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 =17;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 25 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(:,2) = strpad('Ca_i in component intracellular_ion_concentrations (mM)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ca_b in component intracellular_ion_concentrations (mM)');
LEGEND_STATES(:,1) = strpad('TRPN in component intracellular_ion_concentrations (mM)');
LEGEND_CONSTANTS(:,1) = strpad('Ca_TRPN_Max in component troponin (mM)');
LEGEND_ALGEBRAIC(:,17) = strpad('J_TRPN in component troponin (mM_per_ms)');
LEGEND_STATES(:,2) = strpad('z in component tropomyosin (dimensionless)');
LEGEND_ALGEBRAIC(:,10) = strpad('z_max in component tropomyosin (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('k_on in component troponin (per_mM_per_ms)');
LEGEND_CONSTANTS(:,3) = strpad('k_Ref_off in component troponin (per_ms)');
LEGEND_CONSTANTS(:,4) = strpad('gamma_trpn in component troponin (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('alpha_0 in component tropomyosin (per_ms)');
LEGEND_CONSTANTS(:,6) = strpad('alpha_r1 in component tropomyosin (per_ms)');
LEGEND_CONSTANTS(:,7) = strpad('alpha_r2 in component tropomyosin (per_ms)');
LEGEND_CONSTANTS(:,8) = strpad('n_Rel in component tropomyosin (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('K_z in component tropomyosin (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('n_Hill in component tropomyosin (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('Ca_50ref in component tropomyosin (mM)');
LEGEND_CONSTANTS(:,12) = strpad('z_p in component tropomyosin (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('beta_1 in component tropomyosin (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('Ca_50 in component tropomyosin (mM)');
LEGEND_ALGEBRAIC(:,8) = strpad('Ca_TRPN_50 in component tropomyosin (mM)');
LEGEND_CONSTANTS(:,23) = strpad('K_2 in component tropomyosin (per_ms)');
LEGEND_CONSTANTS(:,25) = strpad('K_1 in component tropomyosin (per_ms)');
LEGEND_ALGEBRAIC(:,9) = strpad('alpha_Tm in component tropomyosin (per_ms)');
LEGEND_ALGEBRAIC(:,3) = strpad('beta_Tm in component tropomyosin (per_ms)');
LEGEND_CONSTANTS(:,14) = strpad('beta_0 in component filament_overlap (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('lambda in component Myofilaments (dimensionless)');
LEGEND_ALGEBRAIC(:,16) = strpad('k_off in component troponin (per_ms)');
LEGEND_ALGEBRAIC(:,15) = strpad('Tension in component Cross_Bridges (N_per_mm2)');
LEGEND_CONSTANTS(:,15) = strpad('T_ref in component length_independent_tension (N_per_mm2)');
LEGEND_ALGEBRAIC(:,4) = strpad('ExtensionRatio in component Myofilaments (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('dExtensionRatiodt in component Myofilaments (per_ms)');
LEGEND_ALGEBRAIC(:,6) = strpad('lambda_prev in component Myofilaments (dimensionless)');
