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 =7;
end
% There are a total of 6 entries in each of the rate and state variable arrays.
% There are a total of 10 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 (minute)');
LEGEND_STATES(:,1) = strpad('C2 in component C2 (millimolar)');
LEGEND_CONSTANTS(:,1) = strpad('k6 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k8 in component reaction_constants (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k9 in component reaction_constants (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('M in component M (millimolar)');
LEGEND_CONSTANTS(:,3) = strpad('P in component reaction_constants (millimolar)');
LEGEND_STATES(:,3) = strpad('CP in component CP (millimolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('k3 in component reaction_constants (second_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('Y in component Y (millimolar)');
LEGEND_STATES(:,5) = strpad('pM in component pM (millimolar)');
LEGEND_CONSTANTS(:,10) = strpad('k5 in component reaction_constants (second_order_rate_constant)');
LEGEND_ALGEBRAIC(:,7) = strpad('F in component reaction_constants (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,2) = strpad('k1 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k2 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('aa in component reaction_constants (millimolar)');
LEGEND_STATES(:,6) = strpad('YP in component YP (millimolar)');
LEGEND_CONSTANTS(:,6) = strpad('k7 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k4 in component reaction_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k4_ in component reaction_constants (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('CT in component reaction_constants (millimolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('YT in component reaction_constants (millimolar)');
LEGEND_ALGEBRAIC(:,6) = strpad('YT_CT in component reaction_constants (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('M_CT in component reaction_constants (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt C2 in component C2 (millimolar)');
LEGEND_RATES(:,3) = strpad('d/dt CP in component CP (millimolar)');
LEGEND_RATES(:,5) = strpad('d/dt pM in component pM (millimolar)');
LEGEND_RATES(:,2) = strpad('d/dt M in component M (millimolar)');
LEGEND_RATES(:,4) = strpad('d/dt Y in component Y (millimolar)');
LEGEND_RATES(:,6) = strpad('d/dt YP in component YP (millimolar)');
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) = 0.001;
CONSTANTS(:,1) = 1.0;
CONSTANTS(:,2) = 100.0;
STATES(:,2) = 0.001;
CONSTANTS(:,3) = 1.0;
STATES(:,3) = 0.001;
STATES(:,4) = 0.001;
STATES(:,5) = 0.001;
CONSTANTS(:,4) = 0.0;
CONSTANTS(:,5) = 1.0;
STATES(:,6) = 0.001;
CONSTANTS(:,6) = 0.6;
CONSTANTS(:,7) = 180.0;
CONSTANTS(:,8) = 0.018;
CONSTANTS(:,9) = CONSTANTS(:,2)./CONSTANTS(:,3);
CONSTANTS(:,10) = 0.00000./CONSTANTS(:,3);
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(:,2)+ CONSTANTS(:,2).*STATES(:,3)) - CONSTANTS(:,9).*CONSTANTS(:,3).*STATES(:,1);
RATES(:,6) = CONSTANTS(:,1).*STATES(:,2) - CONSTANTS(:,6).*STATES(:,6);
ALGEBRAIC(:,1) = STATES(:,1)+STATES(:,3)+STATES(:,5)+STATES(:,2);
ALGEBRAIC(:,5) = 200.000./ALGEBRAIC(:,1);
RATES(:,3) = CONSTANTS(:,9).*CONSTANTS(:,3).*STATES(:,1) - ( CONSTANTS(:,2).*STATES(:,3)+ ALGEBRAIC(:,5).*STATES(:,3).*STATES(:,4));
ALGEBRAIC(:,2) = ( 0.0150000.*ALGEBRAIC(:,1))./CONSTANTS(:,5);
RATES(:,4) = CONSTANTS(:,5).*ALGEBRAIC(:,2) - ( ALGEBRAIC(:,5).*STATES(:,3).*STATES(:,4)+ CONSTANTS(:,4).*STATES(:,4));
ALGEBRAIC(:,7) = CONSTANTS(:,8)+ CONSTANTS(:,7).*power(STATES(:,2)./ALGEBRAIC(:,1), 2.00000);
RATES(:,5) = ( ALGEBRAIC(:,5).*STATES(:,3).*STATES(:,4)+ CONSTANTS(:,10).*CONSTANTS(:,3).*STATES(:,2)) - STATES(:,5).*ALGEBRAIC(:,7);
RATES(:,2) = STATES(:,5).*ALGEBRAIC(:,7) - ( CONSTANTS(:,10).*CONSTANTS(:,3).*STATES(:,2)+ CONSTANTS(:,1).*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(:,1)+STATES(:,3)+STATES(:,5)+STATES(:,2);
ALGEBRAIC(:,5) = 200.000./ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = ( 0.0150000.*ALGEBRAIC(:,1))./CONSTANTS(:,5);
ALGEBRAIC(:,7) = CONSTANTS(:,8)+ CONSTANTS(:,7).*power(STATES(:,2)./ALGEBRAIC(:,1), 2.00000);
ALGEBRAIC(:,3) = STATES(:,4)+STATES(:,6)+STATES(:,5)+STATES(:,2);
ALGEBRAIC(:,4) = STATES(:,2)./ALGEBRAIC(:,1);
ALGEBRAIC(:,6) = ALGEBRAIC(:,3)./ALGEBRAIC(:,1);
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