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 =10;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 21 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('Ca_m in component Ca_m (micromolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('J_min in component J_min (micromolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('J_mout in component J_mout (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('k_min in component J_min (micromolar)');
LEGEND_STATES(:,2) = strpad('Ca_cyt in component Ca_cyt (micromolar)');
LEGEND_CONSTANTS(:,2) = strpad('K_m in component J_min (micromolar)');
LEGEND_CONSTANTS(:,3) = strpad('n in component J_min (micromolar)');
LEGEND_CONSTANTS(:,4) = strpad('k_mout in component J_mout (micromolar)');
LEGEND_ALGEBRAIC(:,7) = strpad('J_ERch in component J_ERch (micromolar)');
LEGEND_ALGEBRAIC(:,8) = strpad('J_ERpump in component J_ERpump (micromolar)');
LEGEND_ALGEBRAIC(:,9) = strpad('J_in in component J_in (micromolar)');
LEGEND_ALGEBRAIC(:,10) = strpad('J_out in component J_out (micromolar)');
LEGEND_STATES(:,3) = strpad('Ca_ER in component Ca_ER (micromolar)');
LEGEND_STATES(:,4) = strpad('PLC in component PLC (micromolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('J_PLCact in component J_PLCact (micromolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('J_PLCinact in component J_PLCinact (micromolar)');
LEGEND_STATES(:,5) = strpad('G_alpha in component G_alpha (micromolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('J_actG_alpha in component J_actG_alpha (micromolar)');
LEGEND_ALGEBRAIC(:,6) = strpad('J_inactG_alpha in component J_inactG_alpha (micromolar)');
LEGEND_CONSTANTS(:,5) = strpad('k_10 in component J_ERch (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('K_11 in component J_ERch (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('K_17 in component J_ERpump (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('k_16 in component J_ERpump (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('K_12 in component J_in (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('k_13 in component J_in (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('k_14 in component J_out (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('K_15 in component J_out (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('k_7 in component J_PLCact (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('k_8 in component J_PLCinact (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('K_9 in component J_PLCinact (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('k_1 in component J_actG_alpha (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('k_2 in component J_actG_alpha (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('k_3 in component J_inactG_alpha (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('K_4 in component J_inactG_alpha (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('k_5 in component J_inactG_alpha (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('K_6 in component J_inactG_alpha (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt Ca_m in component Ca_m (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt Ca_cyt in component Ca_cyt (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt Ca_ER in component Ca_ER (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt PLC in component PLC (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt G_alpha in component G_alpha (micromolar)');
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) = 330;
STATES(:,2) = 0.01;
CONSTANTS(:,2) = 1.6;
CONSTANTS(:,3) = 8;
CONSTANTS(:,4) = 0.5;
STATES(:,3) = 20;
STATES(:,4) = 0.01;
STATES(:,5) = 0.01;
CONSTANTS(:,5) = 5;
CONSTANTS(:,6) = 3;
CONSTANTS(:,7) = 0.05;
CONSTANTS(:,8) = 5.37;
CONSTANTS(:,9) = 2.8;
CONSTANTS(:,10) = 13.4;
CONSTANTS(:,11) = 153;
CONSTANTS(:,12) = 0.16;
CONSTANTS(:,13) = 2.08;
CONSTANTS(:,14) = 32.24;
CONSTANTS(:,15) = 29.09;
CONSTANTS(:,16) = 0.01;
CONSTANTS(:,17) = 0.1;
CONSTANTS(:,18) = 0.64;
CONSTANTS(:,19) = 0.09;
CONSTANTS(:,20) = 4.88;
CONSTANTS(:,21) = 1.18;
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(:,1).*power(STATES(:,2), CONSTANTS(:,3)))./(power(CONSTANTS(:,2), CONSTANTS(:,3))+power(STATES(:,2), CONSTANTS(:,3)));
ALGEBRAIC(:,4) = ( CONSTANTS(:,4).*STATES(:,1))./1.00000;
RATES(:,1) = ALGEBRAIC(:,1) - ALGEBRAIC(:,4);
ALGEBRAIC(:,2) = CONSTANTS(:,13).*STATES(:,5);
ALGEBRAIC(:,5) = CONSTANTS(:,14).*(STATES(:,4)./(CONSTANTS(:,15)+STATES(:,4)));
RATES(:,4) = (ALGEBRAIC(:,2) - ALGEBRAIC(:,5)).*1.00000;
ALGEBRAIC(:,3) = CONSTANTS(:,16)+ CONSTANTS(:,17).*STATES(:,5);
ALGEBRAIC(:,6) = CONSTANTS(:,18).*STATES(:,4).*(STATES(:,5)./(CONSTANTS(:,19)+STATES(:,5)))+ CONSTANTS(:,20).*STATES(:,2).*(STATES(:,5)./(CONSTANTS(:,21)+STATES(:,5)));
RATES(:,5) = (ALGEBRAIC(:,3) - ALGEBRAIC(:,6)).*1.00000;
ALGEBRAIC(:,7) = CONSTANTS(:,5).*STATES(:,2).*STATES(:,4).*(STATES(:,3)./(CONSTANTS(:,6)+STATES(:,3)));
ALGEBRAIC(:,8) = CONSTANTS(:,8).*(STATES(:,2)./(CONSTANTS(:,7)+STATES(:,3)));
RATES(:,3) = (ALGEBRAIC(:,8) - ALGEBRAIC(:,7)).*1.00000;
ALGEBRAIC(:,9) = CONSTANTS(:,9).*STATES(:,4)+ CONSTANTS(:,10).*STATES(:,5);
ALGEBRAIC(:,10) = CONSTANTS(:,11).*(STATES(:,2)./(CONSTANTS(:,12)+STATES(:,2)));
RATES(:,2) = (((((ALGEBRAIC(:,7) - ALGEBRAIC(:,8))+ALGEBRAIC(:,9)) - ALGEBRAIC(:,10))+ALGEBRAIC(:,4)) - ALGEBRAIC(:,1)).*1.00000;
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(:,1).*power(STATES(:,2), CONSTANTS(:,3)))./(power(CONSTANTS(:,2), CONSTANTS(:,3))+power(STATES(:,2), CONSTANTS(:,3)));
ALGEBRAIC(:,4) = ( CONSTANTS(:,4).*STATES(:,1))./1.00000;
ALGEBRAIC(:,2) = CONSTANTS(:,13).*STATES(:,5);
ALGEBRAIC(:,5) = CONSTANTS(:,14).*(STATES(:,4)./(CONSTANTS(:,15)+STATES(:,4)));
ALGEBRAIC(:,3) = CONSTANTS(:,16)+ CONSTANTS(:,17).*STATES(:,5);
ALGEBRAIC(:,6) = CONSTANTS(:,18).*STATES(:,4).*(STATES(:,5)./(CONSTANTS(:,19)+STATES(:,5)))+ CONSTANTS(:,20).*STATES(:,2).*(STATES(:,5)./(CONSTANTS(:,21)+STATES(:,5)));
ALGEBRAIC(:,7) = CONSTANTS(:,5).*STATES(:,2).*STATES(:,4).*(STATES(:,3)./(CONSTANTS(:,6)+STATES(:,3)));
ALGEBRAIC(:,8) = CONSTANTS(:,8).*(STATES(:,2)./(CONSTANTS(:,7)+STATES(:,3)));
ALGEBRAIC(:,9) = CONSTANTS(:,9).*STATES(:,4)+ CONSTANTS(:,10).*STATES(:,5);
ALGEBRAIC(:,10) = CONSTANTS(:,11).*(STATES(:,2)./(CONSTANTS(:,12)+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