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 11 entries in each of the rate and state variable arrays.
% There are a total of 15 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('t in component environment (s)');
LEGEND_CONSTANTS(:,1) = strpad('kf8 in component PIPtoDAG (per_s)');
LEGEND_CONSTANTS(:,2) = strpad('kf9 in component PIPtoDAG (per_s)');
LEGEND_CONSTANTS(:,3) = strpad('km6 in component PIPtoDAG (um)');
LEGEND_CONSTANTS(:,4) = strpad('Vmax6 in component PIPtoDAG (per_s)');
LEGEND_CONSTANTS(:,5) = strpad('km7 in component PIPtoDAG (um)');
LEGEND_CONSTANTS(:,6) = strpad('Vmax7 in component PIPtoDAG (per_s)');
LEGEND_STATES(:,1) = strpad('PIP2 in component PIPtoDAG (um)');
LEGEND_STATES(:,2) = strpad('DAG in component PIPtoDAG (um)');
LEGEND_STATES(:,3) = strpad('IP3 in component PIPtoDAG (um)');
LEGEND_STATES(:,4) = strpad('CaPLC in component PLC (um)');
LEGEND_STATES(:,5) = strpad('CaGqPLC in component PLC (um)');
LEGEND_STATES(:,6) = strpad('Inositol in component PIPtoDAG (um)');
LEGEND_STATES(:,7) = strpad('PC in component PIPtoDAG (um)');
LEGEND_CONSTANTS(:,7) = strpad('kf1 in component PLC (per_um_s)');
LEGEND_CONSTANTS(:,8) = strpad('kb1 in component PLC (per_s)');
LEGEND_CONSTANTS(:,9) = strpad('kf2 in component PLC (per_um_s)');
LEGEND_CONSTANTS(:,10) = strpad('kb2 in component PLC (per_s)');
LEGEND_CONSTANTS(:,11) = strpad('kf3 in component PLC (per_um_s)');
LEGEND_CONSTANTS(:,12) = strpad('kb3 in component PLC (per_s)');
LEGEND_CONSTANTS(:,13) = strpad('kf4 in component PLC (per_um_s)');
LEGEND_CONSTANTS(:,14) = strpad('kb4 in component PLC (per_s)');
LEGEND_CONSTANTS(:,15) = strpad('kf5 in component PLC (per_s)');
LEGEND_STATES(:,8) = strpad('PLC in component PLC (um)');
LEGEND_STATES(:,9) = strpad('Gq in component PLC (um)');
LEGEND_STATES(:,10) = strpad('Ca in component PLC (um)');
LEGEND_STATES(:,11) = strpad('GqPLC in component PLC (um)');
LEGEND_RATES(:,1) = strpad('d/dt PIP2 in component PIPtoDAG (um)');
LEGEND_RATES(:,2) = strpad('d/dt DAG in component PIPtoDAG (um)');
LEGEND_RATES(:,3) = strpad('d/dt IP3 in component PIPtoDAG (um)');
LEGEND_RATES(:,7) = strpad('d/dt PC in component PIPtoDAG (um)');
LEGEND_RATES(:,6) = strpad('d/dt Inositol in component PIPtoDAG (um)');
LEGEND_RATES(:,8) = strpad('d/dt PLC in component PLC (um)');
LEGEND_RATES(:,9) = strpad('d/dt Gq in component PLC (um)');
LEGEND_RATES(:,10) = strpad('d/dt Ca in component PLC (um)');
LEGEND_RATES(:,11) = strpad('d/dt GqPLC in component PLC (um)');
LEGEND_RATES(:,4) = strpad('d/dt CaPLC in component PLC (um)');
LEGEND_RATES(:,5) = strpad('d/dt CaGqPLC in component PLC (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) = 0.15;
CONSTANTS(:,2) = 2.5;
CONSTANTS(:,3) = 5;
CONSTANTS(:,4) = 48;
CONSTANTS(:,5) = 19.84166667;
CONSTANTS(:,6) = 10;
STATES(:,1) = 10;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
CONSTANTS(:,7) = 0.000005;
CONSTANTS(:,8) = 1;
CONSTANTS(:,9) = 0.0000042;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 0.00005;
CONSTANTS(:,12) = 1;
CONSTANTS(:,13) = 0.0000042;
CONSTANTS(:,14) = 1;
CONSTANTS(:,15) = 0.0133;
STATES(:,8) = 0.8;
STATES(:,9) = 0.15;
STATES(:,10) = 0.1;
STATES(:,11) = 0;
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) = ( - STATES(:,4).*CONSTANTS(:,6).*STATES(:,1))./(CONSTANTS(:,5)+STATES(:,1)) - ( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,3)+STATES(:,1));
RATES(:,2) = ( STATES(:,4).*CONSTANTS(:,6).*STATES(:,1))./(CONSTANTS(:,5)+STATES(:,1)) - CONSTANTS(:,1).*STATES(:,2);
RATES(:,3) = ( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,3)+STATES(:,1)) - CONSTANTS(:,2).*STATES(:,3);
RATES(:,7) = CONSTANTS(:,1).*STATES(:,2);
RATES(:,6) = CONSTANTS(:,2).*STATES(:,3);
RATES(:,8) = (( - STATES(:,8).*STATES(:,10).*CONSTANTS(:,7)+ STATES(:,4).*CONSTANTS(:,8)) - STATES(:,8).*STATES(:,9).*CONSTANTS(:,9))+ STATES(:,11).*CONSTANTS(:,10);
RATES(:,9) = ( - STATES(:,8).*STATES(:,9).*CONSTANTS(:,9)+ STATES(:,11).*CONSTANTS(:,10)+ STATES(:,5).*CONSTANTS(:,14)) - STATES(:,4).*STATES(:,9).*CONSTANTS(:,13);
RATES(:,10) = (( - STATES(:,8).*STATES(:,10).*CONSTANTS(:,7)+ STATES(:,4).*CONSTANTS(:,8)) - STATES(:,10).*STATES(:,11).*CONSTANTS(:,11))+ STATES(:,5).*CONSTANTS(:,12);
RATES(:,11) = (( STATES(:,8).*STATES(:,9).*CONSTANTS(:,9) - STATES(:,11).*CONSTANTS(:,10)) - STATES(:,10).*STATES(:,11).*CONSTANTS(:,11))+ STATES(:,5).*CONSTANTS(:,12);
RATES(:,4) = (( STATES(:,8).*STATES(:,10).*CONSTANTS(:,7) - STATES(:,4).*CONSTANTS(:,8))+ STATES(:,5).*CONSTANTS(:,15)+ STATES(:,5).*CONSTANTS(:,14)) - STATES(:,4).*STATES(:,9).*CONSTANTS(:,13);
RATES(:,5) = ((( STATES(:,11).*STATES(:,10).*CONSTANTS(:,11) - STATES(:,5).*CONSTANTS(:,12))+ STATES(:,4).*STATES(:,9).*CONSTANTS(:,13)) - STATES(:,5).*CONSTANTS(:,14)) - STATES(:,5).*CONSTANTS(:,15);
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
% 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