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 =13;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 14 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_ALGEBRAIC(:,5) = strpad('phi3_c1 in component phi (per_second)');
LEGEND_STATES(:,1) = strpad('h1 in component h1 (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('phi1_c1 in component phi (second_order_rate)');
LEGEND_ALGEBRAIC(:,3) = strpad('phi2_c1 in component phi (per_second)');
LEGEND_CONSTANTS(:,1) = strpad('p in component model_parameters (micro_molar)');
LEGEND_ALGEBRAIC(:,2) = strpad('phi_1_c1 in component phi (per_second)');
LEGEND_ALGEBRAIC(:,9) = strpad('phi3_c2 in component phi (per_second)');
LEGEND_STATES(:,2) = strpad('h2 in component h2 (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('phi1_c2 in component phi (second_order_rate)');
LEGEND_ALGEBRAIC(:,7) = strpad('phi2_c2 in component phi (per_second)');
LEGEND_ALGEBRAIC(:,6) = strpad('phi_1_c2 in component phi (per_second)');
LEGEND_CONSTANTS(:,2) = strpad('r2 in component model_parameters (second_order_rate)');
LEGEND_CONSTANTS(:,3) = strpad('R1 in component model_parameters (micro_molar)');
LEGEND_CONSTANTS(:,4) = strpad('k1 in component model_parameters (micro_molar_per_second)');
LEGEND_CONSTANTS(:,5) = strpad('R3 in component model_parameters (micro_molar)');
LEGEND_CONSTANTS(:,6) = strpad('k2 in component model_parameters (micro_molar_per_second)');
LEGEND_CONSTANTS(:,7) = strpad('r4 in component model_parameters (per_second)');
LEGEND_CONSTANTS(:,8) = strpad('k3 in component model_parameters (micro_molar_per_second)');
LEGEND_CONSTANTS(:,9) = strpad('R5 in component model_parameters (micro_molar)');
LEGEND_STATES(:,3) = strpad('c1 in component c1 (micro_molar)');
LEGEND_STATES(:,4) = strpad('c2 in component c2 (micro_molar)');
LEGEND_CONSTANTS(:,10) = strpad('Vp in component model_parameters (micro_molar_per_second)');
LEGEND_CONSTANTS(:,11) = strpad('Kp in component model_parameters (micro_molar)');
LEGEND_ALGEBRAIC(:,8) = strpad('j_pump_c1 in component j_pump (micro_molar_per_second)');
LEGEND_ALGEBRAIC(:,10) = strpad('j_pump_c2 in component j_pump (micro_molar_per_second)');
LEGEND_CONSTANTS(:,12) = strpad('kf in component model_parameters (micro_molar_per_second)');
LEGEND_ALGEBRAIC(:,11) = strpad('j_receptor_c1 in component j_receptor (micro_molar_per_second)');
LEGEND_ALGEBRAIC(:,12) = strpad('j_receptor_c2 in component j_receptor (micro_molar_per_second)');
LEGEND_ALGEBRAIC(:,13) = strpad('j_diffusion in component j_diffusion (micro_molar_per_second)');
LEGEND_CONSTANTS(:,13) = strpad('D in component model_parameters (per_second)');
LEGEND_CONSTANTS(:,14) = strpad('j_leak in component model_parameters (micro_molar_per_second)');
LEGEND_RATES(:,1) = strpad('d/dt h1 in component h1 (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt h2 in component h2 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt c1 in component c1 (micro_molar)');
LEGEND_RATES(:,4) = strpad('d/dt c2 in component c2 (micro_molar)');
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) = 0.8;
CONSTANTS(:,1) = 0.2778;
STATES(:,2) = 0.1;
CONSTANTS(:,2) = 100;
CONSTANTS(:,3) = 6;
CONSTANTS(:,4) = 44;
CONSTANTS(:,5) = 50;
CONSTANTS(:,6) = 26.5;
CONSTANTS(:,7) = 20;
CONSTANTS(:,8) = 1.6;
CONSTANTS(:,9) = 1.6;
