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 =5;
end
% There are a total of 13 entries in each of the rate and state variable arrays.
% There are a total of 45 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 (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('c1 in component c1 (dimensionless)');
LEGEND_STATES(:,2) = strpad('c2 in component c2 (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('L in component model_parameters (nanomolar)');
LEGEND_CONSTANTS(:,2) = strpad('kt in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('kxR0 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k_minusx in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('KDL in component model_parameters (nanomolar)');
LEGEND_CONSTANTS(:,6) = strpad('ke in component model_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,2) = strpad('e_PI3K in component e_PI3K (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('kappa_PI3K in component e_PI3K (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('alpha_PI3K in component e_PI3K (dimensionless)');
LEGEND_STATES(:,3) = strpad('m_3PI in component m_3PI (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('k_3PI in component m_3PI (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('e_GEF in component e_GEF (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('K_GR in component e_GEF (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('K_GP in component e_GEF (dimensionless)');
LEGEND_STATES(:,4) = strpad('f_GEF in component f_GEF (dimensionless)');
LEGEND_STATES(:,5) = strpad('m_Ras in component m_Ras (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('k_Ras in component m_Ras (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('gamma in component m_Ras (dimensionless)');
LEGEND_STATES(:,6) = strpad('x1 in component x1 (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('kd_x1 in component x1 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('KM_x11 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('KM_x12 in component model_parameters (dimensionless)');
LEGEND_STATES(:,7) = strpad('y in component y (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('yp in component yp (dimensionless)');
LEGEND_STATES(:,8) = strpad('x2 in component x2 (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('kd_x2 in component x2 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('K_x2 in component x2 (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('KM_x21 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('KM_x22 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('Vmax_yph1_KM_yph1 in component y (first_order_rate_constant)');
LEGEND_CONSTANTS(:,22) = strpad('KM_yph1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('KM_yph2 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('Vmax_x11_KM_x11 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,25) = strpad('Vmax_x21_KM_x21 in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,9) = strpad('ypp in component ypp (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('Vmax_yph2_KM_yph2 in component ypp (first_order_rate_constant)');
LEGEND_CONSTANTS(:,27) = strpad('KM_y1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('KM_y2 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,29) = strpad('Vmax_x12_KM_x12 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,30) = strpad('Vmax_x22_KM_x22 in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,10) = strpad('z in component z (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('zp in component zp (dimensionless)');
LEGEND_CONSTANTS(:,31) = strpad('Vmax_zph1_KM_zph1 in component z (first_order_rate_constant)');
LEGEND_CONSTANTS(:,32) = strpad('Vmax_y1_KM_y1 in component z (first_order_rate_constant)');
