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 =15;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 29 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 (millisecond)');
LEGEND_CONSTANTS(:,1) = strpad('A_iso in component parameters (mN_per_mm2_per_mM)');
LEGEND_CONSTANTS(:,2) = strpad('k_off in component parameters (per_msec)');
LEGEND_CONSTANTS(:,3) = strpad('k_on in component parameters (per_mM_per_msec)');
LEGEND_CONSTANTS(:,4) = strpad('k_onI in component parameters (per_msec)');
LEGEND_CONSTANTS(:,5) = strpad('k_offi in component parameters (per_msec)');
LEGEND_CONSTANTS(:,6) = strpad('k_OFF in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('k_xboff in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('k_tmoff in component parameters (per_msec)');
LEGEND_CONSTANTS(:,9) = strpad('k_tmonc in component parameters (per_msec)');
LEGEND_CONSTANTS(:,10) = strpad('k_tmRU in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('k_tmxb in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('k_12 in component parameters (per_mM_per_msec)');
LEGEND_CONSTANTS(:,13) = strpad('k_minus12 in component parameters (per_msec)');
LEGEND_CONSTANTS(:,14) = strpad('k_Titin in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('k_3c in component parameters (per_msec)');
LEGEND_CONSTANTS(:,16) = strpad('k_3f in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('k_3xb in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('k_minus3 in component parameters (per_msec)');
LEGEND_CONSTANTS(:,19) = strpad('k_4 in component parameters (per_msec)');
LEGEND_CONSTANTS(:,20) = strpad('k_minus4 in component parameters (per_msec)');
LEGEND_CONSTANTS(:,21) = strpad('k_5 in component parameters (per_msec)');
LEGEND_ALGEBRAIC(:,1) = strpad('F_b in component active_force (mN_per_mm2)');
LEGEND_STATES(:,1) = strpad('RUA_MADPPi in component RU_species (mM)');
LEGEND_STATES(:,2) = strpad('RUA_MADP in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,6) = strpad('Q_CaB in component Ca_binding_rate (mM_per_msec)');
LEGEND_ALGEBRAIC(:,4) = strpad('RUNA in component RU_species (mM)');
LEGEND_STATES(:,3) = strpad('Ca in component RU_species (mM)');
LEGEND_STATES(:,4) = strpad('RUTCa_off in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,12) = strpad('Q_TCaA in component TnI_conf_change_rate (mM_per_msec)');
LEGEND_ALGEBRAIC(:,10) = strpad('k_offI in component TnI_conf_change_rate (per_msec)');
LEGEND_STATES(:,5) = strpad('RUTCa_on in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,8) = strpad('RUA in component RU_species (mM)');
LEGEND_CONSTANTS(:,22) = strpad('RU_total in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,3) = strpad('Q_TMA in component Tm_conf_change_rate (mM_per_msec)');
LEGEND_ALGEBRAIC(:,2) = strpad('k_tmon in component Tm_conf_change_rate (per_msec)');
LEGEND_STATES(:,6) = strpad('RUTM_on in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,11) = strpad('Q_MB in component myosin_binding_rate (mM_per_msec)');
LEGEND_CONSTANTS(:,29) = strpad('KTitin in component KTitin (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('L in component length (mmeter)');
