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 =4;
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 (minute)');
LEGEND_STATES(:,1) = strpad('r in component r (nanomolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ir in component r (flux)');
LEGEND_CONSTANTS(:,1) = strpad('k6 in component r (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('s in component s (nanomolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('Is in component model_parameters (flux)');
LEGEND_CONSTANTS(:,2) = strpad('k7 in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('f in component f (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('k1 in component f (second_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k2 in component f (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k3 in component f (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('phi_b_s in component f (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('sb in component f (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('delta_b in component f (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('c in component model_parameters (nanomolar)');
LEGEND_STATES(:,4) = strpad('h in component h (nanomolar)');
LEGEND_CONSTANTS(:,9) = strpad('k4 in component h (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k5 in component h (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('phi_r_s in component h (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('sr in component h (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('delta_r in component h (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('k8 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('j1 in component model_parameters (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt r in component r (nanomolar)');
LEGEND_RATES(:,2) = strpad('d/dt s in component s (nanomolar)');
LEGEND_RATES(:,3) = strpad('d/dt f in component f (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt h in component h (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) = 0.0;
CONSTANTS(:,1) = 5.0;
STATES(:,2) = 0.0;
CONSTANTS(:,2) = 5.0;
STATES(:,3) = 0.3;
CONSTANTS(:,3) = 0.1;
CONSTANTS(:,4) = 0.002;
CONSTANTS(:,5) = 0.018;
CONSTANTS(:,6) = 0.029;
CONSTANTS(:,7) = 0.3;
CONSTANTS(:,8) = 0.01;
STATES(:,4) = 0.0;
CONSTANTS(:,9) = 9.0;
CONSTANTS(:,10) = 71.0;
CONSTANTS(:,11) = -0.56;
CONSTANTS(:,12) = 0.3;
CONSTANTS(:,13) = 0.07;
CONSTANTS(:,14) = 10;
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) = piecewise({VOI>=0.00000&VOI<=90.0000, 0.00000 , VOI>=91.0000&VOI<=92.0000, 10.0000 , VOI>=93.0000&VOI<=113.000, 0.00000 , VOI>=114.000&VOI<=115.000, 10.0000 , VOI>=116.000&VOI<=136.000, 0.00000 , VOI>=137.000&VOI<=138.000, 10.0000 , VOI>=139.000&VOI<=159.000, 0.00000 , VOI>=160.000&VOI<=161.000, 10.0000 , VOI>=162.000&VOI<=252.000, 0.00000 , VOI>=253.000&VOI<=254.000, 10.0000 , VOI>=255.000&VOI<=275.000, 0.00000 , VOI>=276.000&VOI<=277.000, 10.0000 , VOI>=278.000&VOI<=298.000, 0.00000 , VOI>=299.000&VOI<=300.000, 10.0000 , VOI>=301.000&VOI<=321.000, 0.00000 , VOI>=322.000&VOI<=323.000, 10.0000 }, 0.00000);
RATES(:,1) = ALGEBRAIC(:,1) - CONSTANTS(:,1).*STATES(:,1);
ALGEBRAIC(:,2) = piecewise({VOI>0.00000&VOI<=90.0000, 10.0000 , VOI>90.0000&VOI<=180.000, 0.00000 , VOI>180.000&VOI<=270.000, 10.0000 , VOI>270.000&VOI<=360.000, 0.00000 }, 0.00000);
RATES(:,2) = ALGEBRAIC(:,2) - CONSTANTS(:,2).*STATES(:,2);
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*STATES(:,2), 10) - CONSTANTS(:,6))./CONSTANTS(:,7)));
RATES(:,3) = - ( CONSTANTS(:,3).*(STATES(:,1)+CONSTANTS(:,8)).*STATES(:,3))+ (CONSTANTS(:,4)+ CONSTANTS(:,5).*ALGEBRAIC(:,3)).*(1.00000 - STATES(:,3));
ALGEBRAIC(:,4) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*STATES(:,2), 10) - CONSTANTS(:,11))./CONSTANTS(:,12)));
RATES(:,4) = CONSTANTS(:,14).*( (CONSTANTS(:,9)+ CONSTANTS(:,10).*(1.00000 - ALGEBRAIC(:,4))).*( (STATES(:,1)+CONSTANTS(:,8)).*STATES(:,3)) - CONSTANTS(:,13).*STATES(:,4));
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) = piecewise({VOI>=0.00000&VOI<=90.0000, 0.00000 , VOI>=91.0000&VOI<=92.0000, 10.0000 , VOI>=93.0000&VOI<=113.000, 0.00000 , VOI>=114.000&VOI<=115.000, 10.0000 , VOI>=116.000&VOI<=136.000, 0.00000 , VOI>=137.000&VOI<=138.000, 10.0000 , VOI>=139.000&VOI<=159.000, 0.00000 , VOI>=160.000&VOI<=161.000, 10.0000 , VOI>=162.000&VOI<=252.000, 0.00000 , VOI>=253.000&VOI<=254.000, 10.0000 , VOI>=255.000&VOI<=275.000, 0.00000 , VOI>=276.000&VOI<=277.000, 10.0000 , VOI>=278.000&VOI<=298.000, 0.00000 , VOI>=299.000&VOI<=300.000, 10.0000 , VOI>=301.000&VOI<=321.000, 0.00000 , VOI>=322.000&VOI<=323.000, 10.0000 }, 0.00000);
ALGEBRAIC(:,2) = piecewise({VOI>0.00000&VOI<=90.0000, 10.0000 , VOI>90.0000&VOI<=180.000, 0.00000 , VOI>180.000&VOI<=270.000, 10.0000 , VOI>270.000&VOI<=360.000, 0.00000 }, 0.00000);
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*STATES(:,2), 10) - CONSTANTS(:,6))./CONSTANTS(:,7)));
ALGEBRAIC(:,4) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*STATES(:,2), 10) - CONSTANTS(:,11))./CONSTANTS(:,12)));
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
% Compute a logarithm to any base" +
function x = arbitrary_log(a, base)
x = log(a) ./ log(base);
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