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 =3;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 40 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 (hour)');
LEGEND_CONSTANTS(:,1) = strpad('v_sP in component nucleus (nanomolar_hour)');
LEGEND_CONSTANTS(:,2) = strpad('v_mP in component nucleus (nanomolar_hour)');
LEGEND_CONSTANTS(:,3) = strpad('K_IP in component nucleus (nanomolar)');
LEGEND_CONSTANTS(:,4) = strpad('K_mP in component nucleus (nanomolar)');
LEGEND_CONSTANTS(:,5) = strpad('v_sT in component nucleus (nanomolar_hour)');
LEGEND_CONSTANTS(:,6) = strpad('v_mT in component nucleus (nanomolar_hour)');
LEGEND_CONSTANTS(:,7) = strpad('K_IT in component nucleus (nanomolar)');
LEGEND_CONSTANTS(:,8) = strpad('K_mT in component nucleus (nanomolar)');
LEGEND_CONSTANTS(:,9) = strpad('k_d in component cytosol (per_hour)');
LEGEND_CONSTANTS(:,10) = strpad('n in component nucleus (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('k_1 in component cytosol (per_hour)');
LEGEND_CONSTANTS(:,12) = strpad('k_2 in component cytosol (per_hour)');
LEGEND_CONSTANTS(:,13) = strpad('k_dN in component nucleus (per_hour)');
LEGEND_STATES(:,1) = strpad('C in component cytosol (nanomolar)');
LEGEND_STATES(:,2) = strpad('M_P in component nucleus (nanomolar)');
LEGEND_STATES(:,3) = strpad('M_T in component nucleus (nanomolar)');
LEGEND_STATES(:,4) = strpad('C_N in component nucleus (nanomolar)');
LEGEND_CONSTANTS(:,14) = strpad('k_3 in component cytosol (per_nanomolar_hour)');
LEGEND_CONSTANTS(:,15) = strpad('k_4 in component cytosol (per_hour)');
LEGEND_CONSTANTS(:,16) = strpad('k_dC in component cytosol (per_hour)');
LEGEND_STATES(:,5) = strpad('P_0 in component PER (nanomolar)');
LEGEND_STATES(:,6) = strpad('P_1 in component PER (nanomolar)');
LEGEND_STATES(:,7) = strpad('P_2 in component PER (nanomolar)');
LEGEND_STATES(:,8) = strpad('T_0 in component TIM (nanomolar)');
LEGEND_STATES(:,9) = strpad('T_1 in component TIM (nanomolar)');
LEGEND_STATES(:,10) = strpad('T_2 in component TIM (nanomolar)');
LEGEND_CONSTANTS(:,17) = strpad('V_1P in component PER (nanomolar_hour)');
LEGEND_CONSTANTS(:,18) = strpad('V_2P in component PER (nanomolar_hour)');
LEGEND_CONSTANTS(:,19) = strpad('V_3P in component PER (nanomolar_hour)');
LEGEND_CONSTANTS(:,20) = strpad('V_4P in component PER (nanomolar_hour)');
LEGEND_CONSTANTS(:,21) = strpad('K_1P in component PER (nanomolar)');
LEGEND_CONSTANTS(:,22) = strpad('K_2P in component PER (nanomolar)');
LEGEND_CONSTANTS(:,23) = strpad('K_3P in component PER (nanomolar)');
LEGEND_CONSTANTS(:,24) = strpad('K_4P in component PER (nanomolar)');
LEGEND_CONSTANTS(:,25) = strpad('K_dP in component PER (nanomolar)');
LEGEND_CONSTANTS(:,26) = strpad('v_dP in component PER (nanomolar_hour)');
LEGEND_CONSTANTS(:,27) = strpad('k_sP in component PER (per_hour)');
LEGEND_CONSTANTS(:,28) = strpad('V_1T in component TIM (nanomolar_hour)');
