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 =4; end % There are a total of 4 entries in each of the rate and state variable arrays. % There are a total of 10 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_ALGEBRAIC(:,1) = strpad('F in component equations (force)'); LEGEND_STATES(:,1) = strpad('R_on in component equations (dimensionless)'); LEGEND_STATES(:,2) = strpad('A in component equations (dimensionless)'); LEGEND_CONSTANTS(:,1) = strpad('alpha in component equations (dimensionless)'); LEGEND_ALGEBRAIC(:,2) = strpad('D in component equations (dimensionless)'); LEGEND_ALGEBRAIC(:,4) = strpad('k_XB in component equations (per_second)'); LEGEND_CONSTANTS(:,2) = strpad('k_a in component equations (per_second)'); LEGEND_STATES(:,3) = strpad('x in component equations (um)'); LEGEND_CONSTANTS(:,3) = strpad('x_0 in component undefined_parameters (um)'); LEGEND_CONSTANTS(:,4) = strpad('epsilon in component undefined_parameters (force_per_um)'); LEGEND_CONSTANTS(:,5) = strpad('beta in component undefined_parameters (per_um)'); LEGEND_CONSTANTS(:,6) = strpad('g in component undefined_parameters (per_second)'); LEGEND_CONSTANTS(:,7) = strpad('f in component undefined_parameters (per_second)'); LEGEND_CONSTANTS(:,8) = strpad('k_off in component undefined_parameters (per_second)'); LEGEND_CONSTANTS(:,9) = strpad('k_on in component undefined_parameters (per_second)'); LEGEND_STATES(:,4) = strpad('L in component parameters_stelzer_et_al (um)'); LEGEND_CONSTANTS(:,10) = strpad('L_0 in component parameters_stelzer_et_al (um)'); LEGEND_ALGEBRAIC(:,3) = strpad('dL_dt in component parameters_stelzer_et_al (um_per_second)'); LEGEND_RATES(:,1) = strpad('d/dt R_on in component equations (dimensionless)'); LEGEND_RATES(:,2) = strpad('d/dt A in component equations (dimensionless)'); LEGEND_RATES(:,3) = strpad('d/dt x in component equations (um)'); LEGEND_RATES(:,4) = strpad('d/dt L in component parameters_stelzer_et_al (um)'); 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) = 1; STATES(:,2) = 0; CONSTANTS(:,1) = 0.1; CONSTANTS(:,2) = 0; STATES(:,3) = 1; CONSTANTS(:,3) = 1; CONSTANTS(:,4) = 1; CONSTANTS(:,5) = 2; CONSTANTS(:,6) = 1; CONSTANTS(:,7) = 1; CONSTANTS(:,8) = 1; CONSTANTS(:,9) = 1; STATES(:,4) = 2.12; CONSTANTS(:,10) = 2.12; 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) = 1.00000 - STATES(:,2); RATES(:,2) = CONSTANTS(:,7).*ALGEBRAIC(:,2).*STATES(:,1) - CONSTANTS(:,6).*STATES(:,2); ALGEBRAIC(:,3) = piecewise({0.00100000<VOI&VOI<=0.00300000, 10.6000 }, 0.00000); RATES(:,3) = - CONSTANTS(:,6).*(STATES(:,3) - CONSTANTS(:,3))+ALGEBRAIC(:,3); RATES(:,4) = ALGEBRAIC(:,3); ALGEBRAIC(:,4) = CONSTANTS(:,2).*STATES(:,2); RATES(:,1) = - ((CONSTANTS(:,8)+ALGEBRAIC(:,4)+ CONSTANTS(:,1).*CONSTANTS(:,9))./(1.00000+CONSTANTS(:,1))+ CONSTANTS(:,7).*ALGEBRAIC(:,2)).*STATES(:,1)+ (CONSTANTS(:,6) - (ALGEBRAIC(:,4)+ CONSTANTS(:,1).*CONSTANTS(:,9))./(1.00000+CONSTANTS(:,1))).*STATES(:,2)+ (ALGEBRAIC(:,4)+( CONSTANTS(:,1).*CONSTANTS(:,9))./(1.00000+CONSTANTS(:,1))).*CONSTANTS(:,5).*(STATES(:,4) - CONSTANTS(:,10)); 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) = 1.00000 - STATES(:,2); ALGEBRAIC(:,3) = piecewise({0.00100000<VOI&VOI<=0.00300000, 10.6000 }, 0.00000); ALGEBRAIC(:,4) = CONSTANTS(:,2).*STATES(:,2); ALGEBRAIC(:,1) = STATES(:,2).*CONSTANTS(:,4).*STATES(:,3); end % Compute result of a piecewise function function x = piecewise(cases, default) set = [0]; for i = 1:2:length(cases) if (length(cases{i+1}) == 1) x(cases{i} & ~set,:) = cases{i+1}; else x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set); end set = set | cases{i}; if(set), break, end end if (length(default) == 1) x(~set,:) = default; else x(~set,:) = default(~set); 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