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 =6;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 17 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 temporalExistence (second)');
LEGEND_CONSTANTS(:,1) = strpad('alphaTF in component Device_TFgenerator (uM_per_second)');
LEGEND_CONSTANTS(:,15) = strpad('JTF in component Device_TFgenerator (uM_per_second)');
LEGEND_STATES(:,1) = strpad('TFS in component BioEnv_TFSAssociation (uM)');
LEGEND_ALGEBRAIC(:,6) = strpad('Jgain_TF in component BioEnv_TFSAssociation_interface (uM_per_second)');
LEGEND_CONSTANTS(:,16) = strpad('Jgain_TFS in component BioEnv_TFSAssociation_interface (uM_per_second)');
LEGEND_ALGEBRAIC(:,4) = strpad('JTF in component Device_PhzMSgenerator (uM_per_second)');
LEGEND_STATES(:,2) = strpad('TF in component BioEnv_TFSAssociation (uM)');
LEGEND_CONSTANTS(:,2) = strpad('s in component BioEnv_TFSAssociation (uM)');
LEGEND_CONSTANTS(:,3) = strpad('betaTFS in component BioEnv_TFSAssociation (per_uM_per_second)');
LEGEND_CONSTANTS(:,4) = strpad('kd in component BioEnv_TFSAssociation (per_second)');
LEGEND_CONSTANTS(:,5) = strpad('deltaTFS in component BioEnv_TFSAssociation (per_second)');
LEGEND_CONSTANTS(:,6) = strpad('deltaTF in component BioEnv_TFSAssociation (per_second)');
LEGEND_ALGEBRAIC(:,1) = strpad('Jassociation in component BioEnv_TFSAssociation (uM_per_second)');
LEGEND_CONSTANTS(:,7) = strpad('gammaPhzMS in component Device_PhzMSgenerator (uM)');
LEGEND_CONSTANTS(:,8) = strpad('betaPhzMS in component Device_PhzMSgenerator (uM_per_second)');
LEGEND_ALGEBRAIC(:,2) = strpad('JPhzMS in component Device_PhzMSgenerator (uM_per_second)');
LEGEND_CONSTANTS(:,9) = strpad('gammaTF in component Device_PhzMSgenerator (uM)');
LEGEND_CONSTANTS(:,10) = strpad('betaTF in component Device_PhzMSgenerator (uM_per_second)');
LEGEND_CONSTANTS(:,11) = strpad('feedbackOn in component Device_PhzMSgenerator (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('Jgain_PhzMS in component BioEnv_PhzMStoPYO_interface (uM_per_second)');
LEGEND_CONSTANTS(:,17) = strpad('Jgain_PYO in component BioEnv_PhzMStoPYO_interface (uM_per_second)');
LEGEND_STATES(:,3) = strpad('PhzMS in component BioEnv_PhzMStoPYO (uM)');
LEGEND_STATES(:,4) = strpad('PYO in component BioEnv_PhzMStoPYO (uM)');
LEGEND_CONSTANTS(:,12) = strpad('deltaPhzMS in component BioEnv_PhzMStoPYO (per_second)');
LEGEND_CONSTANTS(:,13) = strpad('alphaPYO in component BioEnv_PhzMStoPYO (per_second)');
LEGEND_CONSTANTS(:,14) = strpad('deltaPYO in component BioEnv_PhzMStoPYO (per_second)');
LEGEND_ALGEBRAIC(:,3) = strpad('JPYOformation in component BioEnv_PhzMStoPYO (uM_per_second)');
LEGEND_RATES(:,2) = strpad('d/dt TF in component BioEnv_TFSAssociation (uM)');
LEGEND_RATES(:,1) = strpad('d/dt TFS in component BioEnv_TFSAssociation (uM)');
LEGEND_RATES(:,3) = strpad('d/dt PhzMS in component BioEnv_PhzMStoPYO (uM)');
LEGEND_RATES(:,4) = strpad('d/dt PYO in component BioEnv_PhzMStoPYO (uM)');
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) = 0.05;
STATES(:,1) = 0;
STATES(:,2) = 8.6207;
CONSTANTS(:,2) = 5;
CONSTANTS(:,3) = 1e6;
CONSTANTS(:,4) = 4e6;
CONSTANTS(:,5) = 3.851e-4;
CONSTANTS(:,6) = 5.8e-3;
CONSTANTS(:,7) = 5;
CONSTANTS(:,8) = 0.1;
CONSTANTS(:,9) = 4;
CONSTANTS(:,10) = 0.07;
CONSTANTS(:,11) = 1;
STATES(:,3) = 0;
STATES(:,4) = 0;
CONSTANTS(:,12) = 8.0225e-6;
CONSTANTS(:,13) = 1.3;
CONSTANTS(:,14) = 5.8e-1;
CONSTANTS(:,15) = CONSTANTS(:,1);
CONSTANTS(:,16) = 0.00000;
CONSTANTS(:,17) = 0.00000;
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
ALGEBRAIC(:,1) = CONSTANTS(:,3).*CONSTANTS(:,2).*STATES(:,2) - CONSTANTS(:,4).*STATES(:,1);
RATES(:,1) = (ALGEBRAIC(:,1) - CONSTANTS(:,5).*STATES(:,1))+CONSTANTS(:,16);
ALGEBRAIC(:,3) = CONSTANTS(:,13).*STATES(:,3);
RATES(:,4) = (CONSTANTS(:,17) - CONSTANTS(:,14).*STATES(:,4))+ALGEBRAIC(:,3);
ALGEBRAIC(:,2) = ( CONSTANTS(:,8).*STATES(:,1))./(CONSTANTS(:,7)+STATES(:,1));
ALGEBRAIC(:,5) = ALGEBRAIC(:,2);
RATES(:,3) = ALGEBRAIC(:,5) - CONSTANTS(:,12).*STATES(:,3);
ALGEBRAIC(:,4) = piecewise({CONSTANTS(:,11) ~= 0.00000, ( CONSTANTS(:,10).*STATES(:,1))./(CONSTANTS(:,9)+STATES(:,1)) }, 0.00000);
ALGEBRAIC(:,6) = CONSTANTS(:,15)+ALGEBRAIC(:,4);
RATES(:,2) = ( - ALGEBRAIC(:,1)+ALGEBRAIC(:,6)) - CONSTANTS(:,6).*STATES(:,2);
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(:,3).*CONSTANTS(:,2).*STATES(:,2) - CONSTANTS(:,4).*STATES(:,1);
ALGEBRAIC(:,3) = CONSTANTS(:,13).*STATES(:,3);
ALGEBRAIC(:,2) = ( CONSTANTS(:,8).*STATES(:,1))./(CONSTANTS(:,7)+STATES(:,1));
ALGEBRAIC(:,5) = ALGEBRAIC(:,2);
ALGEBRAIC(:,4) = piecewise({CONSTANTS(:,11) ~= 0.00000, ( CONSTANTS(:,10).*STATES(:,1))./(CONSTANTS(:,9)+STATES(:,1)) }, 0.00000);
ALGEBRAIC(:,6) = CONSTANTS(:,15)+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