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 8 entries in each of the rate and state variable arrays.
% There are a total of 25 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_STATES(:,1) = strpad('Pyr in component Pyr (micromolar)');
LEGEND_CONSTANTS(:,25) = strpad('v1 in component v1 (micromolar_per_second)');
LEGEND_ALGEBRAIC(:,1) = strpad('v2 in component v2 (micromolar_per_second)');
LEGEND_ALGEBRAIC(:,6) = strpad('v7 in component v7 (micromolar_per_second)');
LEGEND_STATES(:,2) = strpad('AcCoA in component AcCoA (micromolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('v3 in component v3 (micromolar_per_second)');
LEGEND_STATES(:,3) = strpad('Cit in component Cit (micromolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('v4 in component v4 (micromolar_per_second)');
LEGEND_STATES(:,4) = strpad('KG in component KG (micromolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('v5 in component v5 (micromolar_per_second)');
LEGEND_ALGEBRAIC(:,5) = strpad('v6 in component v6 (micromolar_per_second)');
LEGEND_STATES(:,5) = strpad('OAA in component OAA (micromolar)');
LEGEND_ALGEBRAIC(:,7) = strpad('v8 in component v8 (micromolar_per_second)');
LEGEND_STATES(:,6) = strpad('NAD in component NAD (micromolar)');
LEGEND_ALGEBRAIC(:,10) = strpad('vresp in component vresp (micromolar_per_second)');
LEGEND_STATES(:,7) = strpad('ATP in component ATP (micromolar)');
LEGEND_ALGEBRAIC(:,13) = strpad('vATP in component vATP (micromolar_per_second)');
LEGEND_ALGEBRAIC(:,8) = strpad('vANT in component vANT (micromolar_per_second)');
LEGEND_STATES(:,8) = strpad('delta_psi in component delta_psi (millivolt)');
LEGEND_CONSTANTS(:,1) = strpad('C in component delta_psi (millimolar_per_millivolt)');
LEGEND_ALGEBRAIC(:,9) = strpad('vleak in component vleak (micromolar_per_second)');
LEGEND_CONSTANTS(:,2) = strpad('k1 in component v1 (micromolar_per_second)');
LEGEND_CONSTANTS(:,3) = strpad('k2 in component v2 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k3 in component v3 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k4 in component v4 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k5 in component v5 (third_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('At in component model_parameters (millimolar)');
LEGEND_CONSTANTS(:,8) = strpad('k6 in component v6 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k7 in component v7 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k8 in component v8 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('kANT in component vANT (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('kleak in component vleak (molar_per_millivolt_per_second)');
LEGEND_CONSTANTS(:,13) = strpad('kresp in component vresp (millimolar_per_second)');
LEGEND_CONSTANTS(:,14) = strpad('K in component vresp (millimolar)');
LEGEND_CONSTANTS(:,15) = strpad('a in component vresp (per_millivolt)');
LEGEND_CONSTANTS(:,16) = strpad('delta_psi_m in component vresp (millivolt)');
LEGEND_CONSTANTS(:,17) = strpad('Nt in component model_parameters (millimolar)');
LEGEND_CONSTANTS(:,18) = strpad('kATP in component vATP (millimolar_per_second)');
LEGEND_CONSTANTS(:,19) = strpad('b in component vATP (per_micromolar)');
LEGEND_ALGEBRAIC(:,12) = strpad('ATP_crit_delta_psi in component ATP_crit_delta_psi (micromolar)');
LEGEND_CONSTANTS(:,20) = strpad('R in component ATP_crit_delta_psi (joule_per_mole_kelvin)');
LEGEND_CONSTANTS(:,21) = strpad('T in component ATP_crit_delta_psi (kelvin)');
LEGEND_CONSTANTS(:,22) = strpad('F in component ATP_crit_delta_psi (coulomb_per_mole)');
LEGEND_CONSTANTS(:,23) = strpad('Kapp in component ATP_crit_delta_psi (per_millimolar)');
LEGEND_CONSTANTS(:,24) = strpad('Pi in component ATP_crit_delta_psi (millimolar)');
LEGEND_ALGEBRAIC(:,11) = strpad('delta_G_transport in component ATP_crit_delta_psi (joule_per_mole)');
LEGEND_RATES(:,1) = strpad('d/dt Pyr in component Pyr (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt AcCoA in component AcCoA (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt Cit in component Cit (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt KG in component KG (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt OAA in component OAA (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt NAD in component NAD (micromolar)');
