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 =4;
end
% There are a total of 3 entries in each of the rate and state variable arrays.
% There are a total of 15 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 (min)');
LEGEND_STATES(:,1) = strpad('Z in component Ca (uM)');
LEGEND_STATES(:,2) = strpad('Y in component Ca (uM)');
LEGEND_STATES(:,3) = strpad('X in component Ca (uM)');
LEGEND_CONSTANTS(:,15) = strpad('V_in in component V_in (uM_per_min)');
LEGEND_ALGEBRAIC(:,1) = strpad('V_2i in component V_2i (uM_per_min)');
LEGEND_ALGEBRAIC(:,2) = strpad('V_3i in component V_3i (uM_per_min)');
LEGEND_ALGEBRAIC(:,3) = strpad('V_2s in component V_2s (uM_per_min)');
LEGEND_ALGEBRAIC(:,4) = strpad('V_3s in component V_3s (uM_per_min)');
LEGEND_CONSTANTS(:,1) = strpad('K_f in component Ca (per_min)');
LEGEND_CONSTANTS(:,2) = strpad('K in component Ca (per_min)');
LEGEND_CONSTANTS(:,3) = strpad('beta in component Ca_flux (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('v_0 in component V_in (uM_per_min)');
LEGEND_CONSTANTS(:,5) = strpad('v_1 in component V_in (uM_per_min)');
LEGEND_CONSTANTS(:,6) = strpad('V_M2i in component V_2i (uM_per_min)');
LEGEND_CONSTANTS(:,7) = strpad('K_2i in component V_2i (uM)');
LEGEND_CONSTANTS(:,8) = strpad('V_M3i in component V_3i (uM_per_min)');
LEGEND_CONSTANTS(:,9) = strpad('K_3z in component V_3i (uM)');
LEGEND_CONSTANTS(:,10) = strpad('K_3y in component V_3i (uM)');
LEGEND_CONSTANTS(:,11) = strpad('V_M2s in component V_2s (uM_per_min)');
LEGEND_CONSTANTS(:,12) = strpad('K_2s in component V_2s (uM)');
LEGEND_CONSTANTS(:,13) = strpad('V_M3s in component V_3s (uM_per_min)');
LEGEND_CONSTANTS(:,14) = strpad('K_3s in component V_3s (uM)');
LEGEND_RATES(:,1) = strpad('d/dt Z in component Ca (uM)');
LEGEND_RATES(:,2) = strpad('d/dt Y in component Ca (uM)');
LEGEND_RATES(:,3) = strpad('d/dt X in component Ca (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) = 0.0;
STATES(:,2) = 0.0;
STATES(:,3) = 0.5;
CONSTANTS(:,1) = 0.5;
CONSTANTS(:,2) = 1;
CONSTANTS(:,3) = 1;
CONSTANTS(:,4) = 0.015;
CONSTANTS(:,5) = 0.012;
CONSTANTS(:,6) = 3.1;
CONSTANTS(:,7) = 0.005;
CONSTANTS(:,8) = 25;
CONSTANTS(:,9) = 0.022;
CONSTANTS(:,10) = 0.065;
CONSTANTS(:,11) = 1.5;
CONSTANTS(:,12) = 0.0265;
CONSTANTS(:,13) = 0.169;
CONSTANTS(:,14) = 0.1;
CONSTANTS(:,15) = CONSTANTS(:,4)+ CONSTANTS(:,5).*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
ALGEBRAIC(:,1) = CONSTANTS(:,6).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,7), 2.00000)+power(STATES(:,1), 2.00000)));
ALGEBRAIC(:,2) = CONSTANTS(:,8).*(power(STATES(:,2), 2.00000)./(power(CONSTANTS(:,10), 2.00000)+power(STATES(:,2), 2.00000))).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,9), 2.00000)+power(STATES(:,1), 2.00000)));
RATES(:,2) = ALGEBRAIC(:,1)+ - ALGEBRAIC(:,2)+ - ( CONSTANTS(:,1).*STATES(:,2));
ALGEBRAIC(:,3) = CONSTANTS(:,11).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,12), 2.00000)+power(STATES(:,1), 2.00000)));
ALGEBRAIC(:,4) = CONSTANTS(:,3).*CONSTANTS(:,13).*(power(STATES(:,3), 2.00000)./(power(CONSTANTS(:,14), 2.00000)+power(STATES(:,3), 2.00000)));
RATES(:,1) = CONSTANTS(:,15)+ - ALGEBRAIC(:,1)+ALGEBRAIC(:,2)+ CONSTANTS(:,1).*STATES(:,2)+ - ALGEBRAIC(:,3)+ALGEBRAIC(:,4)+ CONSTANTS(:,1).*STATES(:,3)+ - ( CONSTANTS(:,2).*STATES(:,1));
RATES(:,3) = ALGEBRAIC(:,3)+ - ALGEBRAIC(:,4)+ - ( CONSTANTS(:,1).*STATES(:,3));
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(:,6).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,7), 2.00000)+power(STATES(:,1), 2.00000)));
ALGEBRAIC(:,2) = CONSTANTS(:,8).*(power(STATES(:,2), 2.00000)./(power(CONSTANTS(:,10), 2.00000)+power(STATES(:,2), 2.00000))).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,9), 2.00000)+power(STATES(:,1), 2.00000)));
ALGEBRAIC(:,3) = CONSTANTS(:,11).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,12), 2.00000)+power(STATES(:,1), 2.00000)));
ALGEBRAIC(:,4) = CONSTANTS(:,3).*CONSTANTS(:,13).*(power(STATES(:,3), 2.00000)./(power(CONSTANTS(:,14), 2.00000)+power(STATES(:,3), 2.00000)));
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