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 =3; end % There are a total of 3 entries in each of the rate and state variable arrays. % There are a total of 20 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('V_0 in component Vin (micromolar_per_minute)'); LEGEND_CONSTANTS(:,2) = strpad('V_1 in component Vin (micromolar_per_minute)'); LEGEND_CONSTANTS(:,3) = strpad('beta in component Vin (dimensionless)'); LEGEND_CONSTANTS(:,20) = strpad('V_in in component Vin (micromolar_per_minute)'); LEGEND_CONSTANTS(:,4) = strpad('V_M2 in component V2 (micromolar_per_minute)'); LEGEND_STATES(:,1) = strpad('Z in component cytosol (micromolar)'); LEGEND_CONSTANTS(:,5) = strpad('K_2 in component V2 (micromolar)'); LEGEND_ALGEBRAIC(:,1) = strpad('V_2 in component V2 (micromolar_per_minute)'); LEGEND_CONSTANTS(:,6) = strpad('V_M3 in component V3 (micromolar_per_minute)'); LEGEND_CONSTANTS(:,7) = strpad('K_Z in component V3 (micromolar)'); LEGEND_CONSTANTS(:,8) = strpad('K_A in component V3 (micromolar)'); LEGEND_CONSTANTS(:,9) = strpad('K_Y in component V3 (micromolar)'); LEGEND_CONSTANTS(:,10) = strpad('m in component V3 (dimensionless)'); LEGEND_STATES(:,2) = strpad('Y in component internal_pool (micromolar)'); LEGEND_STATES(:,3) = strpad('A in component InsP3_conc (micromolar)'); LEGEND_ALGEBRAIC(:,3) = strpad('V_3 in component V3 (micromolar_per_minute)'); LEGEND_CONSTANTS(:,11) = strpad('V_M5 in component V5 (micromolar_per_minute)'); LEGEND_CONSTANTS(:,12) = strpad('K_5 in component V5 (micromolar)'); LEGEND_CONSTANTS(:,13) = strpad('K_d in component V5 (micromolar)'); LEGEND_CONSTANTS(:,14) = strpad('p in component V5 (dimensionless)'); LEGEND_CONSTANTS(:,15) = strpad('n in component V5 (dimensionless)'); LEGEND_ALGEBRAIC(:,2) = strpad('V_5 in component V5 (micromolar_per_minute)'); LEGEND_CONSTANTS(:,16) = strpad('k in component cytosol (per_minute)'); LEGEND_CONSTANTS(:,17) = strpad('k_f in component cytosol (per_minute)'); LEGEND_CONSTANTS(:,18) = strpad('epsilon in component InsP3_conc (per_minute)'); LEGEND_CONSTANTS(:,19) = strpad('V_4 in component InsP3_conc (micromolar_per_minute)'); LEGEND_RATES(:,1) = strpad('d/dt Z in component cytosol (micromolar)'); LEGEND_RATES(:,2) = strpad('d/dt Y in component internal_pool (micromolar)'); LEGEND_RATES(:,3) = strpad('d/dt A in component InsP3_conc (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 = []; CONSTANTS(:,1) = 2; CONSTANTS(:,2) = 2; CONSTANTS(:,3) = 0.6; CONSTANTS(:,4) = 6; STATES(:,1) = 0.15; CONSTANTS(:,5) = 0.1; CONSTANTS(:,6) = 20; CONSTANTS(:,7) = 0.5; CONSTANTS(:,8) = 0.2; CONSTANTS(:,9) = 0.2; CONSTANTS(:,10) = 2; STATES(:,2) = 1; STATES(:,3) = 0.42; CONSTANTS(:,11) = 5; CONSTANTS(:,12) = 1; CONSTANTS(:,13) = 0.4; CONSTANTS(:,14) = 2; CONSTANTS(:,15) = 4; CONSTANTS(:,16) = 10; CONSTANTS(:,17) = 1; CONSTANTS(:,18) = 0.1; CONSTANTS(:,19) = 2; CONSTANTS(:,20) = CONSTANTS(:,1)+ CONSTANTS(:,2).*CONSTANTS(:,3); 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(:,11).*power(STATES(:,3), CONSTANTS(:,14)))./(power(CONSTANTS(:,12), CONSTANTS(:,14))+power(STATES(:,3), CONSTANTS(:,14)))).*power(STATES(:,1), CONSTANTS(:,15)))./(power(CONSTANTS(:,13), CONSTANTS(:,15))+power(STATES(:,1), CONSTANTS(:,15))); RATES(:,3) = ( CONSTANTS(:,3).*CONSTANTS(:,19) - ALGEBRAIC(:,2)) - CONSTANTS(:,18).*STATES(:,3); ALGEBRAIC(:,1) = ( CONSTANTS(:,4).*power(STATES(:,1), 2.00000))./(power(CONSTANTS(:,5), 2.00000)+power(STATES(:,1), 2.00000)); ALGEBRAIC(:,3) = ( (( (( CONSTANTS(:,6).*power(STATES(:,1), CONSTANTS(:,10)))./(power(CONSTANTS(:,7), CONSTANTS(:,10))+power(STATES(:,1), CONSTANTS(:,10)))).*power(STATES(:,2), 2.00000))./(power(CONSTANTS(:,9), 2.00000)+power(STATES(:,2), 2.00000))).*power(STATES(:,3), 4.00000))./(power(CONSTANTS(:,8), 4.00000)+power(STATES(:,3), 4.00000)); RATES(:,1) = ((CONSTANTS(:,20) - ALGEBRAIC(:,1))+ALGEBRAIC(:,3)+ CONSTANTS(:,17).*STATES(:,2)) - CONSTANTS(:,16).*STATES(:,1); RATES(:,2) = (ALGEBRAIC(:,1) - ALGEBRAIC(:,3)) - CONSTANTS(:,17).*STATES(:,2); 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(:,11).*power(STATES(:,3), CONSTANTS(:,14)))./(power(CONSTANTS(:,12), CONSTANTS(:,14))+power(STATES(:,3), CONSTANTS(:,14)))).*power(STATES(:,1), CONSTANTS(:,15)))./(power(CONSTANTS(:,13), CONSTANTS(:,15))+power(STATES(:,1), CONSTANTS(:,15))); ALGEBRAIC(:,1) = ( CONSTANTS(:,4).*power(STATES(:,1), 2.00000))./(power(CONSTANTS(:,5), 2.00000)+power(STATES(:,1), 2.00000)); ALGEBRAIC(:,3) = ( (( (( CONSTANTS(:,6).*power(STATES(:,1), CONSTANTS(:,10)))./(power(CONSTANTS(:,7), CONSTANTS(:,10))+power(STATES(:,1), CONSTANTS(:,10)))).*power(STATES(:,2), 2.00000))./(power(CONSTANTS(:,9), 2.00000)+power(STATES(:,2), 2.00000))).*power(STATES(:,3), 4.00000))./(power(CONSTANTS(:,8), 4.00000)+power(STATES(:,3), 4.00000)); 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