LEGEND_RATES(:,7) = strpad('d/dt ATP in component ATP (micromolar)');
LEGEND_RATES(:,8) = strpad('d/dt delta_psi in component delta_psi (millivolt)');
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) = 0.154;
STATES(:,2) = 0.063;
STATES(:,3) = 0.44;
STATES(:,4) = 0.225;
STATES(:,5) = 0.005;
STATES(:,6) = 0.856;
STATES(:,7) = 3.536;
STATES(:,8) = 150.0;
CONSTANTS(:,1) = 6.75e-06;
CONSTANTS(:,2) = 38.0;
CONSTANTS(:,3) = 152.0;
CONSTANTS(:,4) = 57142.0;
CONSTANTS(:,5) = 53.0;
CONSTANTS(:,6) = 82361.0;
CONSTANTS(:,7) = 4.160;
CONSTANTS(:,8) = 3.2e-3;
CONSTANTS(:,9) = 40.0;
CONSTANTS(:,10) = 3.6;
CONSTANTS(:,11) = 0.1;
CONSTANTS(:,12) = 0.426;
CONSTANTS(:,13) = 2.5;
CONSTANTS(:,14) = 2;
CONSTANTS(:,15) = 0.1;
CONSTANTS(:,16) = 150.0;
CONSTANTS(:,17) = 1.070;
CONSTANTS(:,18) = 131.9;
CONSTANTS(:,19) = 4;
CONSTANTS(:,20) = 8.314;
CONSTANTS(:,21) = 298;
CONSTANTS(:,22) = 96485;
CONSTANTS(:,23) = 4.4e-6;
CONSTANTS(:,24) = 2.440;
CONSTANTS(:,25) = CONSTANTS(:,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(:,1) = CONSTANTS(:,3).*STATES(:,1).*STATES(:,6);
ALGEBRAIC(:,2) = CONSTANTS(:,4).*STATES(:,5).*STATES(:,2);
RATES(:,2) = ALGEBRAIC(:,1) - ALGEBRAIC(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,5).*STATES(:,3).*STATES(:,6);
RATES(:,3) = ALGEBRAIC(:,2) - ALGEBRAIC(:,3);
ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,4).*STATES(:,6).*(CONSTANTS(:,7) - STATES(:,7));
ALGEBRAIC(:,5) = CONSTANTS(:,8).*(STATES(:,5) - STATES(:,4));
RATES(:,4) = (ALGEBRAIC(:,3)+ALGEBRAIC(:,5)) - ALGEBRAIC(:,4);
ALGEBRAIC(:,6) = CONSTANTS(:,9).*STATES(:,1).*STATES(:,7);
RATES(:,1) = CONSTANTS(:,25) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,6));
ALGEBRAIC(:,7) = CONSTANTS(:,10).*STATES(:,5);
RATES(:,5) = (ALGEBRAIC(:,4)+ALGEBRAIC(:,6)) - (ALGEBRAIC(:,2)+ALGEBRAIC(:,7)+ALGEBRAIC(:,5));
ALGEBRAIC(:,10) = CONSTANTS(:,13).*((CONSTANTS(:,17) - STATES(:,6))./((CONSTANTS(:,14)+CONSTANTS(:,17)) - STATES(:,6))).*(1.00000./(1.00000+exp( CONSTANTS(:,15).*(STATES(:,8) - CONSTANTS(:,16)))));
RATES(:,6) = ALGEBRAIC(:,10) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,3)+ 2.00000.*ALGEBRAIC(:,4));
ALGEBRAIC(:,11) = 0.00120000.*CONSTANTS(:,22).*STATES(:,8);
ALGEBRAIC(:,12) = CONSTANTS(:,7)./(1.00000+exp(( -3.00000.*ALGEBRAIC(:,11))./( CONSTANTS(:,20).*CONSTANTS(:,21)))./( CONSTANTS(:,23).*CONSTANTS(:,24)));
ALGEBRAIC(:,13) = CONSTANTS(:,18).*(2.00000./(1.00000+exp( CONSTANTS(:,19).*(STATES(:,7) - ALGEBRAIC(:,12)))) - 1.00000);
ALGEBRAIC(:,8) = CONSTANTS(:,11).*STATES(:,7);
RATES(:,7) = (ALGEBRAIC(:,13)+ALGEBRAIC(:,4)) - (ALGEBRAIC(:,8)+ALGEBRAIC(:,6));
ALGEBRAIC(:,9) = CONSTANTS(:,12).*STATES(:,8);
RATES(:,8) = (1.00000./CONSTANTS(:,1)).*( 10.0000.*ALGEBRAIC(:,10) - ( 3.00000.*ALGEBRAIC(:,13)+ALGEBRAIC(:,9)+ALGEBRAIC(:,8)));
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(:,3).*STATES(:,1).*STATES(:,6);
ALGEBRAIC(:,2) = CONSTANTS(:,4).*STATES(:,5).*STATES(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,5).*STATES(:,3).*STATES(:,6);
ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,4).*STATES(:,6).*(CONSTANTS(:,7) - STATES(:,7));
ALGEBRAIC(:,5) = CONSTANTS(:,8).*(STATES(:,5) - STATES(:,4));
ALGEBRAIC(:,6) = CONSTANTS(:,9).*STATES(:,1).*STATES(:,7);
ALGEBRAIC(:,7) = CONSTANTS(:,10).*STATES(:,5);
ALGEBRAIC(:,10) = CONSTANTS(:,13).*((CONSTANTS(:,17) - STATES(:,6))./((CONSTANTS(:,14)+CONSTANTS(:,17)) - STATES(:,6))).*(1.00000./(1.00000+exp( CONSTANTS(:,15).*(STATES(:,8) - CONSTANTS(:,16)))));
ALGEBRAIC(:,11) = 0.00120000.*CONSTANTS(:,22).*STATES(:,8);
ALGEBRAIC(:,12) = CONSTANTS(:,7)./(1.00000+exp(( -3.00000.*ALGEBRAIC(:,11))./( CONSTANTS(:,20).*CONSTANTS(:,21)))./( CONSTANTS(:,23).*CONSTANTS(:,24)));
ALGEBRAIC(:,13) = CONSTANTS(:,18).*(2.00000./(1.00000+exp( CONSTANTS(:,19).*(STATES(:,7) - ALGEBRAIC(:,12)))) - 1.00000);
ALGEBRAIC(:,8) = CONSTANTS(:,11).*STATES(:,7);
ALGEBRAIC(:,9) = CONSTANTS(:,12).*STATES(:,8);
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