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 =5;
end
% There are a total of 1 entries in each of the rate and state variable arrays.
% There are a total of 28 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 (second)');
LEGEND_CONSTANTS(:,1) = strpad('k_p1 in component SERCA (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k_p2 in component SERCA (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k_p3 in component SERCA (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k_m1 in component SERCA (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k_m2 in component SERCA (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k_m3 in component SERCA (second_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('kdatp in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,7) = strpad('kdcai in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,8) = strpad('kdcasr in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,9) = strpad('kdh1 in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,10) = strpad('kdhi in component SERCA (millimolar_squared)');
LEGEND_CONSTANTS(:,11) = strpad('kdhsr in component SERCA (millimolar_squared)');
LEGEND_CONSTANTS(:,12) = strpad('kdh in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,13) = strpad('n in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('Ca_i in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,15) = strpad('Ca_sr in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,16) = strpad('H_i in component SERCA (millimolar)');
LEGEND_STATES(:,1) = strpad('ATP in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,17) = strpad('ADP in component SERCA (millimolar)');
LEGEND_CONSTANTS(:,18) = strpad('P_i in component SERCA (millimolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('T_ATP in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('T_Cai in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('T_Casr in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('T_H1 in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('T_Hi in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('T_Hsr in component SERCA (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('T_H in component SERCA (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('a_p1 in component SERCA (first_order_rate_constant)');
LEGEND_CONSTANTS(:,26) = strpad('a_p2 in component SERCA (first_order_rate_constant)');
LEGEND_CONSTANTS(:,27) = strpad('a_m1 in component SERCA (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('a_m2 in component SERCA (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('s2 in component SERCA (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,5) = strpad('v_cycle in component SERCA (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt ATP in component SERCA (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 = [];
CONSTANTS(:,1) = 25900;
CONSTANTS(:,2) = 2540;
CONSTANTS(:,3) = 20.5;
CONSTANTS(:,4) = 2;
CONSTANTS(:,5) = 67200;
CONSTANTS(:,6) = 149;
CONSTANTS(:,7) = 0.9;
CONSTANTS(:,8) = 2.24;
CONSTANTS(:,9) = 1.09e-5;
CONSTANTS(:,10) = 3.54e-3;
CONSTANTS(:,11) = 1.05e-8;
CONSTANTS(:,12) = 7.24e-5;
CONSTANTS(:,13) = 2;
CONSTANTS(:,14) = 1e-3;
CONSTANTS(:,15) = 1;
CONSTANTS(:,16) = 1e-4;
STATES(:,1) = 0.01;
CONSTANTS(:,17) = 20e-3;
CONSTANTS(:,18) = 1;
CONSTANTS(:,19) = CONSTANTS(:,4)./CONSTANTS(:,1);
CONSTANTS(:,20) = CONSTANTS(:,14)./CONSTANTS(:,7);
CONSTANTS(:,27) = 0.100000;
CONSTANTS(:,21) = CONSTANTS(:,15)./CONSTANTS(:,8);
CONSTANTS(:,22) = CONSTANTS(:,16)./CONSTANTS(:,9);
CONSTANTS(:,23) = power(CONSTANTS(:,16), CONSTANTS(:,13))./CONSTANTS(:,10);
CONSTANTS(:,24) = power(CONSTANTS(:,16), CONSTANTS(:,13))./CONSTANTS(:,11);
CONSTANTS(:,25) = CONSTANTS(:,16)./CONSTANTS(:,12);
CONSTANTS(:,26) = ( CONSTANTS(:,3).*CONSTANTS(:,24))./( CONSTANTS(:,24).*(1.00000+CONSTANTS(:,25))+ CONSTANTS(:,25).*(1.00000+power(CONSTANTS(:,21), 2.00000)));
CONSTANTS(:,27) = ( CONSTANTS(:,5).*CONSTANTS(:,17).*power(CONSTANTS(:,21), 2.00000).*CONSTANTS(:,25))./( CONSTANTS(:,24).*(1.00000+CONSTANTS(:,25))+ CONSTANTS(:,25).*(1.00000+power(CONSTANTS(:,21), 2.00000)));
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(:,27);
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)./CONSTANTS(:,19);
ALGEBRAIC(:,2) = ( CONSTANTS(:,2).*ALGEBRAIC(:,1).*power(CONSTANTS(:,20), 2.00000))./( ALGEBRAIC(:,1).*power(CONSTANTS(:,20), 2.00000)+ CONSTANTS(:,23).*(1.00000+ ALGEBRAIC(:,1).*(1.00000+CONSTANTS(:,22)+power(CONSTANTS(:,20), 2.00000))));
ALGEBRAIC(:,3) = ( CONSTANTS(:,6).*CONSTANTS(:,18).*CONSTANTS(:,23))./( ALGEBRAIC(:,1).*power(CONSTANTS(:,20), 2.00000)+ CONSTANTS(:,23).*(1.00000+ ALGEBRAIC(:,1).*(1.00000+CONSTANTS(:,22)+power(CONSTANTS(:,20), 2.00000))));
ALGEBRAIC(:,4) = ALGEBRAIC(:,2)+CONSTANTS(:,26)+CONSTANTS(:,27)+ALGEBRAIC(:,3);
ALGEBRAIC(:,5) = ( ALGEBRAIC(:,2).*CONSTANTS(:,26) - CONSTANTS(:,27).*ALGEBRAIC(:,3))./ALGEBRAIC(:,4);
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