LEGEND_ALGEBRAIC(:,11) = strpad('overlap in component filament_overlap (dimensionless)');
LEGEND_ALGEBRAIC(:,12) = strpad('T_Base in component length_independent_tension (N_per_mm2)');
LEGEND_ALGEBRAIC(:,13) = strpad('T_0 in component isometric_tension (N_per_mm2)');
LEGEND_ALGEBRAIC(:,14) = strpad('Q in component Cross_Bridges (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('a in component Cross_Bridges (dimensionless)');
LEGEND_STATES(:,3) = strpad('Q_1 in component Cross_Bridges (dimensionless)');
LEGEND_STATES(:,4) = strpad('Q_2 in component Cross_Bridges (dimensionless)');
LEGEND_STATES(:,5) = strpad('Q_3 in component Cross_Bridges (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('A_1 in component Cross_Bridges (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('A_2 in component Cross_Bridges (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('A_3 in component Cross_Bridges (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('alpha_1 in component Cross_Bridges (per_ms)');
LEGEND_CONSTANTS(:,21) = strpad('alpha_2 in component Cross_Bridges (per_ms)');
LEGEND_CONSTANTS(:,22) = strpad('alpha_3 in component Cross_Bridges (per_ms)');
LEGEND_RATES(:,1) = strpad('d/dt TRPN in component intracellular_ion_concentrations (mM)');
LEGEND_RATES(:,2) = strpad('d/dt z in component tropomyosin (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt Q_1 in component Cross_Bridges (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt Q_2 in component Cross_Bridges (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt Q_3 in component Cross_Bridges (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) = 0.067593139865;
CONSTANTS(:,1) = 70e-3;
STATES(:,2) = 0.014417937837;
CONSTANTS(:,2) = 100;
CONSTANTS(:,3) = 0.2;
CONSTANTS(:,4) = 2;
CONSTANTS(:,5) = 8e-3;
CONSTANTS(:,6) = 2e-3;
CONSTANTS(:,7) = 1.75e-3;
CONSTANTS(:,8) = 3;
CONSTANTS(:,9) = 0.15;
CONSTANTS(:,10) = 3;
CONSTANTS(:,11) = 1.05e-3;
CONSTANTS(:,12) = 0.85;
CONSTANTS(:,13) = -4;
CONSTANTS(:,14) = 4.9;
CONSTANTS(:,15) = 56.2;
CONSTANTS(:,16) = 0.35;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,17) = -29;
CONSTANTS(:,18) = 138;
CONSTANTS(:,19) = 129;
CONSTANTS(:,20) = 0.03;
CONSTANTS(:,21) = 0.13;
CONSTANTS(:,22) = 0.625;
CONSTANTS(:,23) = (( CONSTANTS(:,7).*power(CONSTANTS(:,12), CONSTANTS(:,8)))./(power(CONSTANTS(:,12), CONSTANTS(:,8))+power(CONSTANTS(:,9), CONSTANTS(:,8)))).*(1.00000 - ( CONSTANTS(:,8).*power(CONSTANTS(:,9), CONSTANTS(:,8)))./(power(CONSTANTS(:,12), CONSTANTS(:,8))+power(CONSTANTS(:,9), CONSTANTS(:,8))));
CONSTANTS(:,24) = 0.00000;
CONSTANTS(:,25) = ( CONSTANTS(:,7).*power(CONSTANTS(:,12), CONSTANTS(:,8) - 1.00000).*CONSTANTS(:,8).*power(CONSTANTS(:,9), CONSTANTS(:,8)))./power(power(CONSTANTS(:,12), CONSTANTS(:,8))+power(CONSTANTS(:,9), CONSTANTS(:,8)), 2.00000);
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(:,3) = CONSTANTS(:,17).*CONSTANTS(:,24) - CONSTANTS(:,20).*STATES(:,3);
