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 =1;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 38 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('MP in component MP (nanomolar)');
LEGEND_CONSTANTS(:,1) = strpad('vsP in component MP (flux)');
LEGEND_CONSTANTS(:,2) = strpad('vmP in component MP (flux)');
LEGEND_CONSTANTS(:,3) = strpad('KmP in component MP (nanomolar)');
LEGEND_CONSTANTS(:,4) = strpad('KIP in component MP (nanomolar)');
LEGEND_CONSTANTS(:,5) = strpad('kd in component parameters (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('CN in component CN (nanomolar)');
LEGEND_CONSTANTS(:,6) = strpad('n in component parameters (dimensionless)');
LEGEND_STATES(:,3) = strpad('P0 in component P0 (nanomolar)');
LEGEND_CONSTANTS(:,7) = strpad('ksP in component P0 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('V1P in component parameters (flux)');
LEGEND_CONSTANTS(:,9) = strpad('V2P in component parameters (flux)');
LEGEND_CONSTANTS(:,10) = strpad('K1P in component parameters (nanomolar)');
LEGEND_CONSTANTS(:,11) = strpad('K2P in component parameters (nanomolar)');
LEGEND_STATES(:,4) = strpad('P1 in component P1 (nanomolar)');
LEGEND_CONSTANTS(:,12) = strpad('V3P in component parameters (flux)');
LEGEND_CONSTANTS(:,13) = strpad('V4P in component parameters (flux)');
LEGEND_CONSTANTS(:,14) = strpad('K3P in component parameters (nanomolar)');
LEGEND_CONSTANTS(:,15) = strpad('K4P in component parameters (nanomolar)');
LEGEND_STATES(:,5) = strpad('P2 in component P2 (nanomolar)');
LEGEND_CONSTANTS(:,16) = strpad('vdP in component P2 (flux)');
LEGEND_CONSTANTS(:,17) = strpad('KdP in component P2 (nanomolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('Pt in component P2 (nanomolar)');
LEGEND_CONSTANTS(:,18) = strpad('k3 in component parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('k4 in component parameters (first_order_rate_constant)');
LEGEND_STATES(:,6) = strpad('T2 in component T2 (nanomolar)');
LEGEND_STATES(:,7) = strpad('C in component C (nanomolar)');
LEGEND_STATES(:,8) = strpad('MT in component MT (nanomolar)');
LEGEND_CONSTANTS(:,20) = strpad('vsT in component MT (flux)');
LEGEND_CONSTANTS(:,21) = strpad('vmT in component MT (flux)');
LEGEND_CONSTANTS(:,22) = strpad('KmT in component MT (nanomolar)');
LEGEND_CONSTANTS(:,23) = strpad('KIT in component MT (nanomolar)');
LEGEND_STATES(:,9) = strpad('T0 in component T0 (nanomolar)');
LEGEND_CONSTANTS(:,24) = strpad('ksT in component T0 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,25) = strpad('V1T in component parameters (flux)');
LEGEND_CONSTANTS(:,26) = strpad('V2T in component parameters (flux)');