LEGEND_CONSTANTS(:,33) = strpad('KM_zph1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,34) = strpad('KM_zph2 in component model_parameters (dimensionless)');
LEGEND_STATES(:,11) = strpad('zpp in component zpp (dimensionless)');
LEGEND_STATES(:,12) = strpad('e_ph in component e_ph (dimensionless)');
LEGEND_CONSTANTS(:,35) = strpad('Vmax_zph2_KM_zph2 in component zpp (first_order_rate_constant)');
LEGEND_CONSTANTS(:,36) = strpad('Vmax_y2_KM_y2 in component zpp (first_order_rate_constant)');
LEGEND_CONSTANTS(:,37) = strpad('n in component f_GEF (dimensionless)');
LEGEND_CONSTANTS(:,38) = strpad('Kf in component f_GEF (dimensionless)');
LEGEND_CONSTANTS(:,39) = strpad('Zf in component f_GEF (dimensionless)');
LEGEND_CONSTANTS(:,40) = strpad('k_FB_f in component f_GEF (first_order_rate_constant)');
LEGEND_STATES(:,13) = strpad('w in component w (dimensionless)');
LEGEND_CONSTANTS(:,41) = strpad('kd_w in component w (first_order_rate_constant)');
LEGEND_CONSTANTS(:,42) = strpad('k_FB_ph in component e_ph (first_order_rate_constant)');
LEGEND_CONSTANTS(:,43) = strpad('p in component e_ph (dimensionless)');
LEGEND_CONSTANTS(:,44) = strpad('Wph in component e_ph (dimensionless)');
LEGEND_CONSTANTS(:,45) = strpad('Kph in component e_ph (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt r in component r (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt c2 in component c2 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt m_3PI in component m_3PI (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt m_Ras in component m_Ras (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt x1 in component x1 (dimensionless)');
LEGEND_RATES(:,8) = strpad('d/dt x2 in component x2 (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt y in component y (dimensionless)');
LEGEND_RATES(:,9) = strpad('d/dt ypp in component ypp (dimensionless)');
LEGEND_RATES(:,10) = strpad('d/dt z in component z (dimensionless)');
LEGEND_RATES(:,11) = strpad('d/dt zpp in component zpp (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt f_GEF in component f_GEF (dimensionless)');
LEGEND_RATES(:,13) = strpad('d/dt w in component w (dimensionless)');
LEGEND_RATES(:,12) = strpad('d/dt e_ph in component e_ph (dimensionless)');
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) = 0.5;
STATES(:,2) = 0.0;
CONSTANTS(:,1) = 1.0;
CONSTANTS(:,2) = 0.005;
CONSTANTS(:,3) = 0.3;
CONSTANTS(:,4) = 0.07;
CONSTANTS(:,5) = 1.5;
CONSTANTS(:,6) = 0.2;
CONSTANTS(:,7) = 0.3;
CONSTANTS(:,8) = 80.0;
STATES(:,3) = 0.0;
CONSTANTS(:,9) = 1.0;
CONSTANTS(:,10) = 495.0;
CONSTANTS(:,11) = 5.09;
STATES(:,4) = 1.0;
STATES(:,5) = 0.0;
CONSTANTS(:,12) = 1.0;
CONSTANTS(:,13) = 0.1;
STATES(:,6) = 0.0;
CONSTANTS(:,14) = 0.745;
CONSTANTS(:,15) = 30.3;
CONSTANTS(:,16) = 45.5;
STATES(:,7) = 1.0;
STATES(:,8) = 0.0;
CONSTANTS(:,17) = 2.85;
CONSTANTS(:,18) = 6.77;
CONSTANTS(:,19) = 21.6;
CONSTANTS(:,20) = 15.7;
CONSTANTS(:,21) = 4.40;
CONSTANTS(:,22) = 44.0;
CONSTANTS(:,23) = 12.7;
CONSTANTS(:,24) = 1.18;
CONSTANTS(:,25) = 0.405;
STATES(:,9) = 0.0;
CONSTANTS(:,26) = 6.77;
CONSTANTS(:,27) = 31.9;
CONSTANTS(:,28) = 8.81;
CONSTANTS(:,29) = 4.71;
CONSTANTS(:,30) = 2.41;
STATES(:,10) = 1.0;
CONSTANTS(:,31) = 0.451;
CONSTANTS(:,32) = 11.8;
CONSTANTS(:,33) = 14.0;
CONSTANTS(:,34) = 31.5;
STATES(:,11) = 0.0;
STATES(:,12) = 1.0;
CONSTANTS(:,35) = 0.228;
CONSTANTS(:,36) = 31.9;
CONSTANTS(:,37) = 1.03;
CONSTANTS(:,38) = 3.76;
CONSTANTS(:,39) = 0.272;
CONSTANTS(:,40) = 0.976;
STATES(:,13) = 0.0;
CONSTANTS(:,41) = 0.0333;
CONSTANTS(:,42) = 2.34;
CONSTANTS(:,43) = 1.98;
CONSTANTS(:,44) = 0.385;
CONSTANTS(:,45) = 4.64;