RATES(:,4) = CONSTANTS(:,18).*CONSTANTS(:,24) - CONSTANTS(:,21).*STATES(:,4);
RATES(:,5) = CONSTANTS(:,19).*CONSTANTS(:,24) - CONSTANTS(:,22).*STATES(:,5);
ALGEBRAIC(:,1) = CONSTANTS(:,1) - STATES(:,1);
ALGEBRAIC(:,4) = piecewise({VOI>1000.00, 1.00000 }, 1.00000);
ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,4)>0.800000&ALGEBRAIC(:,4)<=1.15000, ALGEBRAIC(:,4) , ALGEBRAIC(:,4)>1.15000, 1.15000 }, 0.800000);
ALGEBRAIC(:,7) = CONSTANTS(:,11).*(1.00000+ CONSTANTS(:,13).*(ALGEBRAIC(:,5) - 1.00000));
ALGEBRAIC(:,8) = ( ALGEBRAIC(:,7).*CONSTANTS(:,1))./(ALGEBRAIC(:,7)+ (CONSTANTS(:,3)./CONSTANTS(:,2)).*(1.00000 - ( (1.00000+ CONSTANTS(:,14).*(ALGEBRAIC(:,5) - 1.00000)).*0.500000)./CONSTANTS(:,4)));
ALGEBRAIC(:,9) = CONSTANTS(:,5).*power(ALGEBRAIC(:,1)./ALGEBRAIC(:,8), CONSTANTS(:,10));
ALGEBRAIC(:,3) = CONSTANTS(:,6)+( CONSTANTS(:,7).*power(STATES(:,2), CONSTANTS(:,8) - 1.00000))./(power(STATES(:,2), CONSTANTS(:,8))+power(CONSTANTS(:,9), CONSTANTS(:,8)));
RATES(:,2) = ALGEBRAIC(:,9).*(1.00000 - STATES(:,2)) - ALGEBRAIC(:,3).*STATES(:,2);
ALGEBRAIC(:,2) = piecewise({VOI<1.00000, 1000.00.*1.84330e-07 , VOI>=10.0000&VOI<15.0000, 1000.00.*((( 1.05500.*power(VOI./1000.00, 3.00000) - 0.0350700.*power(VOI./1000.00, 2.00000))+( 0.000399200.*VOI)./1000.00) - 1.35600e-06) , VOI>=15.0000&VOI<55.0000, 1000.00.*((( 0.0140000.*power(VOI./1000.00, 3.00000) - 0.00255500.*power(VOI./1000.00, 2.00000))+( 0.000149400.*VOI)./1000.00) - 1.42800e-06) , VOI>=55.0000&VOI<250.000, 1000.00.*((( 1.73900e-05.*power(VOI./1000.00, 3.00000) - 3.20900e-06.*power(VOI./1000.00, 2.00000)) - ( 5.68900e-06.*VOI)./1000.00)+1.71900e-06) , VOI>=250.000&VOI<490.000, 1000.00.*(((( 0.000132100.*power(VOI./1000.00, 4.00000) - 0.000219700.*power(VOI./1000.00, 3.00000))+ 0.000137400.*power(VOI./1000.00, 2.00000)) - ( 3.89500e-05.*VOI)./1000.00)+4.44100e-06) }, 1000.00.*1.21480e-07);
ALGEBRAIC(:,11) = 1.00000+ CONSTANTS(:,14).*(ALGEBRAIC(:,5) - 1.00000);
ALGEBRAIC(:,10) = (CONSTANTS(:,5)./power(ALGEBRAIC(:,8)./CONSTANTS(:,1), CONSTANTS(:,10)) - CONSTANTS(:,23))./(CONSTANTS(:,6)+CONSTANTS(:,25)+CONSTANTS(:,5)./power(ALGEBRAIC(:,8)./CONSTANTS(:,1), CONSTANTS(:,10)));
ALGEBRAIC(:,12) = ( CONSTANTS(:,15).*STATES(:,2))./ALGEBRAIC(:,10);
ALGEBRAIC(:,13) = ALGEBRAIC(:,12).*ALGEBRAIC(:,11);
ALGEBRAIC(:,14) = STATES(:,3)+STATES(:,4)+STATES(:,5);
ALGEBRAIC(:,15) = piecewise({ALGEBRAIC(:,14)<0.00000, ( ALGEBRAIC(:,13).*( CONSTANTS(:,16).*ALGEBRAIC(:,14)+1.00000))./(1.00000 - ALGEBRAIC(:,14)) }, ( ALGEBRAIC(:,13).*(1.00000+ (CONSTANTS(:,16)+2.00000).*ALGEBRAIC(:,14)))./(1.00000+ALGEBRAIC(:,14)));
ALGEBRAIC(:,16) = piecewise({1.00000 - ALGEBRAIC(:,15)./( CONSTANTS(:,4).*CONSTANTS(:,15))>0.100000, CONSTANTS(:,3).*(1.00000 - ALGEBRAIC(:,15)./( CONSTANTS(:,4).*CONSTANTS(:,15))) }, CONSTANTS(:,3).*0.100000);