LEGEND_CONSTANTS(:,27) = strpad('K1T in component parameters (nanomolar)');
LEGEND_CONSTANTS(:,28) = strpad('K2T in component parameters (nanomolar)');
LEGEND_STATES(:,10) = strpad('T1 in component T1 (nanomolar)');
LEGEND_CONSTANTS(:,29) = strpad('V3T in component parameters (flux)');
LEGEND_CONSTANTS(:,30) = strpad('V4T in component parameters (flux)');
LEGEND_CONSTANTS(:,31) = strpad('K3T in component parameters (nanomolar)');
LEGEND_CONSTANTS(:,32) = strpad('K4T in component parameters (nanomolar)');
LEGEND_CONSTANTS(:,33) = strpad('vdT in component T2 (flux)');
LEGEND_CONSTANTS(:,34) = strpad('KdT in component T2 (nanomolar)');
LEGEND_CONSTANTS(:,35) = strpad('kdC in component C (first_order_rate_constant)');
LEGEND_CONSTANTS(:,36) = strpad('k1 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,37) = strpad('k2 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,38) = strpad('kdN in component CN (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt MP in component MP (nanomolar)');
LEGEND_RATES(:,3) = strpad('d/dt P0 in component P0 (nanomolar)');
LEGEND_RATES(:,4) = strpad('d/dt P1 in component P1 (nanomolar)');
LEGEND_RATES(:,5) = strpad('d/dt P2 in component P2 (nanomolar)');
LEGEND_RATES(:,8) = strpad('d/dt MT in component MT (nanomolar)');
LEGEND_RATES(:,9) = strpad('d/dt T0 in component T0 (nanomolar)');
LEGEND_RATES(:,10) = strpad('d/dt T1 in component T1 (nanomolar)');
LEGEND_RATES(:,6) = strpad('d/dt T2 in component T2 (nanomolar)');
LEGEND_RATES(:,7) = strpad('d/dt C in component C (nanomolar)');
LEGEND_RATES(:,2) = strpad('d/dt CN in component CN (nanomolar)');
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) = 0.1;
CONSTANTS(:,1) = 1;
CONSTANTS(:,2) = 0.7;
CONSTANTS(:,3) = 0.2;
CONSTANTS(:,4) = 1.0;
CONSTANTS(:,5) = 0.01;
STATES(:,2) = 1.25;
CONSTANTS(:,6) = 4.0;
STATES(:,3) = 0.1;
CONSTANTS(:,7) = 0.9;
CONSTANTS(:,8) = 8.0;
CONSTANTS(:,9) = 1.0;
CONSTANTS(:,10) = 2.0;
CONSTANTS(:,11) = 2.0;
STATES(:,4) = 0.1;
CONSTANTS(:,12) = 8.0;
CONSTANTS(:,13) = 1.0;
CONSTANTS(:,14) = 2.0;
CONSTANTS(:,15) = 1;
STATES(:,5) = 0.1;
CONSTANTS(:,16) = 2;
CONSTANTS(:,17) = 0.2;
CONSTANTS(:,18) = 1.2;
CONSTANTS(:,19) = 0.6;
STATES(:,6) = 0.1;
STATES(:,7) = 0.1;
STATES(:,8) = 1.6;
CONSTANTS(:,20) = 1.0;
CONSTANTS(:,21) = 0.7;
CONSTANTS(:,22) = 0.2;
CONSTANTS(:,23) = 1.0;
STATES(:,9) = 0.1;
CONSTANTS(:,24) = 0.9;
CONSTANTS(:,25) = 8.0;
CONSTANTS(:,26) = 1.0;
CONSTANTS(:,27) = 2.0;
CONSTANTS(:,28) = 2.0;
STATES(:,10) = 0.1;
CONSTANTS(:,29) = 8.0;
CONSTANTS(:,30) = 1.0;
CONSTANTS(:,31) = 2.0;
CONSTANTS(:,32) = 1;
CONSTANTS(:,33) = 2;
CONSTANTS(:,34) = 0.2;
CONSTANTS(:,35) = 0.01;
CONSTANTS(:,36) = 0.6;
