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 =10;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 28 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('ract in component r (dimensionless)');
LEGEND_ALGEBRAIC(:,10) = strpad('hr in component r (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('Ir in component r (flux)');
LEGEND_ALGEBRAIC(:,7) = strpad('Ir2 in component r (flux)');
LEGEND_CONSTANTS(:,1) = strpad('k6 in component r (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('n1 in component r (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('theta_1 in component r (nanomolar)');
LEGEND_CONSTANTS(:,4) = strpad('n3 in component r (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('theta_3 in component r (dimensionless)');
LEGEND_STATES(:,2) = strpad('s in component s (nanomolar)');
LEGEND_ALGEBRAIC(:,9) = strpad('h_delta1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('j1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('Is2 in component s (flux)');
LEGEND_ALGEBRAIC(:,8) = strpad('Is in component model_parameters (flux)');
LEGEND_CONSTANTS(:,8) = strpad('k7 in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('g in component g (dimensionless)');
LEGEND_STATES(:,4) = strpad('se in component se (nanomolar)');
LEGEND_CONSTANTS(:,9) = strpad('Ise in component se (flux)');
LEGEND_STATES(:,5) = strpad('f in component f (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('k1 in component f (second_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('k2 in component f (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('k3 in component f (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('phi_b_s in component f (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('sb in component f (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('delta_b in component f (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('c in component model_parameters (nanomolar)');
LEGEND_STATES(:,6) = strpad('h in component h (nanomolar)');
LEGEND_CONSTANTS(:,16) = strpad('k4 in component h (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('k5 in component h (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('phi_r_s in component h (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('sr in component h (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('delta_r in component h (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('k8 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('g1 in component g (first_order_rate_constant)');
LEGEND_CONSTANTS(:,22) = strpad('gmax in component g (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('g2 in component g (per_nanomolar)');
LEGEND_ALGEBRAIC(:,6) = strpad('hact in component g (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('n2 in component g (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('theta_2 in component g (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('h_delta in component model_parameters (dimensionless)');
LEGEND_STATES(:,7) = strpad('hh in component hh (nanomolar)');
LEGEND_CONSTANTS(:,26) = strpad('Ih in component hh (flux)');
LEGEND_CONSTANTS(:,27) = strpad('delta in component model_parameters (per_nanomolar)');
LEGEND_CONSTANTS(:,28) = strpad('delta1 in component model_parameters (per_nanomolar)');
LEGEND_RATES(:,1) = strpad('d/dt r in component r (nanomolar)');
LEGEND_RATES(:,2) = strpad('d/dt s in component s (nanomolar)');
LEGEND_RATES(:,4) = strpad('d/dt se in component se (nanomolar)');
LEGEND_RATES(:,5) = strpad('d/dt f in component f (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt h in component h (nanomolar)');
LEGEND_RATES(:,3) = strpad('d/dt g in component g (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt hh in component hh (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;
CONSTANTS(:,2) = 4.0;
CONSTANTS(:,3) = 1.0;
CONSTANTS(:,4) = 5.0;
CONSTANTS(:,5) = 30.0;
STATES(:,2) = 0.0;
CONSTANTS(:,6) = 10;
CONSTANTS(:,7) = 50.0;
CONSTANTS(:,8) = 5.0;
STATES(:,3) = 2.0;
STATES(:,4) = 0.0;
CONSTANTS(:,9) = 10.0;
STATES(:,5) = 0.3;
CONSTANTS(:,10) = 0.1;
CONSTANTS(:,11) = 0.002;
CONSTANTS(:,12) = 0.018;
CONSTANTS(:,13) = 0.029;
CONSTANTS(:,14) = 0.3;
CONSTANTS(:,15) = 0.01;
STATES(:,6) = 0.0;
CONSTANTS(:,16) = 0.5;
CONSTANTS(:,17) = 71.0;
CONSTANTS(:,18) = -0.56;
CONSTANTS(:,19) = 0.2;
CONSTANTS(:,20) = 0.07;
