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 =1;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 10 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 (second)');
LEGEND_STATES(:,1) = strpad('x1 in component x1 (nanomolar)');
LEGEND_STATES(:,2) = strpad('x2 in component x2 (nanomolar)');
LEGEND_STATES(:,3) = strpad('x3 in component x3 (nanomolar)');
LEGEND_STATES(:,4) = strpad('x4 in component x4 (nanomolar)');
LEGEND_STATES(:,5) = strpad('x5 in component x5 (nanomolar)');
LEGEND_STATES(:,6) = strpad('x6 in component x6 (nanomolar)');
LEGEND_STATES(:,7) = strpad('x7 in component x7 (nanomolar)');
LEGEND_STATES(:,8) = strpad('x8 in component x8 (nanomolar)');
LEGEND_STATES(:,9) = strpad('x9 in component x9 (nanomolar)');
LEGEND_CONSTANTS(:,1) = strpad('k1 in component rate_variables (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k1_ in component rate_variables (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k2 in component rate_variables (second_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k2_ in component rate_variables (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k4 in component rate_variables (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k4_ in component rate_variables (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k5 in component rate_variables (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k5_ in component rate_variables (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('scatchard in component x1 (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('k3 in component rate_variables (second_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k3_ in component rate_variables (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt x1 in component x1 (nanomolar)');
LEGEND_RATES(:,2) = strpad('d/dt x2 in component x2 (nanomolar)');
LEGEND_RATES(:,3) = strpad('d/dt x3 in component x3 (nanomolar)');
LEGEND_RATES(:,4) = strpad('d/dt x4 in component x4 (nanomolar)');
LEGEND_RATES(:,5) = strpad('d/dt x5 in component x5 (nanomolar)');
LEGEND_RATES(:,6) = strpad('d/dt x6 in component x6 (nanomolar)');
LEGEND_RATES(:,7) = strpad('d/dt x7 in component x7 (nanomolar)');
LEGEND_RATES(:,8) = strpad('d/dt x8 in component x8 (nanomolar)');
LEGEND_RATES(:,9) = strpad('d/dt x9 in component x9 (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 = [];
STATES(:,1) = 10;
STATES(:,2) = 0.1;
STATES(:,3) = 1.0;
STATES(:,4) = 1.0;
STATES(:,5) = 1.0;
STATES(:,6) = 1.0;
STATES(:,7) = 1.0;
STATES(:,8) = 1.0;
STATES(:,9) = 1.0;
CONSTANTS(:,1) = 1000000;
CONSTANTS(:,2) = 0.0004;
CONSTANTS(:,3) = 1000000;
CONSTANTS(:,4) = 0.04;
CONSTANTS(:,5) = 1000000;
CONSTANTS(:,6) = 0.0004;
CONSTANTS(:,7) = 10000000;
CONSTANTS(:,8) = 0.004;
CONSTANTS(:,9) = 1000000;
CONSTANTS(:,10) = 0.0004;
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).*STATES(:,3) - CONSTANTS(:,1).*STATES(:,1).*STATES(:,2))+ CONSTANTS(:,4).*STATES(:,4)) - CONSTANTS(:,3).*STATES(:,1).*STATES(:,3))+ CONSTANTS(:,6).*(STATES(:,6)+STATES(:,7))) - CONSTANTS(:,5).*STATES(:,1).*(STATES(:,5)+STATES(:,9)))+ CONSTANTS(:,8).*(STATES(:,7)+STATES(:,8)+STATES(:,9))) - CONSTANTS(:,7).*STATES(:,1).*(STATES(:,5)+STATES(:,6)+STATES(:,7));
RATES(:,2) = (( CONSTANTS(:,2).*STATES(:,3) - CONSTANTS(:,1).*STATES(:,1).*STATES(:,2))+ CONSTANTS(:,10).*(STATES(:,5)+STATES(:,9))) - CONSTANTS(:,9).*STATES(:,2).*(STATES(:,3)+STATES(:,4));
RATES(:,3) = ((((( CONSTANTS(:,1).*STATES(:,1).*STATES(:,2) - CONSTANTS(:,2).*STATES(:,3))+ CONSTANTS(:,4).*STATES(:,4)) - CONSTANTS(:,3).*STATES(:,1).*STATES(:,3))+ CONSTANTS(:,10).*STATES(:,5)) - CONSTANTS(:,9).*STATES(:,2).*STATES(:,3));
RATES(:,4) = (( CONSTANTS(:,3).*STATES(:,1).*STATES(:,3) - CONSTANTS(:,4).*STATES(:,4))+ CONSTANTS(:,10).*STATES(:,9)) - CONSTANTS(:,3).*STATES(:,2).*STATES(:,4);
RATES(:,5) = (((( CONSTANTS(:,9).*STATES(:,2).*STATES(:,3) - CONSTANTS(:,10).*STATES(:,5))+ CONSTANTS(:,6).*STATES(:,6)) - CONSTANTS(:,5).*STATES(:,1).*STATES(:,5))+ CONSTANTS(:,8).*STATES(:,9)) - CONSTANTS(:,7).*STATES(:,1).*STATES(:,5);
RATES(:,6) = (( CONSTANTS(:,5).*STATES(:,1).*STATES(:,5) - CONSTANTS(:,6).*STATES(:,6))+ CONSTANTS(:,8).*STATES(:,7)) - CONSTANTS(:,7).*STATES(:,1).*STATES(:,6);
RATES(:,7) = ( CONSTANTS(:,5).*STATES(:,1).*STATES(:,9) - CONSTANTS(:,6).*STATES(:,7))+ CONSTANTS(:,8).*(STATES(:,8) - STATES(:,7))+ CONSTANTS(:,7).*STATES(:,1).*(STATES(:,6) - STATES(:,7));
RATES(:,8) = CONSTANTS(:,7).*STATES(:,1).*STATES(:,7) - CONSTANTS(:,8).*STATES(:,8);
RATES(:,9) = (((( CONSTANTS(:,9).*STATES(:,2).*STATES(:,4) - CONSTANTS(:,10).*STATES(:,9))+ CONSTANTS(:,6).*STATES(:,7)) - CONSTANTS(:,5).*STATES(:,1).*STATES(:,9))+ CONSTANTS(:,7).*STATES(:,1).*STATES(:,5)) - CONSTANTS(:,8).*STATES(:,9);
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) = (STATES(:,3)+STATES(:,4)+STATES(:,7)+STATES(:,8)+STATES(:,9))./STATES(:,1);
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