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 =21;
end
% There are a total of 11 entries in each of the rate and state variable arrays.
% There are a total of 33 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_CONSTANTS(:,1) = strpad('k1 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k1_ in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k1__ in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('kn1 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k2 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('kn2 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k3 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k3_ in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('kn4 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k5 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('kn6 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('k8 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('k9 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('k10 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('k17 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('k18 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('k19 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('k20 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('k21 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,20) = strpad('k22 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('k24 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,22) = strpad('k25 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,23) = strpad('k25_ in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,24) = strpad('k26 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,25) = strpad('k26_ in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,26) = strpad('k28 in component rate_constants (first_order_rate_constant)');
LEGEND_CONSTANTS(:,27) = strpad('k29 in component rate_constants (first_order_rate_constant)');
LEGEND_STATES(:,1) = strpad('a_CyclinE_Cdk2 in component a_CyclinE_Cdk2 (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('V_2 in component V_2 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,14) = strpad('V_10 in component V_10 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('V_n2 in component V_n2 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,13) = strpad('V_9 in component V_9 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,15) = strpad('V_21 in component V_21 (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('i_CyclinE_Cdk2 in component i_CyclinE_Cdk2 (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('V_3 in component V_3 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,10) = strpad('V_5 in component V_5 (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('pRB_E2F in component pRB_E2F (dimensionless)');
LEGEND_CONSTANTS(:,33) = strpad('V_n1 in component V_n1 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,2) = strpad('V_1 in component V_1 (first_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('E2F in component E2F (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('V_4 in component E2F (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,7) = strpad('V_18 in component V_18 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('V_n4 in component V_n4 (first_order_rate_constant)');
LEGEND_STATES(:,5) = strpad('pRB in component pRB (dimensionless)');
LEGEND_CONSTANTS(:,29) = strpad('V_27 in component pRB (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,5) = strpad('V_26 in component V_26 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,11) = strpad('V_29 in component V_29 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,8) = strpad('V_28 in component V_28 (first_order_rate_constant)');
