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 3 entries in each of the rate and state variable arrays.
% There are a total of 17 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_ALGEBRAIC(:,1) = strpad('Ca_Pr in component total_calcium (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('Ca_tot in component total_calcium (micromolar)');
LEGEND_CONSTANTS(:,2) = strpad('rho_ER in component ER_calcium (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('beta_ER in component ER_calcium (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('rho_m in component mitochondrial_calcium (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('beta_m in component mitochondrial_calcium (dimensionless)');
LEGEND_STATES(:,1) = strpad('Ca_cyt in component cytosolic_calcium (micromolar)');
LEGEND_STATES(:,2) = strpad('Ca_ER in component ER_calcium (micromolar)');
LEGEND_STATES(:,3) = strpad('Ca_m in component mitochondrial_calcium (micromolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('Pr in component total_protein (micromolar)');
LEGEND_CONSTANTS(:,6) = strpad('Pr_tot in component total_protein (micromolar)');
LEGEND_CONSTANTS(:,7) = strpad('k_plus in component cytosolic_calcium (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k_minus in component cytosolic_calcium (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('J_ch in component Ca_efflux_from_the_ER (flux)');
LEGEND_ALGEBRAIC(:,5) = strpad('J_leak in component Ca_leak_flux_from_the_ER (flux)');
LEGEND_ALGEBRAIC(:,3) = strpad('J_pump in component ATP_dependent_Ca_uptake_into_the_ER (flux)');
LEGEND_ALGEBRAIC(:,7) = strpad('J_out in component mitochondrial_Ca_release (flux)');
LEGEND_ALGEBRAIC(:,6) = strpad('J_in in component mitochondrial_Ca_uptake (flux)');
LEGEND_CONSTANTS(:,9) = strpad('k_pump in component ATP_dependent_Ca_uptake_into_the_ER (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k_ch in component Ca_efflux_from_the_ER (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('K1 in component Ca_efflux_from_the_ER (micromolar)');
LEGEND_CONSTANTS(:,12) = strpad('k_leak in component Ca_leak_flux_from_the_ER (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('k_in in component mitochondrial_Ca_uptake (flux)');
LEGEND_CONSTANTS(:,14) = strpad('K2 in component mitochondrial_Ca_uptake (micromolar)');
LEGEND_CONSTANTS(:,15) = strpad('k_out in component mitochondrial_Ca_release (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('k_m in component mitochondrial_Ca_release (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('K3 in component mitochondrial_Ca_release (micromolar)');
LEGEND_RATES(:,1) = strpad('d/dt Ca_cyt in component cytosolic_calcium (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt Ca_ER in component ER_calcium (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt Ca_m in component mitochondrial_calcium (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 = [];
CONSTANTS(:,1) = 90.0;
CONSTANTS(:,2) = 0.01;
CONSTANTS(:,3) = 0.0025;
CONSTANTS(:,4) = 0.01;
CONSTANTS(:,5) = 0.0025;
STATES(:,1) = 0.05;
STATES(:,2) = 1.0;
STATES(:,3) = 0.4;
CONSTANTS(:,6) = 120.0;
CONSTANTS(:,7) = 0.1;
CONSTANTS(:,8) = 0.01;
CONSTANTS(:,9) = 20.0;
CONSTANTS(:,10) = 4100.0;
CONSTANTS(:,11) = 5.0;
CONSTANTS(:,12) = 0.05;
CONSTANTS(:,13) = 300.0;
CONSTANTS(:,14) = 0.8;
CONSTANTS(:,15) = 125.0;
CONSTANTS(:,16) = 0.00625;
CONSTANTS(:,17) = 5.0;
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(:,4) = CONSTANTS(:,10).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,1), 2.00000))).*(STATES(:,2) - STATES(:,1));
ALGEBRAIC(:,5) = CONSTANTS(:,12).*(STATES(:,2) - STATES(:,1));
ALGEBRAIC(:,3) = CONSTANTS(:,9).*STATES(:,1);
RATES(:,2) = (CONSTANTS(:,3)./CONSTANTS(:,2)).*(ALGEBRAIC(:,3) - (ALGEBRAIC(:,4)+ALGEBRAIC(:,5)));
ALGEBRAIC(:,1) = CONSTANTS(:,1) - (STATES(:,1)+ (CONSTANTS(:,2)./CONSTANTS(:,3)).*STATES(:,2)+ (CONSTANTS(:,4)./CONSTANTS(:,5)).*STATES(:,3));
ALGEBRAIC(:,2) = CONSTANTS(:,6) - ALGEBRAIC(:,1);
ALGEBRAIC(:,7) = ( CONSTANTS(:,15).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,17), 2.00000)+power(STATES(:,1), 2.00000)))+CONSTANTS(:,16)).*STATES(:,3);
ALGEBRAIC(:,6) = CONSTANTS(:,13).*(power(STATES(:,1), 8.00000)./(power(CONSTANTS(:,14), 8.00000)+power(STATES(:,1), 8.00000)));
RATES(:,1) = (ALGEBRAIC(:,4)+ALGEBRAIC(:,5)+ALGEBRAIC(:,7)+ CONSTANTS(:,8).*ALGEBRAIC(:,1)) - (ALGEBRAIC(:,3)+ALGEBRAIC(:,6)+ CONSTANTS(:,7).*STATES(:,1).*ALGEBRAIC(:,2));
RATES(:,3) = (CONSTANTS(:,5)./CONSTANTS(:,4)).*(ALGEBRAIC(:,6) - ALGEBRAIC(:,7));
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(:,4) = CONSTANTS(:,10).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,1), 2.00000))).*(STATES(:,2) - STATES(:,1));
ALGEBRAIC(:,5) = CONSTANTS(:,12).*(STATES(:,2) - STATES(:,1));
ALGEBRAIC(:,3) = CONSTANTS(:,9).*STATES(:,1);
ALGEBRAIC(:,1) = CONSTANTS(:,1) - (STATES(:,1)+ (CONSTANTS(:,2)./CONSTANTS(:,3)).*STATES(:,2)+ (CONSTANTS(:,4)./CONSTANTS(:,5)).*STATES(:,3));
ALGEBRAIC(:,2) = CONSTANTS(:,6) - ALGEBRAIC(:,1);
ALGEBRAIC(:,7) = ( CONSTANTS(:,15).*(power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,17), 2.00000)+power(STATES(:,1), 2.00000)))+CONSTANTS(:,16)).*STATES(:,3);
ALGEBRAIC(:,6) = CONSTANTS(:,13).*(power(STATES(:,1), 8.00000)./(power(CONSTANTS(:,14), 8.00000)+power(STATES(:,1), 8.00000)));
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