LEGEND_CONSTANTS(:,29) = strpad('V_2T in component TIM (nanomolar_hour)');
LEGEND_CONSTANTS(:,30) = strpad('V_3T in component TIM (nanomolar_hour)');
LEGEND_CONSTANTS(:,31) = strpad('V_4T in component TIM (nanomolar_hour)');
LEGEND_CONSTANTS(:,32) = strpad('K_1T in component TIM (nanomolar)');
LEGEND_CONSTANTS(:,33) = strpad('K_2T in component TIM (nanomolar)');
LEGEND_CONSTANTS(:,34) = strpad('K_3T in component TIM (nanomolar)');
LEGEND_CONSTANTS(:,35) = strpad('K_4T in component TIM (nanomolar)');
LEGEND_CONSTANTS(:,36) = strpad('K_dT in component TIM (nanomolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('v_dT in component LD_cycle (nanomolar_hour)');
LEGEND_CONSTANTS(:,37) = strpad('k_sT in component TIM (per_hour)');
LEGEND_CONSTANTS(:,38) = strpad('PI in component LD_cycle (dimensionless)');
LEGEND_CONSTANTS(:,39) = strpad('v_dT_dark in component LD_cycle (nanomolar_hour)');
LEGEND_CONSTANTS(:,40) = strpad('v_dT_light in component LD_cycle (nanomolar_hour)');
LEGEND_ALGEBRAIC(:,2) = strpad('P_t in component PER_total (nanomolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('T_t in component TIM_total (nanomolar)');
LEGEND_RATES(:,2) = strpad('d/dt M_P in component nucleus (nanomolar)');
LEGEND_RATES(:,3) = strpad('d/dt M_T in component nucleus (nanomolar)');
LEGEND_RATES(:,4) = strpad('d/dt C_N in component nucleus (nanomolar)');
LEGEND_RATES(:,1) = strpad('d/dt C in component cytosol (nanomolar)');
LEGEND_RATES(:,5) = strpad('d/dt P_0 in component PER (nanomolar)');
LEGEND_RATES(:,6) = strpad('d/dt P_1 in component PER (nanomolar)');
LEGEND_RATES(:,7) = strpad('d/dt P_2 in component PER (nanomolar)');
LEGEND_RATES(:,8) = strpad('d/dt T_0 in component TIM (nanomolar)');
LEGEND_RATES(:,9) = strpad('d/dt T_1 in component TIM (nanomolar)');
LEGEND_RATES(:,10) = strpad('d/dt T_2 in component TIM (nanomolar)');
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) = 0.8;
CONSTANTS(:,2) = 0.8;
CONSTANTS(:,3) = 1;
CONSTANTS(:,4) = 0.2;
CONSTANTS(:,5) = 1;
CONSTANTS(:,6) = 0.7;
CONSTANTS(:,7) = 1;
CONSTANTS(:,8) = 0.2;
CONSTANTS(:,9) = 0.01;
CONSTANTS(:,10) = 4;
CONSTANTS(:,11) = 1.2;
CONSTANTS(:,12) = 0.2;
CONSTANTS(:,13) = 0.01;
STATES(:,1) = 0.1790;
STATES(:,2) = 0.09107;
STATES(:,3) = 1.427;
STATES(:,4) = 1.203;
CONSTANTS(:,14) = 1.2;
CONSTANTS(:,15) = 0.6;
CONSTANTS(:,16) = 0.01;
STATES(:,5) = 0.02324;
STATES(:,6) = 0.02210;
STATES(:,7) = 0.01251;
STATES(:,8) = 0.5420;
STATES(:,9) = 0.8000;
STATES(:,10) = 4.733;
CONSTANTS(:,17) = 8;
CONSTANTS(:,18) = 1;
CONSTANTS(:,19) = 8;
CONSTANTS(:,20) = 1;
CONSTANTS(:,21) = 2;
CONSTANTS(:,22) = 2;
CONSTANTS(:,23) = 2;
CONSTANTS(:,24) = 2;
CONSTANTS(:,25) = 0.2;
CONSTANTS(:,26) = 2;
CONSTANTS(:,27) = 0.9;
CONSTANTS(:,28) = 8;
CONSTANTS(:,29) = 1;
CONSTANTS(:,30) = 8;
CONSTANTS(:,31) = 1;
CONSTANTS(:,32) = 2;
CONSTANTS(:,33) = 2;
CONSTANTS(:,34) = 2;
CONSTANTS(:,35) = 2;
CONSTANTS(:,36) = 0.2;
CONSTANTS(:,37) = 0.9;
CONSTANTS(:,38) = 3.141592653589793;
CONSTANTS(:,39) = 2;