LEGEND_STATES(:,6) = strpad('CycD_Cdk4 in component CycD_Cdk4 (dimensionless)');
LEGEND_CONSTANTS(:,30) = strpad('V_6 in component CycD_Cdk4 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,19) = strpad('V_20 in component V_20 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,9) = strpad('V_n6 in component V_n6 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,17) = strpad('V_19 in component V_19 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,16) = strpad('V_17 in component V_17 (first_order_rate_constant)');
LEGEND_STATES(:,7) = strpad('p27 in component p27 (dimensionless)');
LEGEND_CONSTANTS(:,31) = strpad('V_7 in component p27 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,12) = strpad('V_8 in component V_8 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,21) = strpad('V_22 in component V_22 (first_order_rate_constant)');
LEGEND_STATES(:,8) = strpad('CycE_Cdk2_p27 in component CycE_Cdk2_p27 (dimensionless)');
LEGEND_STATES(:,9) = strpad('CycD_Cdk4_p27 in component CycD_Cdk4_p27 (dimensionless)');
LEGEND_STATES(:,10) = strpad('p16 in component p16 (dimensionless)');
LEGEND_CONSTANTS(:,32) = strpad('V_23 in component p16 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,20) = strpad('V_25 in component V_25 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,18) = strpad('V_24 in component V_24 (first_order_rate_constant)');
LEGEND_STATES(:,11) = strpad('pRB_P in component pRB_P (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt a_CyclinE_Cdk2 in component a_CyclinE_Cdk2 (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt i_CyclinE_Cdk2 in component i_CyclinE_Cdk2 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt pRB_E2F in component pRB_E2F (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt E2F in component E2F (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt pRB in component pRB (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt CycD_Cdk4 in component CycD_Cdk4 (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt p27 in component p27 (dimensionless)');
LEGEND_RATES(:,8) = strpad('d/dt CycE_Cdk2_p27 in component CycE_Cdk2_p27 (dimensionless)');
LEGEND_RATES(:,9) = strpad('d/dt CycD_Cdk4_p27 in component CycD_Cdk4_p27 (dimensionless)');
LEGEND_RATES(:,10) = strpad('d/dt p16 in component p16 (dimensionless)');
LEGEND_RATES(:,11) = strpad('d/dt pRB_P in component pRB_P (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 = [];
CONSTANTS(:,1) = 0.1;
CONSTANTS(:,2) = 0.5;
CONSTANTS(:,3) = 0.5;
CONSTANTS(:,4) = 0.001;
CONSTANTS(:,5) = 0.1;
CONSTANTS(:,6) = 1;
CONSTANTS(:,7) = 1.42;
CONSTANTS(:,8) = 0;
CONSTANTS(:,9) = 0.016;
CONSTANTS(:,10) = 0.02;
CONSTANTS(:,11) = 5;
CONSTANTS(:,12) = 2;
CONSTANTS(:,13) = 2;
CONSTANTS(:,14) = 0.035;
CONSTANTS(:,15) = 3.5;
CONSTANTS(:,16) = 0.0001;
CONSTANTS(:,17) = 0.05;
CONSTANTS(:,18) = 0.01;
CONSTANTS(:,19) = 0.1;
CONSTANTS(:,20) = 0.001;
CONSTANTS(:,21) = 0.1;
CONSTANTS(:,22) = 0.01;
CONSTANTS(:,23) = 0.02;
CONSTANTS(:,24) = 0.01;
CONSTANTS(:,25) = 0.1;
CONSTANTS(:,26) = 0.01;
CONSTANTS(:,27) = 0.001;
STATES(:,1) = 0;
STATES(:,2) = 0.01;
STATES(:,3) = 1.95;
STATES(:,4) = 0;
CONSTANTS(:,28) = 0.000001;
STATES(:,5) = 0.05;
CONSTANTS(:,29) = 0.01;
STATES(:,6) = 0;
CONSTANTS(:,30) = 0.018;
STATES(:,7) = 5;
CONSTANTS(:,31) = 0.0001;
STATES(:,8) = 1;
STATES(:,9) = 0;
STATES(:,10) = 5;
CONSTANTS(:,32) = 0.2;
STATES(:,11) = 0.01;
CONSTANTS(:,33) = CONSTANTS(:,4);