LEGEND_CONSTANTS(:,23) = strpad('L_0 in component length (mmeter)');
LEGEND_CONSTANTS(:,24) = strpad('MADPPi in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,9) = strpad('RUTM_on_eff in component RU_species (mM)');
LEGEND_STATES(:,7) = strpad('RUAMADPPi in component RU_species (mM)');
LEGEND_CONSTANTS(:,26) = strpad('f_titinNormal in component KTitin (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('f_titinDamaged in component KTitin (dimensionless)');
LEGEND_ALGEBRAIC(:,15) = strpad('Q_Fgen in component Force_Generating_rate (mM_per_msec)');
LEGEND_ALGEBRAIC(:,14) = strpad('k_3 in component Force_Generating_rate (per_msec)');
LEGEND_ALGEBRAIC(:,13) = strpad('RUTCa_on_eff in component RU_species (mM)');
LEGEND_ALGEBRAIC(:,5) = strpad('Q_PiR in component Pi_release_rate (mM_per_msec)');
LEGEND_ALGEBRAIC(:,7) = strpad('Q_ADPR in component ADP_release_rate (mM_per_msec)');
LEGEND_CONSTANTS(:,27) = strpad('alpha in component alpha (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt RUTCa_off in component RU_species (mM)');
LEGEND_RATES(:,5) = strpad('d/dt RUTCa_on in component RU_species (mM)');
LEGEND_RATES(:,6) = strpad('d/dt RUTM_on in component RU_species (mM)');
LEGEND_RATES(:,7) = strpad('d/dt RUAMADPPi in component RU_species (mM)');
LEGEND_RATES(:,1) = strpad('d/dt RUA_MADPPi in component RU_species (mM)');
LEGEND_RATES(:,2) = strpad('d/dt RUA_MADP in component RU_species (mM)');
LEGEND_RATES(:,3) = strpad('d/dt Ca in component RU_species (mM)');
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) = 9000;
CONSTANTS(:,2) = 0.2;
CONSTANTS(:,3) = 17.3;
CONSTANTS(:,4) = 0.2;
CONSTANTS(:,5) = 0.075;
CONSTANTS(:,6) = -0.32;
CONSTANTS(:,7) = -1.37;
CONSTANTS(:,8) = 0.067;
CONSTANTS(:,9) = 0.014;
CONSTANTS(:,10) = 10;
CONSTANTS(:,11) = -1.86;
CONSTANTS(:,12) = 2;
CONSTANTS(:,13) = 0.6;
CONSTANTS(:,14) = 0.2;
CONSTANTS(:,15) = 0.025;
CONSTANTS(:,16) = 50;
CONSTANTS(:,17) = -1.23;
CONSTANTS(:,18) = 0.008;
CONSTANTS(:,19) = 0.077;
CONSTANTS(:,20) = 0.001;
CONSTANTS(:,21) = 0.03723;
STATES(:,1) = 0;
STATES(:,2) = 0;
STATES(:,3) = 0.01;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,22) = 0.0726;
STATES(:,6) = 0;
CONSTANTS(:,23) = 0.001;
CONSTANTS(:,24) = 0.1375;
STATES(:,7) = 0;
CONSTANTS(:,25) = CONSTANTS(:,23);
CONSTANTS(:,26) = CONSTANTS(:,14).*(9.96630./(1.00000+exp((CONSTANTS(:,25)./CONSTANTS(:,23)+1.06390)./0.0696000)));
CONSTANTS(:,27) = piecewise({CONSTANTS(:,25)<1.00000, 1.50000.*(CONSTANTS(:,25)./CONSTANTS(:,23)) - 0.500000 , 1.00000<=CONSTANTS(:,25)&CONSTANTS(:,25)<1.10000, 1.00000 }, - 1.60000.*(CONSTANTS(:,25)./CONSTANTS(:,23))+2.76000);
CONSTANTS(:,28) = CONSTANTS(:,14).*( - 31.0000.*(CONSTANTS(:,25)./CONSTANTS(:,23))+40.0000);
CONSTANTS(:,29) = piecewise({CONSTANTS(:,25)<=1.10000, CONSTANTS(:,26) }, CONSTANTS(:,28));
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(:,5) = CONSTANTS(:,19).*STATES(:,1) - CONSTANTS(:,20).*STATES(:,2);
ALGEBRAIC(:,7) = CONSTANTS(:,21).*STATES(:,2);
RATES(:,2) = ALGEBRAIC(:,5) - ALGEBRAIC(:,7);
ALGEBRAIC(:,4) = CONSTANTS(:,22) - (STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2));
