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 4 entries in each of the rate and state variable arrays.
% There are a total of 11 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('sigma in component parameters (dm)');
LEGEND_CONSTANTS(:,2) = strpad('CNG_tot in component parameters (mole_per_dm_squared)');
LEGEND_CONSTANTS(:,3) = strpad('CaM_tot in component parameters (mole_per_dm_cubed)');
LEGEND_CONSTANTS(:,4) = strpad('km_CNG_0 in component parameters (per_second)');
LEGEND_CONSTANTS(:,5) = strpad('km_CaM4 in component parameters (per_second)');
LEGEND_CONSTANTS(:,6) = strpad('kp_CaM4 in component parameters (dm_6_per_second_per_mole_squared)');
LEGEND_CONSTANTS(:,7) = strpad('kp_CNG_i in component parameters (dm_3_per_second_per_mole)');
LEGEND_CONSTANTS(:,8) = strpad('km_CNG_i in component parameters (per_second)');
LEGEND_CONSTANTS(:,9) = strpad('i_Ca in component parameters (per_second)');
LEGEND_CONSTANTS(:,10) = strpad('k_Ca in component parameters (mole_per_dm_squared_per_second)');
LEGEND_CONSTANTS(:,11) = strpad('K_Ca in component parameters (mole_per_dm_cubed)');
LEGEND_ALGEBRAIC(:,1) = strpad('kp_act in component parameters (per_second)');
LEGEND_STATES(:,1) = strpad('CNG_o in component dCNG_o_dt (mole_per_dm_squared)');
LEGEND_ALGEBRAIC(:,2) = strpad('CNG_o_normalized in component dCNG_o_dt (dimensionless)');
LEGEND_STATES(:,2) = strpad('CNG_i in component dCNG_i_dt (mole_per_dm_squared)');
LEGEND_STATES(:,3) = strpad('CaM4 in component dCaM4_dt (mole_per_dm_cubed)');
LEGEND_STATES(:,4) = strpad('Ca in component dCa_dt (mole_per_dm_cubed)');
LEGEND_ALGEBRAIC(:,3) = strpad('Ca_normalized in component dCa_dt (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('CaM4_normalized in component dCaM4_dt (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('CNG_i_normalized in component dCNG_i_dt (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('CNG_c in component dCNG_c_dt (mole_per_dm_squared)');
LEGEND_ALGEBRAIC(:,7) = strpad('CaM in component dCaM_dt (mole_per_dm_cubed)');
LEGEND_RATES(:,1) = strpad('d/dt CNG_o in component dCNG_o_dt (mole_per_dm_squared)');
LEGEND_RATES(:,4) = strpad('d/dt Ca in component dCa_dt (mole_per_dm_cubed)');
LEGEND_RATES(:,3) = strpad('d/dt CaM4 in component dCaM4_dt (mole_per_dm_cubed)');
LEGEND_RATES(:,2) = strpad('d/dt CNG_i in component dCNG_i_dt (mole_per_dm_squared)');
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) = 5e-7;
CONSTANTS(:,2) = 1.3e-13;
CONSTANTS(:,3) = 2e-5;
CONSTANTS(:,4) = 1e-2;
CONSTANTS(:,5) = 2.5;
CONSTANTS(:,6) = 1.1e9;
CONSTANTS(:,7) = 2.1e6;
CONSTANTS(:,8) = 3.4e-1;
CONSTANTS(:,9) = 2e4;
CONSTANTS(:,10) = 1e-10;
CONSTANTS(:,11) = 1.2e-7;
STATES(:,1) = 0;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 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
RATES(:,4) = ( (STATES(:,1)./CONSTANTS(:,1)).*CONSTANTS(:,9) - ( (CONSTANTS(:,10)./CONSTANTS(:,1)).*STATES(:,4))./(STATES(:,4)+CONSTANTS(:,11))) - 4.00000.*( CONSTANTS(:,6).*power(STATES(:,4), 2.00000).*((CONSTANTS(:,3) - STATES(:,3)) - STATES(:,2)./CONSTANTS(:,1)) - CONSTANTS(:,5).*STATES(:,3));
RATES(:,3) = (( CONSTANTS(:,6).*power(STATES(:,4), 2.00000).*((CONSTANTS(:,3) - STATES(:,3)) - STATES(:,2)./CONSTANTS(:,1)) - CONSTANTS(:,5).*STATES(:,3)) - (CONSTANTS(:,7)./CONSTANTS(:,1)).*STATES(:,3).*(CONSTANTS(:,2) - STATES(:,1)))+ (CONSTANTS(:,8)./CONSTANTS(:,1)).*STATES(:,2);
RATES(:,2) = - CONSTANTS(:,8).*STATES(:,2)+ CONSTANTS(:,7).*STATES(:,3).*(CONSTANTS(:,2) - STATES(:,2));
ALGEBRAIC(:,1) = piecewise({VOI>0.100000&VOI<0.200000, 5.50000 , VOI>4.10000&VOI<4.20000, 5.50000 }, 1.60000e-05);
RATES(:,1) = ( ALGEBRAIC(:,1).*((CONSTANTS(:,2) - STATES(:,1)) - STATES(:,2)) - CONSTANTS(:,4).*STATES(:,1)) - CONSTANTS(:,7).*STATES(:,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) = piecewise({VOI>0.100000&VOI<0.200000, 5.50000 , VOI>4.10000&VOI<4.20000, 5.50000 }, 1.60000e-05);
ALGEBRAIC(:,2) = STATES(:,1)./CONSTANTS(:,2);
ALGEBRAIC(:,3) = STATES(:,4).*10000.0;
ALGEBRAIC(:,4) = STATES(:,3)./CONSTANTS(:,3);
ALGEBRAIC(:,5) = STATES(:,2)./CONSTANTS(:,2);
ALGEBRAIC(:,6) = (CONSTANTS(:,2) - STATES(:,1)) - STATES(:,2);
ALGEBRAIC(:,7) = (CONSTANTS(:,3) - STATES(:,3)) - (1.00000./CONSTANTS(:,1)).*STATES(:,2);
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
end
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