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(:,2) = CONSTANTS(:,2).*STATES(:,6).*STATES(:,3)+ CONSTANTS(:,3).*STATES(:,9).*STATES(:,3)+ CONSTANTS(:,1).*STATES(:,1).*STATES(:,3);
RATES(:,3) = CONSTANTS(:,33) - ALGEBRAIC(:,2);
ALGEBRAIC(:,7) = CONSTANTS(:,16).*STATES(:,4);
ALGEBRAIC(:,4) = CONSTANTS(:,9).*STATES(:,4);
RATES(:,4) = (ALGEBRAIC(:,2)+CONSTANTS(:,28)+ALGEBRAIC(:,7)) - (CONSTANTS(:,33)+ALGEBRAIC(:,4));
ALGEBRAIC(:,1) = CONSTANTS(:,5).*STATES(:,1).*STATES(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,6).*STATES(:,1);
ALGEBRAIC(:,6) = CONSTANTS(:,7).*STATES(:,4)+CONSTANTS(:,8);
ALGEBRAIC(:,10) = CONSTANTS(:,10).*STATES(:,2);
RATES(:,2) = (ALGEBRAIC(:,6)+ALGEBRAIC(:,3)) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,10));
ALGEBRAIC(:,5) = CONSTANTS(:,24)./( (1.00000+ CONSTANTS(:,25).*STATES(:,10)).*1.00000);
ALGEBRAIC(:,11) = CONSTANTS(:,27).*STATES(:,11);
ALGEBRAIC(:,8) = CONSTANTS(:,26).*STATES(:,5);
RATES(:,5) = (CONSTANTS(:,29)+ALGEBRAIC(:,5)+ALGEBRAIC(:,11)) - (CONSTANTS(:,33)+ALGEBRAIC(:,8));
RATES(:,11) = ALGEBRAIC(:,2) - ALGEBRAIC(:,11);
ALGEBRAIC(:,14) = CONSTANTS(:,14).*STATES(:,8);
ALGEBRAIC(:,13) = CONSTANTS(:,13).*STATES(:,7).*STATES(:,1);
RATES(:,8) = ALGEBRAIC(:,13) - ALGEBRAIC(:,14);
ALGEBRAIC(:,15) = CONSTANTS(:,19).*power(STATES(:,1), 2.00000);
RATES(:,1) = (ALGEBRAIC(:,1)+ALGEBRAIC(:,14)) - (ALGEBRAIC(:,3)+ALGEBRAIC(:,13)+ALGEBRAIC(:,15));
ALGEBRAIC(:,19) = CONSTANTS(:,18).*STATES(:,9);
ALGEBRAIC(:,9) = CONSTANTS(:,11).*STATES(:,6);
ALGEBRAIC(:,17) = CONSTANTS(:,17).*STATES(:,7).*STATES(:,6);
ALGEBRAIC(:,16) = CONSTANTS(:,15).*STATES(:,10).*STATES(:,6);
RATES(:,6) = (CONSTANTS(:,30)+ALGEBRAIC(:,19)) - (ALGEBRAIC(:,9)+ALGEBRAIC(:,17)+ALGEBRAIC(:,16));
RATES(:,9) = ALGEBRAIC(:,17) - ALGEBRAIC(:,19);
ALGEBRAIC(:,20) = CONSTANTS(:,22)./( (1.00000+ CONSTANTS(:,23).*STATES(:,5)).*1.00000);
ALGEBRAIC(:,18) = CONSTANTS(:,21).*STATES(:,10);
RATES(:,10) = (CONSTANTS(:,32)+ALGEBRAIC(:,20)) - (ALGEBRAIC(:,16)+ALGEBRAIC(:,18));
ALGEBRAIC(:,12) = CONSTANTS(:,12).*STATES(:,7).*STATES(:,1);
ALGEBRAIC(:,21) = CONSTANTS(:,20).*STATES(:,7);
RATES(:,7) = (CONSTANTS(:,31)+ALGEBRAIC(:,14)+ALGEBRAIC(:,19)) - (ALGEBRAIC(:,12)+ALGEBRAIC(:,13)+ALGEBRAIC(:,17)+ALGEBRAIC(:,21));
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(:,2) = CONSTANTS(:,2).*STATES(:,6).*STATES(:,3)+ CONSTANTS(:,3).*STATES(:,9).*STATES(:,3)+ CONSTANTS(:,1).*STATES(:,1).*STATES(:,3);
ALGEBRAIC(:,7) = CONSTANTS(:,16).*STATES(:,4);
ALGEBRAIC(:,4) = CONSTANTS(:,9).*STATES(:,4);
ALGEBRAIC(:,1) = CONSTANTS(:,5).*STATES(:,1).*STATES(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,6).*STATES(:,1);
ALGEBRAIC(:,6) = CONSTANTS(:,7).*STATES(:,4)+CONSTANTS(:,8);
ALGEBRAIC(:,10) = CONSTANTS(:,10).*STATES(:,2);
ALGEBRAIC(:,5) = CONSTANTS(:,24)./( (1.00000+ CONSTANTS(:,25).*STATES(:,10)).*1.00000);
ALGEBRAIC(:,11) = CONSTANTS(:,27).*STATES(:,11);
ALGEBRAIC(:,8) = CONSTANTS(:,26).*STATES(:,5);
ALGEBRAIC(:,14) = CONSTANTS(:,14).*STATES(:,8);
ALGEBRAIC(:,13) = CONSTANTS(:,13).*STATES(:,7).*STATES(:,1);
ALGEBRAIC(:,15) = CONSTANTS(:,19).*power(STATES(:,1), 2.00000);
ALGEBRAIC(:,19) = CONSTANTS(:,18).*STATES(:,9);
ALGEBRAIC(:,9) = CONSTANTS(:,11).*STATES(:,6);
ALGEBRAIC(:,17) = CONSTANTS(:,17).*STATES(:,7).*STATES(:,6);
ALGEBRAIC(:,16) = CONSTANTS(:,15).*STATES(:,10).*STATES(:,6);
ALGEBRAIC(:,20) = CONSTANTS(:,22)./( (1.00000+ CONSTANTS(:,23).*STATES(:,5)).*1.00000);
ALGEBRAIC(:,18) = CONSTANTS(:,21).*STATES(:,10);
ALGEBRAIC(:,12) = CONSTANTS(:,12).*STATES(:,7).*STATES(:,1);
ALGEBRAIC(:,21) = CONSTANTS(:,20).*STATES(:,7);
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