CONSTANTS(:,37) = 0.2;
CONSTANTS(:,38) = 0.01;
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).*(power(CONSTANTS(:,4), CONSTANTS(:,6))./(power(CONSTANTS(:,4), CONSTANTS(:,6))+power(STATES(:,2), CONSTANTS(:,6)))) - ( CONSTANTS(:,2).*(STATES(:,1)./(CONSTANTS(:,3)+STATES(:,1)))+ CONSTANTS(:,5).*STATES(:,1));
RATES(:,3) = ( CONSTANTS(:,7).*STATES(:,1)+ CONSTANTS(:,9).*(STATES(:,4)./(CONSTANTS(:,11)+STATES(:,4)))) - ( CONSTANTS(:,8).*(STATES(:,3)./(CONSTANTS(:,10)+STATES(:,3)))+ CONSTANTS(:,5).*STATES(:,3));
RATES(:,4) = ( CONSTANTS(:,8).*(STATES(:,3)./(CONSTANTS(:,10)+STATES(:,3)))+ CONSTANTS(:,13).*(STATES(:,5)./(CONSTANTS(:,15)+STATES(:,5)))) - ( CONSTANTS(:,9).*(STATES(:,4)./(CONSTANTS(:,11)+STATES(:,4)))+ CONSTANTS(:,12).*(STATES(:,4)./(CONSTANTS(:,14)+STATES(:,4)))+ CONSTANTS(:,5).*STATES(:,4));
RATES(:,5) = ( CONSTANTS(:,12).*(STATES(:,4)./(CONSTANTS(:,14)+STATES(:,4)))+ CONSTANTS(:,19).*STATES(:,7)) - ( CONSTANTS(:,13).*(STATES(:,5)./(CONSTANTS(:,15)+STATES(:,5)))+ CONSTANTS(:,18).*STATES(:,5).*STATES(:,6)+ CONSTANTS(:,16).*(STATES(:,5)./(CONSTANTS(:,17)+STATES(:,5)))+ CONSTANTS(:,5).*STATES(:,5));
RATES(:,8) = CONSTANTS(:,20).*(power(CONSTANTS(:,23), CONSTANTS(:,6))./(power(CONSTANTS(:,23), CONSTANTS(:,6))+power(STATES(:,2), CONSTANTS(:,6)))) - ( CONSTANTS(:,21).*(STATES(:,8)./(CONSTANTS(:,22)+STATES(:,8)))+ CONSTANTS(:,5).*STATES(:,8));
RATES(:,9) = ( CONSTANTS(:,24).*STATES(:,8)+ CONSTANTS(:,26).*(STATES(:,10)./(CONSTANTS(:,28)+STATES(:,10)))) - ( CONSTANTS(:,25).*(STATES(:,9)./(CONSTANTS(:,27)+STATES(:,9)))+ CONSTANTS(:,5).*STATES(:,9));
RATES(:,10) = ( CONSTANTS(:,25).*(STATES(:,9)./(CONSTANTS(:,27)+STATES(:,9)))+ CONSTANTS(:,30).*(STATES(:,6)./(CONSTANTS(:,32)+STATES(:,6)))) - ( CONSTANTS(:,26).*(STATES(:,10)./(CONSTANTS(:,28)+STATES(:,10)))+ CONSTANTS(:,29).*(STATES(:,10)./(CONSTANTS(:,31)+STATES(:,10)))+ CONSTANTS(:,5).*STATES(:,10));
RATES(:,6) = ( CONSTANTS(:,29).*(STATES(:,10)./(CONSTANTS(:,31)+STATES(:,10)))+ CONSTANTS(:,19).*STATES(:,7)) - ( CONSTANTS(:,30).*(STATES(:,6)./(CONSTANTS(:,32)+STATES(:,6)))+ CONSTANTS(:,18).*STATES(:,5).*STATES(:,6)+ CONSTANTS(:,33).*(STATES(:,6)./(CONSTANTS(:,34)+STATES(:,6)))+ CONSTANTS(:,5).*STATES(:,6));
RATES(:,7) = ( CONSTANTS(:,18).*STATES(:,5).*STATES(:,6)+ CONSTANTS(:,37).*STATES(:,2)) - ( CONSTANTS(:,19).*STATES(:,7)+ CONSTANTS(:,36).*STATES(:,7)+ CONSTANTS(:,35).*STATES(:,7));
RATES(:,2) = CONSTANTS(:,36).*STATES(:,7) - ( CONSTANTS(:,37).*STATES(:,2)+ CONSTANTS(:,38).*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) = STATES(:,3)+STATES(:,4)+STATES(:,5)+STATES(:,7)+STATES(:,2);
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