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 =2;
end
% There are a total of 8 entries in each of the rate and state variable arrays.
% There are a total of 14 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(:,2) = 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_STATES(:,3) = strpad('J_ERch in component J_ERch (micromolar)');
LEGEND_STATES(:,4) = strpad('J_ERpump in component J_ERpump (micromolar)');
LEGEND_STATES(:,5) = strpad('J_ERleak in component J_ERleak (micromolar)');
LEGEND_STATES(:,6) = strpad('J_in in component J_in (micromolar)');
LEGEND_STATES(:,7) = strpad('J_out in component J_out (micromolar)');
LEGEND_STATES(:,8) = strpad('Ca_ER in component Ca_ER (micromolar)');
LEGEND_CONSTANTS(:,5) = strpad('beta in component J_ERch (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('k_0ch in component J_ERch (micromolar_per_minute)');
LEGEND_CONSTANTS(:,7) = strpad('K_chcyt in component J_ERch (micromolar)');
LEGEND_CONSTANTS(:,8) = strpad('K_chER in component J_ERch (micromolar)');
LEGEND_CONSTANTS(:,9) = strpad('K_ERpump in component J_ERpump (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('K_pump in component J_ERpump (micromolar)');
LEGEND_CONSTANTS(:,11) = strpad('K_ERleak in component J_ERleak (per_minute)');
LEGEND_CONSTANTS(:,12) = strpad('K_0in in component J_in (micromolar_per_minute)');
LEGEND_CONSTANTS(:,13) = strpad('K_out in component J_out (per_minute)');
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(:,8) = strpad('d/dt Ca_ER in component Ca_ER (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt J_ERch in component J_ERch (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt J_ERpump in component J_ERpump (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt J_ERleak in component J_ERleak (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt J_in in component J_in (micromolar)');
LEGEND_RATES(:,7) = strpad('d/dt J_out in component J_out (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) = 0.1;
STATES(:,4) = 0.1;
STATES(:,5) = 0.1;
STATES(:,6) = 0.1;
STATES(:,7) = 0.1;
STATES(:,8) = 20;
CONSTANTS(:,5) = 1.7;
CONSTANTS(:,6) = 325;
CONSTANTS(:,7) = 0.45;
CONSTANTS(:,8) = 1;
CONSTANTS(:,9) = 25;
CONSTANTS(:,10) = 0.5;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 1.7;
CONSTANTS(:,13) = 10;
CONSTANTS(:,13) = CONSTANTS(:,12).*1.00000;
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(:,6) = CONSTANTS(:,13);
RATES(:,8) = ((STATES(:,4) - STATES(:,5)) - STATES(:,3)).*1.00000;
RATES(:,3) = CONSTANTS(:,5).*CONSTANTS(:,6).*( (power(STATES(:,2), 4.00000)./(power(CONSTANTS(:,7), 4.00000)+power(STATES(:,2), 4.00000))).*(power(STATES(:,8), 2.00000)./(power(CONSTANTS(:,8), 2.00000)+power(STATES(:,8), 2.00000)))).*1.00000;
RATES(:,4) = CONSTANTS(:,9).*(power(STATES(:,2), 2.00000)./(power(CONSTANTS(:,10), 2.00000)+power(STATES(:,2), 2.00000)));
RATES(:,5) = (( CONSTANTS(:,11).*STATES(:,8))./1.00000).*1.00000;
RATES(:,7) = (( CONSTANTS(:,13).*STATES(:,2))./1.00000).*1.00000;
ALGEBRAIC(:,1) = ( CONSTANTS(:,1).*power(STATES(:,2), CONSTANTS(:,3)))./(power(CONSTANTS(:,2), CONSTANTS(:,3))+power(STATES(:,2), CONSTANTS(:,3)));
ALGEBRAIC(:,2) = ( CONSTANTS(:,4).*STATES(:,1))./1.00000;
RATES(:,1) = ALGEBRAIC(:,1) - ALGEBRAIC(:,2);
RATES(:,2) = (((((STATES(:,3) - STATES(:,4))+STATES(:,5)+STATES(:,6)) - STATES(:,7))+ALGEBRAIC(:,2)) - 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(:,2) = ( CONSTANTS(:,4).*STATES(:,1))./1.00000;
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