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 9 entries in each of the rate and state variable arrays.
% There are a total of 20 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('kf1 in component PKC (per_s)');
LEGEND_CONSTANTS(:,2) = strpad('kb1 in component PKC (per_s)');
LEGEND_CONSTANTS(:,3) = strpad('kf2 in component PKC (per_um_s)');
LEGEND_CONSTANTS(:,4) = strpad('kb2 in component PKC (per_s)');
LEGEND_CONSTANTS(:,5) = strpad('kf3 in component PKC (per_s)');
LEGEND_CONSTANTS(:,6) = strpad('kb3 in component PKC (per_s)');
LEGEND_CONSTANTS(:,7) = strpad('kf4 in component PKC (per_um_s)');
LEGEND_CONSTANTS(:,8) = strpad('kb4 in component PKC (per_s)');
LEGEND_CONSTANTS(:,9) = strpad('kf5 in component PKC (per_s)');
LEGEND_CONSTANTS(:,10) = strpad('kb5 in component PKC (per_s)');
LEGEND_CONSTANTS(:,11) = strpad('kf6 in component PKC (per_s)');
LEGEND_CONSTANTS(:,12) = strpad('kb6 in component PKC (per_s)');
LEGEND_CONSTANTS(:,13) = strpad('kf7 in component PKC (per_um_s)');
LEGEND_CONSTANTS(:,14) = strpad('kb7 in component PKC (per_s)');
LEGEND_CONSTANTS(:,15) = strpad('kf8 in component PKC (per_um_s)');
LEGEND_CONSTANTS(:,16) = strpad('kb8 in component PKC (per_s)');
LEGEND_CONSTANTS(:,17) = strpad('kf9 in component PKC (per_um_s)');
LEGEND_CONSTANTS(:,18) = strpad('kb9 in component PKC (per_s)');
LEGEND_CONSTANTS(:,19) = strpad('kf10 in component PKC (per_um_s)');
LEGEND_CONSTANTS(:,20) = strpad('kb10 in component PKC (per_s)');
LEGEND_STATES(:,1) = strpad('PKC_i in component PKC (um)');
LEGEND_STATES(:,2) = strpad('AA in component PKC (um)');
LEGEND_STATES(:,3) = strpad('DAG in component PKC (um)');
LEGEND_STATES(:,4) = strpad('Ca in component PKC (um)');
LEGEND_STATES(:,5) = strpad('DAGPKC in component PKC (um)');
LEGEND_STATES(:,6) = strpad('AADAGPKC in component PKC (um)');
LEGEND_STATES(:,7) = strpad('DAGCaPKC in component PKC (um)');
LEGEND_STATES(:,8) = strpad('CaPKC in component PKC (um)');
LEGEND_STATES(:,9) = strpad('PKC_a in component PKC (um)');
LEGEND_RATES(:,1) = strpad('d/dt PKC_i in component PKC (um)');
LEGEND_RATES(:,5) = strpad('d/dt DAGPKC in component PKC (um)');
LEGEND_RATES(:,6) = strpad('d/dt AADAGPKC in component PKC (um)');
LEGEND_RATES(:,8) = strpad('d/dt CaPKC in component PKC (um)');
LEGEND_RATES(:,7) = strpad('d/dt DAGCaPKC in component PKC (um)');
LEGEND_RATES(:,9) = strpad('d/dt PKC_a in component PKC (um)');
LEGEND_RATES(:,2) = strpad('d/dt AA in component PKC (um)');
LEGEND_RATES(:,3) = strpad('d/dt DAG in component PKC (um)');
LEGEND_RATES(:,4) = strpad('d/dt Ca in component PKC (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) = 1;
CONSTANTS(:,2) = 50;