ALGEBRAIC(:,6) = CONSTANTS(:,3).*ALGEBRAIC(:,4).*STATES(:,3) - CONSTANTS(:,2).*STATES(:,4);
RATES(:,3) = - ALGEBRAIC(:,6);
ALGEBRAIC(:,2) = CONSTANTS(:,9).*(STATES(:,5)./CONSTANTS(:,22)).*power(1.00000+ CONSTANTS(:,10).*(STATES(:,6)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,11).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 2.00000);
ALGEBRAIC(:,3) = ALGEBRAIC(:,2).*STATES(:,5) - CONSTANTS(:,8).*STATES(:,6);
ALGEBRAIC(:,9) = CONSTANTS(:,27).*STATES(:,6);
ALGEBRAIC(:,11) = CONSTANTS(:,12).*CONSTANTS(:,29).*CONSTANTS(:,24).*ALGEBRAIC(:,9) - CONSTANTS(:,13).*STATES(:,7);
RATES(:,6) = (ALGEBRAIC(:,3) - ALGEBRAIC(:,11))+ALGEBRAIC(:,7);
ALGEBRAIC(:,8) = STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2);
ALGEBRAIC(:,10) = CONSTANTS(:,5).*power(1.00000+ CONSTANTS(:,6).*(ALGEBRAIC(:,8)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,7).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 4.40000);
ALGEBRAIC(:,12) = CONSTANTS(:,4).*STATES(:,4) - ALGEBRAIC(:,10).*STATES(:,5);
RATES(:,4) = ALGEBRAIC(:,6) - ALGEBRAIC(:,12);
RATES(:,5) = ALGEBRAIC(:,12) - ALGEBRAIC(:,3);
ALGEBRAIC(:,13) = CONSTANTS(:,27).*STATES(:,5);
ALGEBRAIC(:,14) = CONSTANTS(:,15).*power(1.00000+( CONSTANTS(:,16).*(ALGEBRAIC(:,13)+ALGEBRAIC(:,9)+STATES(:,7)))./CONSTANTS(:,22), 2.00000).*power(1.00000+( CONSTANTS(:,17).*(STATES(:,1)+STATES(:,2)))./CONSTANTS(:,22), 2.00000);
ALGEBRAIC(:,15) = ALGEBRAIC(:,14).*STATES(:,7) - CONSTANTS(:,18).*STATES(:,1);
RATES(:,7) = ALGEBRAIC(:,11) - ALGEBRAIC(:,15);
RATES(:,1) = ALGEBRAIC(:,15) - ALGEBRAIC(:,5);
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(:,5) = CONSTANTS(:,19).*STATES(:,1) - CONSTANTS(:,20).*STATES(:,2);
ALGEBRAIC(:,7) = CONSTANTS(:,21).*STATES(:,2);
ALGEBRAIC(:,4) = CONSTANTS(:,22) - (STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2));
ALGEBRAIC(:,6) = CONSTANTS(:,3).*ALGEBRAIC(:,4).*STATES(:,3) - CONSTANTS(:,2).*STATES(:,4);
ALGEBRAIC(:,2) = CONSTANTS(:,9).*(STATES(:,5)./CONSTANTS(:,22)).*power(1.00000+ CONSTANTS(:,10).*(STATES(:,6)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,11).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 2.00000);
ALGEBRAIC(:,3) = ALGEBRAIC(:,2).*STATES(:,5) - CONSTANTS(:,8).*STATES(:,6);
ALGEBRAIC(:,9) = CONSTANTS(:,27).*STATES(:,6);
ALGEBRAIC(:,11) = CONSTANTS(:,12).*CONSTANTS(:,29).*CONSTANTS(:,24).*ALGEBRAIC(:,9) - CONSTANTS(:,13).*STATES(:,7);
ALGEBRAIC(:,8) = STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2);
ALGEBRAIC(:,10) = CONSTANTS(:,5).*power(1.00000+ CONSTANTS(:,6).*(ALGEBRAIC(:,8)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,7).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 4.40000);
ALGEBRAIC(:,12) = CONSTANTS(:,4).*STATES(:,4) - ALGEBRAIC(:,10).*STATES(:,5);
ALGEBRAIC(:,13) = CONSTANTS(:,27).*STATES(:,5);
ALGEBRAIC(:,14) = CONSTANTS(:,15).*power(1.00000+( CONSTANTS(:,16).*(ALGEBRAIC(:,13)+ALGEBRAIC(:,9)+STATES(:,7)))./CONSTANTS(:,22), 2.00000).*power(1.00000+( CONSTANTS(:,17).*(STATES(:,1)+STATES(:,2)))./CONSTANTS(:,22), 2.00000);
ALGEBRAIC(:,15) = ALGEBRAIC(:,14).*STATES(:,7) - CONSTANTS(:,18).*STATES(:,1);
ALGEBRAIC(:,1) = CONSTANTS(:,1).*(STATES(:,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