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(:,40).*( (power(STATES(:,11), CONSTANTS(:,37))./(power(CONSTANTS(:,39), CONSTANTS(:,37))+power(STATES(:,11), CONSTANTS(:,37)))).*STATES(:,4) - (1.00000./CONSTANTS(:,38)).*(1.00000 - STATES(:,4)));
RATES(:,13) = CONSTANTS(:,41).*(STATES(:,11) - STATES(:,13));
RATES(:,12) = CONSTANTS(:,42).*(power(STATES(:,13), CONSTANTS(:,43))./(power(CONSTANTS(:,44), CONSTANTS(:,43))+power(STATES(:,13), CONSTANTS(:,43))) - (1.00000./CONSTANTS(:,45)).*(STATES(:,12) - 1.00000));
ALGEBRAIC(:,1) = ( CONSTANTS(:,1).*STATES(:,1))./CONSTANTS(:,5);
RATES(:,1) = power(1.00000+CONSTANTS(:,1)./CONSTANTS(:,5), -1.00000).*( CONSTANTS(:,2).*(1.00000 - (STATES(:,1)+ALGEBRAIC(:,1)))+ 2.00000.*( CONSTANTS(:,4).*STATES(:,2) - CONSTANTS(:,3).*power(ALGEBRAIC(:,1), 2.00000)));
RATES(:,2) = CONSTANTS(:,3).*power(ALGEBRAIC(:,1), 2.00000) - (CONSTANTS(:,4)+CONSTANTS(:,6)).*STATES(:,2);
ALGEBRAIC(:,2) = ((1.00000+CONSTANTS(:,7)+ 2.00000.*CONSTANTS(:,8).*STATES(:,2)) - power(power(1.00000+CONSTANTS(:,7)+ 2.00000.*CONSTANTS(:,8).*STATES(:,2), 2.00000), 1.0 ./ 2))./2.00000;
RATES(:,3) = CONSTANTS(:,9).*(ALGEBRAIC(:,2) - STATES(:,3));
ALGEBRAIC(:,3) = (( CONSTANTS(:,10).*STATES(:,2)+ CONSTANTS(:,11).*STATES(:,3))./(1.00000+ CONSTANTS(:,10).*STATES(:,2)+ CONSTANTS(:,11).*STATES(:,3))).*STATES(:,4);
RATES(:,5) = CONSTANTS(:,12).*( (1.00000+CONSTANTS(:,13)).*ALGEBRAIC(:,3) - (1.00000+ CONSTANTS(:,13).*ALGEBRAIC(:,3)).*STATES(:,5));
ALGEBRAIC(:,4) = 1.00000 - (STATES(:,7)+STATES(:,9));
RATES(:,6) = CONSTANTS(:,14).*(STATES(:,5) - STATES(:,6)./(1.00000+STATES(:,7)./CONSTANTS(:,15)+ALGEBRAIC(:,4)./CONSTANTS(:,16)));
RATES(:,8) = CONSTANTS(:,17).*(( (1.00000+CONSTANTS(:,18)).*STATES(:,3))./(1.00000+ CONSTANTS(:,18).*STATES(:,3)) - STATES(:,8)./(1.00000+STATES(:,7)./CONSTANTS(:,19)+ALGEBRAIC(:,4)./CONSTANTS(:,20)));
RATES(:,7) = ( CONSTANTS(:,21).*ALGEBRAIC(:,4))./(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,22)+STATES(:,9)./CONSTANTS(:,23)) - (( CONSTANTS(:,24).*STATES(:,6).*STATES(:,7))./(1.00000+STATES(:,7)./CONSTANTS(:,15)+ALGEBRAIC(:,4)./CONSTANTS(:,16))+( CONSTANTS(:,25).*STATES(:,8).*STATES(:,7))./(1.00000+STATES(:,7)./CONSTANTS(:,19)+ALGEBRAIC(:,4)./CONSTANTS(:,20)));
ALGEBRAIC(:,5) = 1.00000 - (STATES(:,10)+STATES(:,11));
RATES(:,9) = (( CONSTANTS(:,29).*STATES(:,6).*ALGEBRAIC(:,4))./(1.00000+STATES(:,7)./CONSTANTS(:,15)+ALGEBRAIC(:,4)./CONSTANTS(:,16))+( CONSTANTS(:,30).*STATES(:,8).*ALGEBRAIC(:,4))./(1.00000+STATES(:,7)./CONSTANTS(:,19)+ALGEBRAIC(:,4)./CONSTANTS(:,20))) - (( CONSTANTS(:,26).*STATES(:,9))./( (1.00000+STATES(:,10)./CONSTANTS(:,27)+ALGEBRAIC(:,5)./CONSTANTS(:,16)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,22))+STATES(:,9)./CONSTANTS(:,23)));
RATES(:,10) = ( CONSTANTS(:,31).*STATES(:,12).*ALGEBRAIC(:,5))./(1.00000+ALGEBRAIC(:,5)./CONSTANTS(:,33)+STATES(:,11)./CONSTANTS(:,34)) - ( CONSTANTS(:,32).*STATES(:,9))./(1.00000+STATES(:,10)./CONSTANTS(:,27)+ALGEBRAIC(:,5)./CONSTANTS(:,28));
RATES(:,11) = ( CONSTANTS(:,36).*ALGEBRAIC(:,5))./(1.00000+STATES(:,10)./CONSTANTS(:,27)+ALGEBRAIC(:,5)./CONSTANTS(:,28)) - ( CONSTANTS(:,35).*STATES(:,12).*STATES(:,11))./(1.00000+ALGEBRAIC(:,5)./CONSTANTS(:,33)+STATES(:,11)./CONSTANTS(:,34));
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) = ( CONSTANTS(:,1).*STATES(:,1))./CONSTANTS(:,5);
ALGEBRAIC(:,2) = ((1.00000+CONSTANTS(:,7)+ 2.00000.*CONSTANTS(:,8).*STATES(:,2)) - power(power(1.00000+CONSTANTS(:,7)+ 2.00000.*CONSTANTS(:,8).*STATES(:,2), 2.00000), 1.0 ./ 2))./2.00000;
ALGEBRAIC(:,3) = (( CONSTANTS(:,10).*STATES(:,2)+ CONSTANTS(:,11).*STATES(:,3))./(1.00000+ CONSTANTS(:,10).*STATES(:,2)+ CONSTANTS(:,11).*STATES(:,3))).*STATES(:,4);
ALGEBRAIC(:,4) = 1.00000 - (STATES(:,7)+STATES(:,9));
ALGEBRAIC(:,5) = 1.00000 - (STATES(:,10)+STATES(:,11));
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