CONSTANTS(:,3) = 0.0000000002;
CONSTANTS(:,4) = 0.1;
CONSTANTS(:,5) = 1.2705;
CONSTANTS(:,6) = 3.5026;
CONSTANTS(:,7) = 0.000000002;
CONSTANTS(:,8) = 0.1;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 0.1;
CONSTANTS(:,11) = 2;
CONSTANTS(:,12) = 0.2;
CONSTANTS(:,13) = 0.000001;
CONSTANTS(:,14) = 0.5;
CONSTANTS(:,15) = 0.000000013333;
CONSTANTS(:,16) = 8.6348;
CONSTANTS(:,17) = 0.000000001;
CONSTANTS(:,18) = 0.1;
CONSTANTS(:,19) = 0.00000003;
CONSTANTS(:,20) = 2;
STATES(:,1) = 1;
STATES(:,2) = 1;
STATES(:,3) = 0.1;
STATES(:,4) = 0.1;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 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(:,1).*CONSTANTS(:,1)+ STATES(:,9).*CONSTANTS(:,2)) - STATES(:,1).*STATES(:,2).*CONSTANTS(:,3))+ STATES(:,9).*CONSTANTS(:,4)) - STATES(:,1).*STATES(:,3).*CONSTANTS(:,17))+ STATES(:,5).*CONSTANTS(:,18)) - STATES(:,1).*STATES(:,4).*CONSTANTS(:,13))+ STATES(:,8).*CONSTANTS(:,14);
RATES(:,5) = (( STATES(:,1).*STATES(:,3).*CONSTANTS(:,17) - STATES(:,5).*CONSTANTS(:,18)) - STATES(:,5).*STATES(:,2).*CONSTANTS(:,19))+ STATES(:,6).*CONSTANTS(:,20);
RATES(:,6) = (( STATES(:,5).*STATES(:,2).*CONSTANTS(:,19) - STATES(:,6).*CONSTANTS(:,20)) - STATES(:,6).*CONSTANTS(:,11))+ STATES(:,9).*CONSTANTS(:,12);
RATES(:,8) = (((((( STATES(:,1).*STATES(:,4).*CONSTANTS(:,13) - STATES(:,8).*CONSTANTS(:,14)) - STATES(:,8).*CONSTANTS(:,5))+ STATES(:,9).*CONSTANTS(:,6)) - STATES(:,8).*STATES(:,2).*CONSTANTS(:,7))+ STATES(:,9).*CONSTANTS(:,8)) - STATES(:,3).*STATES(:,8).*CONSTANTS(:,15))+ STATES(:,7).*CONSTANTS(:,16);
RATES(:,7) = (( STATES(:,3).*STATES(:,8).*CONSTANTS(:,15) - STATES(:,7).*CONSTANTS(:,16)) - STATES(:,7).*CONSTANTS(:,9))+ STATES(:,9).*CONSTANTS(:,10);
RATES(:,9) = (((((((((( STATES(:,1).*CONSTANTS(:,1) - STATES(:,9).*CONSTANTS(:,2))+ STATES(:,1).*STATES(:,2).*CONSTANTS(:,3)) - STATES(:,9).*CONSTANTS(:,4))+ STATES(:,8).*CONSTANTS(:,5)) - STATES(:,9).*CONSTANTS(:,6))+ STATES(:,8).*STATES(:,2).*CONSTANTS(:,7)) - STATES(:,9).*CONSTANTS(:,8))+ STATES(:,7).*CONSTANTS(:,9)) - STATES(:,9).*CONSTANTS(:,10))+ STATES(:,6).*CONSTANTS(:,11)) - STATES(:,9).*CONSTANTS(:,12);
RATES(:,2) = (((( - STATES(:,1).*STATES(:,2).*CONSTANTS(:,3)+ STATES(:,9).*CONSTANTS(:,4)) - STATES(:,8).*STATES(:,2).*CONSTANTS(:,7))+ STATES(:,9).*CONSTANTS(:,8)) - STATES(:,5).*STATES(:,2).*CONSTANTS(:,19))+ STATES(:,6).*CONSTANTS(:,20);
RATES(:,3) = (( - STATES(:,1).*STATES(:,3).*CONSTANTS(:,17)+ STATES(:,5).*CONSTANTS(:,18)) - STATES(:,3).*STATES(:,8).*CONSTANTS(:,15))+ STATES(:,7).*CONSTANTS(:,16);
RATES(:,4) = - STATES(:,1).*STATES(:,4).*CONSTANTS(:,13)+ STATES(:,8).*CONSTANTS(:,14);
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