ALGEBRAIC(:,17) = (CONSTANTS(:,1) - STATES(:,1)).*ALGEBRAIC(:,16) - ALGEBRAIC(:,2).*STATES(:,1).*CONSTANTS(:,2);
RATES(:,1) = ALGEBRAIC(:,17);
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) - STATES(:,1);
ALGEBRAIC(:,4) = piecewise({VOI>1000.00, 1.00000 }, 1.00000);
ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,4)>0.800000&ALGEBRAIC(:,4)<=1.15000, ALGEBRAIC(:,4) , ALGEBRAIC(:,4)>1.15000, 1.15000 }, 0.800000);
ALGEBRAIC(:,7) = CONSTANTS(:,11).*(1.00000+ CONSTANTS(:,13).*(ALGEBRAIC(:,5) - 1.00000));
ALGEBRAIC(:,8) = ( ALGEBRAIC(:,7).*CONSTANTS(:,1))./(ALGEBRAIC(:,7)+ (CONSTANTS(:,3)./CONSTANTS(:,2)).*(1.00000 - ( (1.00000+ CONSTANTS(:,14).*(ALGEBRAIC(:,5) - 1.00000)).*0.500000)./CONSTANTS(:,4)));
ALGEBRAIC(:,9) = CONSTANTS(:,5).*power(ALGEBRAIC(:,1)./ALGEBRAIC(:,8), CONSTANTS(:,10));
ALGEBRAIC(:,3) = CONSTANTS(:,6)+( CONSTANTS(:,7).*power(STATES(:,2), CONSTANTS(:,8) - 1.00000))./(power(STATES(:,2), CONSTANTS(:,8))+power(CONSTANTS(:,9), CONSTANTS(:,8)));
ALGEBRAIC(:,2) = piecewise({VOI<1.00000, 1000.00.*1.84330e-07 , VOI>=10.0000&VOI<15.0000, 1000.00.*((( 1.05500.*power(VOI./1000.00, 3.00000) - 0.0350700.*power(VOI./1000.00, 2.00000))+( 0.000399200.*VOI)./1000.00) - 1.35600e-06) , VOI>=15.0000&VOI<55.0000, 1000.00.*((( 0.0140000.*power(VOI./1000.00, 3.00000) - 0.00255500.*power(VOI./1000.00, 2.00000))+( 0.000149400.*VOI)./1000.00) - 1.42800e-06) , VOI>=55.0000&VOI<250.000, 1000.00.*((( 1.73900e-05.*power(VOI./1000.00, 3.00000) - 3.20900e-06.*power(VOI./1000.00, 2.00000)) - ( 5.68900e-06.*VOI)./1000.00)+1.71900e-06) , VOI>=250.000&VOI<490.000, 1000.00.*(((( 0.000132100.*power(VOI./1000.00, 4.00000) - 0.000219700.*power(VOI./1000.00, 3.00000))+ 0.000137400.*power(VOI./1000.00, 2.00000)) - ( 3.89500e-05.*VOI)./1000.00)+4.44100e-06) }, 1000.00.*1.21480e-07);
ALGEBRAIC(:,11) = 1.00000+ CONSTANTS(:,14).*(ALGEBRAIC(:,5) - 1.00000);
ALGEBRAIC(:,10) = (CONSTANTS(:,5)./power(ALGEBRAIC(:,8)./CONSTANTS(:,1), CONSTANTS(:,10)) - CONSTANTS(:,23))./(CONSTANTS(:,6)+CONSTANTS(:,25)+CONSTANTS(:,5)./power(ALGEBRAIC(:,8)./CONSTANTS(:,1), CONSTANTS(:,10)));
ALGEBRAIC(:,12) = ( CONSTANTS(:,15).*STATES(:,2))./ALGEBRAIC(:,10);
ALGEBRAIC(:,13) = ALGEBRAIC(:,12).*ALGEBRAIC(:,11);
ALGEBRAIC(:,14) = STATES(:,3)+STATES(:,4)+STATES(:,5);
ALGEBRAIC(:,15) = piecewise({ALGEBRAIC(:,14)<0.00000, ( ALGEBRAIC(:,13).*( CONSTANTS(:,16).*ALGEBRAIC(:,14)+1.00000))./(1.00000 - ALGEBRAIC(:,14)) }, ( ALGEBRAIC(:,13).*(1.00000+ (CONSTANTS(:,16)+2.00000).*ALGEBRAIC(:,14)))./(1.00000+ALGEBRAIC(:,14)));
ALGEBRAIC(:,16) = piecewise({1.00000 - ALGEBRAIC(:,15)./( CONSTANTS(:,4).*CONSTANTS(:,15))>0.100000, CONSTANTS(:,3).*(1.00000 - ALGEBRAIC(:,15)./( CONSTANTS(:,4).*CONSTANTS(:,15))) }, CONSTANTS(:,3).*0.100000);
ALGEBRAIC(:,17) = (CONSTANTS(:,1) - STATES(:,1)).*ALGEBRAIC(:,16) - ALGEBRAIC(:,2).*STATES(:,1).*CONSTANTS(:,2);
ALGEBRAIC(:,6) = ALGEBRAIC(:,4);
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