,2) = ALGEBRAIC(:,1) - CONSTANTS(:,30).*STATES(:,4);
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
end
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