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 =6;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 20 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 (ms)');
LEGEND_ALGEBRAIC(:,4) = strpad('Ca_i in component intracellular_ion_concentrations (uM)');
LEGEND_ALGEBRAIC(:,1) = strpad('mtime in component intracellular_ion_concentrations (dimensionless)');
LEGEND_STATES(:,1) = strpad('xb in component crossbridges (dimensionless)');
LEGEND_STATES(:,2) = strpad('TRPN in component troponin (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('k_xb in component crossbridges (per_ms)');
LEGEND_CONSTANTS(:,2) = strpad('nperm in component crossbridges (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('perm50 in component crossbridges (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('permtot in component crossbridges (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('Ca_50ref in component troponin (uM)');
LEGEND_CONSTANTS(:,5) = strpad('beta_1 in component troponin (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('k_off in component troponin (per_ms)');
LEGEND_CONSTANTS(:,7) = strpad('n_TRPN in component troponin (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('lambda_m in component filament_overlap (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('Ca_50 in component troponin (uM)');
LEGEND_CONSTANTS(:,15) = strpad('lambda in component Myofilaments (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('dlambdadt in component Myofilaments (per_ms)');
LEGEND_CONSTANTS(:,20) = strpad('overlap in component filament_overlap (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('beta_0 in component filament_overlap (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('lambda_s in component filament_overlap (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('T_ref in component isometric_tension (kPa)');
LEGEND_ALGEBRAIC(:,3) = strpad('T_0 in component isometric_tension (kPa)');
LEGEND_ALGEBRAIC(:,5) = strpad('Q in component dynamic_stiffness (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('a in component dynamic_stiffness (dimensionless)');
LEGEND_STATES(:,3) = strpad('Q_1 in component dynamic_stiffness (dimensionless)');
LEGEND_STATES(:,4) = strpad('Q_2 in component dynamic_stiffness (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('A_1 in component dynamic_stiffness (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('A_2 in component dynamic_stiffness (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('alpha_1 in component dynamic_stiffness (per_ms)');
LEGEND_CONSTANTS(:,14) = strpad('alpha_2 in component dynamic_stiffness (per_ms)');
LEGEND_ALGEBRAIC(:,6) = strpad('Tension in component dynamic_stiffness (kPa)');
LEGEND_RATES(:,1) = strpad('d/dt xb in component crossbridges (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt TRPN in component troponin (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt Q_1 in component dynamic_stiffness (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt Q_2 in component dynamic_stiffness (dimensionless)');
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) = 0.00046;
STATES(:,2) = 0.0752;
CONSTANTS(:,1) = 0.1;
CONSTANTS(:,2) = 5;
CONSTANTS(:,3) = 0.35;
CONSTANTS(:,4) = 0.8;
CONSTANTS(:,5) = -1.5;
CONSTANTS(:,6) = 0.1;
CONSTANTS(:,7) = 2;
CONSTANTS(:,8) = 1.65;
CONSTANTS(:,9) = 120;
CONSTANTS(:,10) = 0.35;
STATES(:,3) = 0;
STATES(:,4) = 0;
CONSTANTS(:,11) = -29;
CONSTANTS(:,12) = 116;
CONSTANTS(:,13) = 0.1;
CONSTANTS(:,14) = 0.5;
CONSTANTS(:,15) = 1.00000;
CONSTANTS(:,16) = 0.00000;
CONSTANTS(:,17) = piecewise({CONSTANTS(:,15)>1.20000, 1.20000 }, CONSTANTS(:,15));
CONSTANTS(:,18) = CONSTANTS(:,4).*(1.00000+ CONSTANTS(:,5).*(CONSTANTS(:,17) - 1.00000));
CONSTANTS(:,19) = piecewise({CONSTANTS(:,17)>=0.870000, 0.870000 }, CONSTANTS(:,17));
CONSTANTS(:,20) = 1.00000+ CONSTANTS(:,8).*((CONSTANTS(:,17)+CONSTANTS(:,19)) - 1.87000);
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(:,3) = CONSTANTS(:,11).*CONSTANTS(:,16) - CONSTANTS(:,13).*STATES(:,3);
RATES(:,4) = CONSTANTS(:,12).*CONSTANTS(:,16) - CONSTANTS(:,14).*STATES(:,4);
ALGEBRAIC(:,2) = power(power(STATES(:,2)./CONSTANTS(:,3), CONSTANTS(:,2)), 1.0 ./ 2);
RATES(:,1) = CONSTANTS(:,1).*( ALGEBRAIC(:,2).*(1.00000 - STATES(:,1)) - (1.00000./ALGEBRAIC(:,2)).*STATES(:,1));
ALGEBRAIC(:,1) = (VOI - 167.000.*floor(VOI./167.000))./1.00000;
ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,1)>=1.17000&ALGEBRAIC(:,1)<30.8400, 1.00000.*1.85358e-05.*power(ALGEBRAIC(:,1), 3.00000)+ - 0.00159034.*power(ALGEBRAIC(:,1), 2.00000)+ 0.0436459.*power(ALGEBRAIC(:,1), 1.00000)+0.167079 , ALGEBRAIC(:,1)>=30.8400, (( 1.00000.* - 5.74585e-08.*power(ALGEBRAIC(:,1), 3.00000)+ 3.11222e-05.*power(ALGEBRAIC(:,1), 2.00000)) - 0.00661849.*power(ALGEBRAIC(:,1), 1.00000))+0.720442 }, 0.216000);
RATES(:,2) = CONSTANTS(:,6).*( power(ALGEBRAIC(:,4)./CONSTANTS(:,18), CONSTANTS(:,7)).*(1.00000 - STATES(:,2)) - STATES(:,2));
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(:,2) = power(power(STATES(:,2)./CONSTANTS(:,3), CONSTANTS(:,2)), 1.0 ./ 2);
ALGEBRAIC(:,1) = (VOI - 167.000.*floor(VOI./167.000))./1.00000;
ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,1)>=1.17000&ALGEBRAIC(:,1)<30.8400, 1.00000.*1.85358e-05.*power(ALGEBRAIC(:,1), 3.00000)+ - 0.00159034.*power(ALGEBRAIC(:,1), 2.00000)+ 0.0436459.*power(ALGEBRAIC(:,1), 1.00000)+0.167079 , ALGEBRAIC(:,1)>=30.8400, (( 1.00000.* - 5.74585e-08.*power(ALGEBRAIC(:,1), 3.00000)+ 3.11222e-05.*power(ALGEBRAIC(:,1), 2.00000)) - 0.00661849.*power(ALGEBRAIC(:,1), 1.00000))+0.720442 }, 0.216000);
ALGEBRAIC(:,3) = CONSTANTS(:,9).*STATES(:,1).*CONSTANTS(:,20);
ALGEBRAIC(:,5) = STATES(:,3)+STATES(:,4);
ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,5)<0.00000, ( ALGEBRAIC(:,3).*( CONSTANTS(:,10).*ALGEBRAIC(:,5)+1.00000))./(1.00000 - ALGEBRAIC(:,5)) }, ( ALGEBRAIC(:,3).*(1.00000+ (CONSTANTS(:,10)+2.00000).*ALGEBRAIC(:,5)))./(1.00000+ALGEBRAIC(:,5)));
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