CONSTANTS(:,21) = 1.0;
CONSTANTS(:,22) = 5.0;
CONSTANTS(:,23) = 0.008;
CONSTANTS(:,24) = 2.0;
CONSTANTS(:,25) = 30.0;
STATES(:,7) = 0.0;
CONSTANTS(:,26) = 50.0;
CONSTANTS(:,27) = 60.0;
CONSTANTS(:,28) = 15.0;
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(:,4) = CONSTANTS(:,9) - CONSTANTS(:,8).*STATES(:,4);
RATES(:,7) = CONSTANTS(:,6).*(CONSTANTS(:,26) - CONSTANTS(:,20).*STATES(:,7));
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*(STATES(:,2)+STATES(:,4)), 10) - CONSTANTS(:,13))./CONSTANTS(:,14)));
RATES(:,5) = - ( CONSTANTS(:,10).*(STATES(:,1)+CONSTANTS(:,15)).*STATES(:,5))+ (CONSTANTS(:,11)+ CONSTANTS(:,12).*ALGEBRAIC(:,3)).*(1.00000 - STATES(:,5));
ALGEBRAIC(:,4) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*(STATES(:,2)+STATES(:,4)), 10) - CONSTANTS(:,18))./CONSTANTS(:,19)));
RATES(:,6) = CONSTANTS(:,6).*( (CONSTANTS(:,16)+ CONSTANTS(:,17).*(1.00000 - ALGEBRAIC(:,4))).*( (STATES(:,1)+CONSTANTS(:,15)).*STATES(:,5)) - CONSTANTS(:,20).*STATES(:,6));
ALGEBRAIC(:,8) = 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(:,8).*STATES(:,3) - CONSTANTS(:,8).*STATES(:,2))+CONSTANTS(:,7);
ALGEBRAIC(:,2) = (STATES(:,6)+STATES(:,7)).*CONSTANTS(:,27);
ALGEBRAIC(:,6) = power(ALGEBRAIC(:,2), CONSTANTS(:,24))./(power(ALGEBRAIC(:,2), CONSTANTS(:,24))+power( CONSTANTS(:,6).*CONSTANTS(:,25), CONSTANTS(:,24)));
RATES(:,3) = CONSTANTS(:,21).*ALGEBRAIC(:,6).*((CONSTANTS(:,22) - STATES(:,3))./CONSTANTS(:,22)) - CONSTANTS(:,23).*ALGEBRAIC(:,8).*STATES(:,3);
ALGEBRAIC(:,1) = 1.00000 - power(STATES(:,2), CONSTANTS(:,2))./(power(STATES(:,2), CONSTANTS(:,2))+power(CONSTANTS(:,3), CONSTANTS(:,2)));
ALGEBRAIC(:,9) = (STATES(:,6)+STATES(:,7)).*CONSTANTS(:,28);
ALGEBRAIC(:,10) = 1.00000 - power(ALGEBRAIC(:,9), CONSTANTS(:,4))./(power(ALGEBRAIC(:,9), CONSTANTS(:,4))+power( CONSTANTS(:,6).*CONSTANTS(:,5), CONSTANTS(:,4)));
ALGEBRAIC(:,5) = 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(:,7) = piecewise({VOI>=0.00000&VOI<=5.00000, 0.00000 , VOI>=6.00000&VOI<=7.00000, 1000.00 , VOI>=8.00000&VOI<=12.0000, 0.00000 , VOI>=13.0000&VOI<=14.0000, 1000.00 , VOI>=15.0000&VOI<=21.0000, 0.00000 , VOI>=22.0000&VOI<=23.0000, 1000.00 , VOI>=24.0000&VOI<=204.000, 0.00000 , VOI>=205.000&VOI<=206.000, 1000.00 , VOI>=207.000&VOI<=217.000, 0.00000 , VOI>=218.000&VOI<=219.000, 1000.00 , VOI>=220.000&VOI<=227.000, 0.00000 , VOI>=228.000&VOI<=229.000, 1000.00 , VOI>=230.000&VOI<=310.000, 0.00000 , VOI>=311.000&VOI<=312.000, 1000.00 , VOI>=313.000&VOI<=321.000, 0.00000 , VOI>=322.000&VOI<=323.000, 1000.00 }, 0.00000);
RATES(:,1) = ( ALGEBRAIC(:,1).*ALGEBRAIC(:,10).*ALGEBRAIC(:,5) - CONSTANTS(:,1).*STATES(:,1))+ALGEBRAIC(:,7);
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(:,3) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*(STATES(:,2)+STATES(:,4)), 10) - CONSTANTS(:,13))./CONSTANTS(:,14)));
ALGEBRAIC(:,4) = 1.00000./(1.00000+exp( - (arbitrary_log( 1.00000.*(STATES(:,2)+STATES(:,4)), 10) - CONSTANTS(:,18))./CONSTANTS(:,19)));
ALGEBRAIC(:,8) = 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(:,2) = (STATES(:,6)+STATES(:,7)).*CONSTANTS(:,27);
ALGEBRAIC(:,6) = power(ALGEBRAIC(:,2), CONSTANTS(:,24))./(power(ALGEBRAIC(:,2), CONSTANTS(:,24))+power( CONSTANTS(:,6).*CONSTANTS(:,25), CONSTANTS(:,24)));
ALGEBRAIC(:,1) = 1.00000 - power(STATES(:,2), CONSTANTS(:,2))./(power(STATES(:,2), CONSTANTS(:,2))+power(CONSTANTS(:,3), CONSTANTS(:,2)));
ALGEBRAIC(:,9) = (STATES(:,6)+STATES(:,7)).*CONSTANTS(:,28);
ALGEBRAIC(:,10) = 1.00000 - power(ALGEBRAIC(:,9), CONSTANTS(:,4))./(power(ALGEBRAIC(:,9), CONSTANTS(:,4))+power( CONSTANTS(:,6).*CONSTANTS(:,5), CONSTANTS(:,4)));
ALGEBRAIC(:,5) = 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(:,7) = piecewise({VOI>=0.00000&VOI<=5.00000, 0.00000 , VOI>=6.00000&VOI<=7.00000, 1000.00 , VOI>=8.00000&VOI<=12.0000, 0.00000 , VOI>=13.0000&VOI<=14.0000, 1000.00 , VOI>=15.0000&VOI<=21.0000, 0.00000 , VOI>=22.0000&VOI<=23.0000, 1000.00 , VOI>=24.0000&VOI<=204.000, 0.00000 , VOI>=205.000&VOI<=206.000, 1000.00 , VOI>=207.000&VOI<=217.000, 0.00000 , VOI>=218.000&VOI<=219.000, 1000.00 , VOI>=220.000&VOI<=227.000, 0.00000 , VOI>=228.000&VOI<=229.000, 1000.00 , VOI>=230.000&VOI<=310.000, 0.00000 , VOI>=311.000&VOI<=312.000, 1000.00 , VOI>=313.000&VOI<=321.000, 0.00000 , VOI>=322.000&VOI<=323.000, 1000.00 }, 0.00000);
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