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 =0;
end
% There are a total of 1 entries in each of the rate and state variable arrays.
% There are a total of 19 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 (minute)');
LEGEND_CONSTANTS(:,16) = strpad('C in component C (nanomolar)');
LEGEND_CONSTANTS(:,1) = strpad('kf1 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('kr1 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('k_x1 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('kt in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('ke in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('L in component model_parameters (nanomolar)');
LEGEND_CONSTANTS(:,17) = strpad('R in component R (nanomolar)');
LEGEND_CONSTANTS(:,15) = strpad('K_X in component D (per_nanomolar)');
LEGEND_CONSTANTS(:,18) = strpad('D in component D (nanomolar)');
LEGEND_CONSTANTS(:,5) = strpad('kx2 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k_x2 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('R_initial in component R (nanomolar)');
LEGEND_CONSTANTS(:,8) = strpad('krec in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('kdeg in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,1) = strpad('Ri in component Ri (nanomolar)');
LEGEND_CONSTANTS(:,19) = strpad('signal in component signal (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('kappaE in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('Vs in component model_parameters (flux)');
LEGEND_CONSTANTS(:,12) = strpad('KD in component model_parameters (nanomolar)');
LEGEND_RATES(:,1) = strpad('d/dt Ri in component Ri (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) = 0.1;
CONSTANTS(:,2) = 0.005;
CONSTANTS(:,3) = 0.10;
CONSTANTS(:,4) = 0.01;
CONSTANTS(:,5) = 4.83;
CONSTANTS(:,6) = 0.016;
CONSTANTS(:,7) = 2000.0;
CONSTANTS(:,8) = 0.0;
CONSTANTS(:,9) = 0.05;
STATES(:,1) = 200.0;
CONSTANTS(:,10) = 0.20;
CONSTANTS(:,11) = 10.0;
CONSTANTS(:,12) = 1.0;
CONSTANTS(:,13) = CONSTANTS(:,12).*CONSTANTS(:,1);
CONSTANTS(:,14) = 0.0100000.*CONSTANTS(:,13);
CONSTANTS(:,15) = CONSTANTS(:,5)./(CONSTANTS(:,6)+CONSTANTS(:,14)+CONSTANTS(:,3));
[CONSTANTS, STATES, ALGEBRAIC] = rootfind_0(VOI, CONSTANTS, STATES, ALGEBRAIC);
CONSTANTS(:,19) = (( 2.00000.*CONSTANTS(:,18))./200.000)./(CONSTANTS(:,10)+( 2.00000.*CONSTANTS(:,18))./200.000);
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(:,1) = CONSTANTS(:,2).*(CONSTANTS(:,17)+CONSTANTS(:,16)) - (CONSTANTS(:,8)+CONSTANTS(:,9)).*STATES(:,1);
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
end
% Functions required for solving differential algebraic equation
function [CONSTANTS, STATES, ALGEBRAIC] = rootfind_0(VOI, CONSTANTS_IN, STATES_IN, ALGEBRAIC_IN)
ALGEBRAIC = ALGEBRAIC_IN;
CONSTANTS = CONSTANTS_IN;
STATES = STATES_IN;
global initialGuess_0;
if (length(initialGuess_0) ~= 3), initialGuess_0 = [0.1,0.1,0.1];, end
options = optimset('Display', 'off', 'TolX', 1E-6);
if length(VOI) == 1
residualfn = @(algebraicCandidate)residualSN_0(algebraicCandidate, ALGEBRAIC, VOI, CONSTANTS, STATES);
soln = fsolve(residualfn, initialGuess_0, options);
initialGuess_0 = soln;
CONSTANTS(:,16) = soln(1);
CONSTANTS(:,17) = soln(2);
CONSTANTS(:,18) = soln(3);
else
SET_CONSTANTS(:,16) = logical(1);
SET_CONSTANTS(:,17) = logical(1);
SET_CONSTANTS(:,18) = logical(1);
for i=1:length(VOI)
residualfn = @(algebraicCandidate)residualSN_0(algebraicCandidate, ALGEBRAIC(i,:), VOI(i), CONSTANTS, STATES(i,:));
soln = fsolve(residualfn, initialGuess_0, options);
initialGuess_0 = soln;
TEMP_CONSTANTS(:,16) = soln(1);
TEMP_CONSTANTS(:,17) = soln(2);
TEMP_CONSTANTS(:,18) = soln(3);
ALGEBRAIC(i,SET_ALGEBRAIC) = TEMP_ALGEBRAIC(SET_ALGEBRAIC);
end
end
end
function resid = residualSN_0(algebraicCandidate, ALGEBRAIC, VOI, CONSTANTS, STATES)
CONSTANTS(:,16) = algebraicCandidate(1);
CONSTANTS(:,17) = algebraicCandidate(2);
CONSTANTS(:,18) = algebraicCandidate(3);
resid(1) = CONSTANTS(:,16) - ( CONSTANTS(:,1).*CONSTANTS(:,4).*CONSTANTS(:,17))./(CONSTANTS(:,13)+CONSTANTS(:,2)+ (CONSTANTS(:,14)+CONSTANTS(:,3)).*CONSTANTS(:,15).*CONSTANTS(:,17));
resid(2) = CONSTANTS(:,18) - CONSTANTS(:,15).*CONSTANTS(:,17).*CONSTANTS(:,16);
resid(3) = CONSTANTS(:,17) - (CONSTANTS(:,7) - (CONSTANTS(:,16)+ 2.00000.*(CONSTANTS(:,3)./CONSTANTS(:,2)).*(1.00000+CONSTANTS(:,8)./CONSTANTS(:,9)).*CONSTANTS(:,18)));
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