CONSTANTS(:,40) = 4;
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);
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
end
RATES(:,2) = CONSTANTS(:,1).*CONSTANTS(:,3) .^ CONSTANTS(:,10)./(CONSTANTS(:,3) .^ CONSTANTS(:,10)+STATES(:,4) .^ CONSTANTS(:,10)) - CONSTANTS(:,2).*STATES(:,2)./(CONSTANTS(:,4)+STATES(:,2)) - CONSTANTS(:,9).*STATES(:,2);
RATES(:,3) = CONSTANTS(:,5).*CONSTANTS(:,7) .^ CONSTANTS(:,10)./(CONSTANTS(:,7) .^ CONSTANTS(:,10)+STATES(:,4) .^ CONSTANTS(:,10)) - CONSTANTS(:,6).*STATES(:,3)./(CONSTANTS(:,8)+STATES(:,3)) - CONSTANTS(:,9).*STATES(:,3);
RATES(:,4) = CONSTANTS(:,11).*STATES(:,1) - CONSTANTS(:,12).*STATES(:,4) - CONSTANTS(:,13).*STATES(:,4);
RATES(:,1) = CONSTANTS(:,14).*STATES(:,7).*STATES(:,10) - CONSTANTS(:,15).*STATES(:,1) - CONSTANTS(:,11).*STATES(:,1)+ CONSTANTS(:,12).*STATES(:,4) - CONSTANTS(:,16).*STATES(:,1);
RATES(:,5) = CONSTANTS(:,27).*STATES(:,2) - CONSTANTS(:,17).*STATES(:,5)./(CONSTANTS(:,21)+STATES(:,5))+ CONSTANTS(:,18).*STATES(:,6)./(CONSTANTS(:,22)+STATES(:,6)) - CONSTANTS(:,9).*STATES(:,5);
RATES(:,6) = CONSTANTS(:,17).*STATES(:,5)./(CONSTANTS(:,21)+STATES(:,5)) - CONSTANTS(:,18).*STATES(:,6)./(CONSTANTS(:,22)+STATES(:,6)) - CONSTANTS(:,19).*STATES(:,6)./(CONSTANTS(:,23)+STATES(:,6))+ CONSTANTS(:,20).*STATES(:,7)./(CONSTANTS(:,24)+STATES(:,7)) - CONSTANTS(:,9).*STATES(:,6);
RATES(:,7) = CONSTANTS(:,19).*STATES(:,6)./(CONSTANTS(:,23)+STATES(:,6)) - CONSTANTS(:,20).*STATES(:,7)./(CONSTANTS(:,24)+STATES(:,7)) - CONSTANTS(:,14).*STATES(:,7).*STATES(:,10)+ CONSTANTS(:,15).*STATES(:,1) - CONSTANTS(:,26).*STATES(:,7)./(CONSTANTS(:,25)+STATES(:,7)) - CONSTANTS(:,9).*STATES(:,7);
RATES(:,8) = CONSTANTS(:,37).*STATES(:,3) - CONSTANTS(:,28).*STATES(:,8)./(CONSTANTS(:,32)+STATES(:,8))+ CONSTANTS(:,29).*STATES(:,9)./(CONSTANTS(:,33)+STATES(:,9)) - CONSTANTS(:,9).*STATES(:,8);
RATES(:,9) = CONSTANTS(:,28).*STATES(:,8)./(CONSTANTS(:,32)+STATES(:,8)) - CONSTANTS(:,29).*STATES(:,9)./(CONSTANTS(:,33)+STATES(:,9)) - CONSTANTS(:,30).*STATES(:,9)./(CONSTANTS(:,34)+STATES(:,9))+ CONSTANTS(:,31).*STATES(:,10)./(CONSTANTS(:,35)+STATES(:,10)) - CONSTANTS(:,9).*STATES(:,9);
ALGEBRAIC(:,1) = piecewise({ sin( CONSTANTS(:,38).*VOI./12.0000)<=0.00000, CONSTANTS(:,39) }, CONSTANTS(:,40));
RATES(:,10) = CONSTANTS(:,30).*STATES(:,9)./(CONSTANTS(:,34)+STATES(:,9)) - CONSTANTS(:,31).*STATES(:,10)./(CONSTANTS(:,35)+STATES(:,10)) - CONSTANTS(:,14).*STATES(:,7).*STATES(:,10)+ CONSTANTS(:,15).*STATES(:,1) - ALGEBRAIC(:,1).*STATES(:,10)./(CONSTANTS(:,36)+STATES(:,10)) - CONSTANTS(:,9).*STATES(:,10);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
ALGEBRAIC(:,1) = piecewise({ sin( CONSTANTS(:,38).*VOI./12.0000)<=0.00000, CONSTANTS(:,39) }, CONSTANTS(:,40));
ALGEBRAIC(:,2) = STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,4);
ALGEBRAIC(:,3) = STATES(:,8)+STATES(:,9)+STATES(:,10)+STATES(:,1)+STATES(:,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