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 =0; end % There are a total of 9 entries in each of the rate and state variable arrays. % There are a total of 11 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 (hour)'); LEGEND_STATES(:,1) = strpad('Pfr in component Pfr (micromolar)'); LEGEND_STATES(:,2) = strpad('Pr in component Pr (micromolar)'); LEGEND_CONSTANTS(:,1) = strpad('Ifr_sigma_fr_phi_fr in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,2) = strpad('Ir_sigma_r_phi_r in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,3) = strpad('kd in component Pr (first_order_rate_constant)'); LEGEND_STATES(:,3) = strpad('Xi in component Xi (micromolar)'); LEGEND_STATES(:,4) = strpad('Xa in component Xa (micromolar)'); LEGEND_CONSTANTS(:,4) = strpad('kia in component model_parameters (second_order_rate_constant)'); LEGEND_CONSTANTS(:,5) = strpad('kai in component model_parameters (first_order_rate_constant)'); LEGEND_STATES(:,5) = strpad('prepreS in component prepreS (micromolar)'); LEGEND_CONSTANTS(:,6) = strpad('kx in component model_parameters (second_order_rate_constant)'); LEGEND_STATES(:,6) = strpad('preS in component preS (micromolar)'); LEGEND_STATES(:,7) = strpad('Ya in component Ya (micromolar)'); LEGEND_CONSTANTS(:,7) = strpad('ky in component model_parameters (second_order_rate_constant)'); LEGEND_STATES(:,8) = strpad('S in component S (micromolar)'); LEGEND_CONSTANTS(:,8) = strpad('alpha1 in component S (micromolar)'); LEGEND_STATES(:,9) = strpad('V in component V (micromolar)'); LEGEND_CONSTANTS(:,9) = strpad('alpha2 in component V (micromolar)'); LEGEND_CONSTANTS(:,10) = strpad('kG in component Ya (second_order_rate_constant)'); LEGEND_CONSTANTS(:,11) = strpad('glucose in component model_parameters (micromolar)'); LEGEND_RATES(:,1) = strpad('d/dt Pfr in component Pfr (micromolar)'); LEGEND_RATES(:,2) = strpad('d/dt Pr in component Pr (micromolar)'); LEGEND_RATES(:,3) = strpad('d/dt Xi in component Xi (micromolar)'); LEGEND_RATES(:,4) = strpad('d/dt Xa in component Xa (micromolar)'); LEGEND_RATES(:,5) = strpad('d/dt prepreS in component prepreS (micromolar)'); LEGEND_RATES(:,6) = strpad('d/dt preS in component preS (micromolar)'); LEGEND_RATES(:,8) = strpad('d/dt S in component S (micromolar)'); LEGEND_RATES(:,9) = strpad('d/dt V in component V (micromolar)'); LEGEND_RATES(:,7) = strpad('d/dt Ya in component Ya (micromolar)'); 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) = 10.0; STATES(:,2) = 0.0; CONSTANTS(:,1) = 0.1; CONSTANTS(:,2) = 0.0; CONSTANTS(:,3) = 0.1; STATES(:,3) = 6.0; STATES(:,4) = 0.0; CONSTANTS(:,4) = 0.1; CONSTANTS(:,5) = 0.8; STATES(:,5) = 200.0; CONSTANTS(:,6) = 0.2; STATES(:,6) = 0.0; STATES(:,7) = 0.9; CONSTANTS(:,7) = 1.0; STATES(:,8) = 0.0; CONSTANTS(:,8) = 30.0; STATES(:,9) = 50.0; CONSTANTS(:,9) = 50.0; CONSTANTS(:,10) = 0.1; CONSTANTS(:,11) = 1.0; 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(:,1) = CONSTANTS(:,2).*STATES(:,2) - CONSTANTS(:,1).*STATES(:,1); RATES(:,2) = CONSTANTS(:,1).*STATES(:,2) - ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,3).*STATES(:,2)); RATES(:,3) = CONSTANTS(:,5).*STATES(:,4) - CONSTANTS(:,4).*STATES(:,2).*STATES(:,3); RATES(:,4) = CONSTANTS(:,4).*STATES(:,2).*STATES(:,3) - CONSTANTS(:,5).*STATES(:,4); RATES(:,5) = - ( CONSTANTS(:,6).*STATES(:,4).*STATES(:,5)); RATES(:,6) = CONSTANTS(:,6).*STATES(:,4).*STATES(:,5) - CONSTANTS(:,7).*STATES(:,7).*STATES(:,6); RATES(:,8) = ( CONSTANTS(:,7).*STATES(:,7).*STATES(:,6)+CONSTANTS(:,8)./(1.00000+power(STATES(:,9), 3.00000))) - STATES(:,8); RATES(:,9) = CONSTANTS(:,9)./(1.00000+power(STATES(:,8), 3.00000)) - STATES(:,9); RATES(:,7) = - ( CONSTANTS(:,10).*CONSTANTS(:,11).*STATES(:,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 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