STATES(:,3) = 0.3;
STATES(:,4) = 0.1;
CONSTANTS(:,10) = 1.2;
CONSTANTS(:,11) = 0.18;
CONSTANTS(:,12) = 28;
CONSTANTS(:,13) = 0.01;
CONSTANTS(:,14) = 0.2;
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(:,5) = CONSTANTS(:,8)./(CONSTANTS(:,9)+STATES(:,3));
ALGEBRAIC(:,1) = ( CONSTANTS(:,2).*STATES(:,3))./(CONSTANTS(:,3)+STATES(:,3));
ALGEBRAIC(:,3) = (CONSTANTS(:,6)+ CONSTANTS(:,7).*STATES(:,3))./(CONSTANTS(:,5)+STATES(:,3));
ALGEBRAIC(:,2) = CONSTANTS(:,4)./(CONSTANTS(:,5)+STATES(:,3));
RATES(:,1) = ALGEBRAIC(:,5).*(1.00000 - STATES(:,1)) - ( ALGEBRAIC(:,1).*ALGEBRAIC(:,3).*STATES(:,1).*CONSTANTS(:,1))./( ALGEBRAIC(:,1).*CONSTANTS(:,1)+ALGEBRAIC(:,2));
ALGEBRAIC(:,9) = CONSTANTS(:,8)./(CONSTANTS(:,9)+STATES(:,4));
ALGEBRAIC(:,4) = ( CONSTANTS(:,2).*STATES(:,4))./(CONSTANTS(:,3)+STATES(:,4));
ALGEBRAIC(:,7) = (CONSTANTS(:,6)+ CONSTANTS(:,7).*STATES(:,4))./(CONSTANTS(:,5)+STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,4)./(CONSTANTS(:,5)+STATES(:,4));
RATES(:,2) = ALGEBRAIC(:,9).*(1.00000 - STATES(:,2)) - ( ALGEBRAIC(:,4).*ALGEBRAIC(:,7).*STATES(:,2).*CONSTANTS(:,1))./( ALGEBRAIC(:,4).*CONSTANTS(:,1)+ALGEBRAIC(:,6));
ALGEBRAIC(:,8) = ( CONSTANTS(:,10).*power(STATES(:,3), 2.00000))./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,3), 2.00000));
ALGEBRAIC(:,11) = CONSTANTS(:,12).*power(( CONSTANTS(:,1).*STATES(:,1).*ALGEBRAIC(:,1))./( ALGEBRAIC(:,1).*CONSTANTS(:,1)+ALGEBRAIC(:,2)), 4.00000);
ALGEBRAIC(:,13) = CONSTANTS(:,13).*(STATES(:,4) - STATES(:,3));
RATES(:,3) = (ALGEBRAIC(:,11) - ALGEBRAIC(:,8))+CONSTANTS(:,14)+ALGEBRAIC(:,13);
ALGEBRAIC(:,10) = ( CONSTANTS(:,10).*power(STATES(:,4), 2.00000))./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,4), 2.00000));
ALGEBRAIC(:,12) = CONSTANTS(:,12).*power(( CONSTANTS(:,1).*STATES(:,2).*ALGEBRAIC(:,4))./( ALGEBRAIC(:,4).*CONSTANTS(:,1)+ALGEBRAIC(:,6)), 4.00000);
RATES(:,4) = (ALGEBRAIC(:,12) - ALGEBRAIC(:,10))+CONSTANTS(:,14)+ALGEBRAIC(:,13);
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(:,5) = CONSTANTS(:,8)./(CONSTANTS(:,9)+STATES(:,3));
ALGEBRAIC(:,1) = ( CONSTANTS(:,2).*STATES(:,3))./(CONSTANTS(:,3)+STATES(:,3));
ALGEBRAIC(:,3) = (CONSTANTS(:,6)+ CONSTANTS(:,7).*STATES(:,3))./(CONSTANTS(:,5)+STATES(:,3));
ALGEBRAIC(:,2) = CONSTANTS(:,4)./(CONSTANTS(:,5)+STATES(:,3));
ALGEBRAIC(:,9) = CONSTANTS(:,8)./(CONSTANTS(:,9)+STATES(:,4));
ALGEBRAIC(:,4) = ( CONSTANTS(:,2).*STATES(:,4))./(CONSTANTS(:,3)+STATES(:,4));
ALGEBRAIC(:,7) = (CONSTANTS(:,6)+ CONSTANTS(:,7).*STATES(:,4))./(CONSTANTS(:,5)+STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,4)./(CONSTANTS(:,5)+STATES(:,4));
ALGEBRAIC(:,8) = ( CONSTANTS(:,10).*power(STATES(:,3), 2.00000))./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,3), 2.00000));
ALGEBRAIC(:,11) = CONSTANTS(:,12).*power(( CONSTANTS(:,1).*STATES(:,1).*ALGEBRAIC(:,1))./( ALGEBRAIC(:,1).*CONSTANTS(:,1)+ALGEBRAIC(:,2)), 4.00000);
ALGEBRAIC(:,13) = CONSTANTS(:,13).*(STATES(:,4) - STATES(:,3));
ALGEBRAIC(:,10) = ( CONSTANTS(:,10).*power(STATES(:,4), 2.00000))./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,4), 2.00000));
ALGEBRAIC(:,12) = CONSTANTS(:,12).*power(( CONSTANTS(:,1).*STATES(:,2).*ALGEBRAIC(:,4))./( ALGEBRAIC(:,4).*CONSTANTS(:,1)+ALGEBRAIC(:,6)), 4.00000);
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