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 6 entries in each of the rate and state variable arrays. % There are a total of 8 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('x_1 in component x_1 (picomolar)'); LEGEND_CONSTANTS(:,1) = strpad('k_t in component model_parameters (per_minute)'); LEGEND_CONSTANTS(:,2) = strpad('B_max in component model_parameters (picomolar)'); LEGEND_CONSTANTS(:,3) = strpad('k_on in component model_parameters (per_picomolar_per_minute)'); LEGEND_STATES(:,2) = strpad('x_2 in component x_2 (picomolar)'); LEGEND_CONSTANTS(:,4) = strpad('k_off in component model_parameters (per_minute)'); LEGEND_STATES(:,3) = strpad('x_3 in component x_3 (picomolar)'); LEGEND_CONSTANTS(:,5) = strpad('k_ex in component model_parameters (per_minute)'); LEGEND_STATES(:,4) = strpad('x_4 in component x_4 (picomolar)'); LEGEND_CONSTANTS(:,6) = strpad('k_e in component model_parameters (per_minute)'); LEGEND_CONSTANTS(:,7) = strpad('k_di in component model_parameters (per_minute)'); LEGEND_CONSTANTS(:,8) = strpad('k_de in component model_parameters (per_minute)'); LEGEND_STATES(:,5) = strpad('x_5 in component x_5 (picomolar)'); LEGEND_STATES(:,6) = strpad('x_6 in component x_6 (picomolar)'); LEGEND_RATES(:,1) = strpad('d/dt x_1 in component x_1 (picomolar)'); LEGEND_RATES(:,2) = strpad('d/dt x_2 in component x_2 (picomolar)'); LEGEND_RATES(:,3) = strpad('d/dt x_3 in component x_3 (picomolar)'); LEGEND_RATES(:,4) = strpad('d/dt x_4 in component x_4 (picomolar)'); LEGEND_RATES(:,5) = strpad('d/dt x_5 in component x_5 (picomolar)'); LEGEND_RATES(:,6) = strpad('d/dt x_6 in component x_6 (picomolar)'); 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) = 516; CONSTANTS(:,1) = 0.03294; CONSTANTS(:,2) = 129; CONSTANTS(:,3) = 0.10496e-3; STATES(:,2) = 2030.19; CONSTANTS(:,4) = 0.01721; STATES(:,3) = 0; CONSTANTS(:,5) = 0.00994; STATES(:,4) = 0; CONSTANTS(:,6) = 0.07483; CONSTANTS(:,7) = 0.003179; CONSTANTS(:,8) = 0.0164; STATES(:,5) = 0; STATES(:,6) = 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(:,1).*CONSTANTS(:,2) - CONSTANTS(:,1).*STATES(:,1)) - CONSTANTS(:,3).*STATES(:,1).*STATES(:,2))+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4); RATES(:,2) = - CONSTANTS(:,3).*STATES(:,1).*STATES(:,2)+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4); RATES(:,3) = ( CONSTANTS(:,3).*STATES(:,1).*STATES(:,2) - CONSTANTS(:,4).*STATES(:,3)) - CONSTANTS(:,6).*STATES(:,3); RATES(:,4) = (( CONSTANTS(:,6).*STATES(:,3) - CONSTANTS(:,5).*STATES(:,4)) - CONSTANTS(:,7).*STATES(:,4)) - CONSTANTS(:,8).*STATES(:,4); RATES(:,5) = CONSTANTS(:,7).*STATES(:,4); RATES(:,6) = CONSTANTS(:,8).*STATES(:,4); 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