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 =15; end % There are a total of 7 entries in each of the rate and state variable arrays. % There are a total of 40 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_CONSTANTS(:,1) = strpad('cap in component parameters (nanofarad)'); LEGEND_CONSTANTS(:,2) = strpad('cc1lin in component parameters (per_second)'); LEGEND_CONSTANTS(:,3) = strpad('cc_2 in component parameters (per_second)'); LEGEND_CONSTANTS(:,4) = strpad('ck1lin in component parameters (per_second)'); LEGEND_CONSTANTS(:,5) = strpad('ck_2 in component parameters (per_second)'); LEGEND_CONSTANTS(:,6) = strpad('clmax in component parameters (nanosiemens)'); LEGEND_CONSTANTS(:,7) = strpad('cnmax in component parameters (nanosiemens)'); LEGEND_CONSTANTS(:,8) = strpad('cx1lin in component parameters (per_second)'); LEGEND_CONSTANTS(:,9) = strpad('cx2 in component parameters (per_second)'); LEGEND_CONSTANTS(:,10) = strpad('ef in component parameters (per_second)'); LEGEND_CONSTANTS(:,11) = strpad('gl in component parameters (nanosiemens)'); LEGEND_CONSTANTS(:,12) = strpad('hmc_1 in component parameters (uM)'); LEGEND_CONSTANTS(:,13) = strpad('hmc_2 in component parameters (uM)'); LEGEND_CONSTANTS(:,14) = strpad('inf in component parameters (uM_per_picocoulomb)'); LEGEND_CONSTANTS(:,15) = strpad('inhmax in component parameters (dimensionless)'); LEGEND_CONSTANTS(:,16) = strpad('k_1 in component parameters (per_uM_per_second)'); LEGEND_CONSTANTS(:,17) = strpad('k_2 in component parameters (per_second)'); LEGEND_CONSTANTS(:,18) = strpad('kI in component parameters (uM)'); LEGEND_CONSTANTS(:,19) = strpad('kinh in component parameters (uM)'); LEGEND_CONSTANTS(:,20) = strpad('kinhcng in component parameters (uM)'); LEGEND_CONSTANTS(:,21) = strpad('n_1 in component parameters (dimensionless)'); LEGEND_CONSTANTS(:,22) = strpad('n_2 in component parameters (dimensionless)'); LEGEND_CONSTANTS(:,23) = strpad('nI in component parameters (dimensionless)'); LEGEND_CONSTANTS(:,24) = strpad('ninh in component parameters (dimensionless)'); LEGEND_CONSTANTS(:,25) = strpad('ninhcng in component parameters (dimensionless)'); LEGEND_CONSTANTS(:,26) = strpad('pd in component parameters (per_second)'); LEGEND_CONSTANTS(:,27) = strpad('r_1 in component parameters (per_second)'); LEGEND_CONSTANTS(:,28) = strpad('r_2 in component parameters (per_second)'); LEGEND_CONSTANTS(:,29) = strpad('smax in component parameters (uM_per_second)'); LEGEND_CONSTANTS(:,30) = strpad('V_Cl in component parameters (millivolt)'); LEGEND_CONSTANTS(:,31) = strpad('V_cng in component parameters (millivolt)'); LEGEND_CONSTANTS(:,32) = strpad('V_l in component parameters (millivolt)'); LEGEND_CONSTANTS(:,40) = strpad('F_vol in component parameters (picocoulomb_per_uM)'); LEGEND_CONSTANTS(:,33) = strpad('F in component parameters (coulombs_per_mole)'); LEGEND_CONSTANTS(:,34) = strpad('C_vol in component parameters (liter)'); LEGEND_ALGEBRAIC(:,10) = strpad('O_stim in component O_stim (uM)'); LEGEND_CONSTANTS(:,35) = strpad('od in component O_stim (uM)'); LEGEND_CONSTANTS(:,36) = strpad('t_0 in component O_stim (second)'); LEGEND_CONSTANTS(:,37) = strpad('t_1 in component O_stim (second)'); LEGEND_ALGEBRAIC(:,1) = strpad('H_0 in component O_stim (dimensionless)'); LEGEND_ALGEBRAIC(:,6) = strpad('H_1 in component O_stim (dimensionless)'); LEGEND_STATES(:,1) = strpad('bLR in component bLR (dimensionless)'); LEGEND_CONSTANTS(:,38) = strpad('R_tot in component bLR (dimensionless)'); LEGEND_STATES(:,2) = strpad('aG in component aG (dimensionless)'); LEGEND_CONSTANTS(:,39) = strpad('G_tot in component aG (dimensionless)'); LEGEND_ALGEBRAIC(:,2) = strpad('k_G in component k_G (per_second)'); LEGEND_ALGEBRAIC(:,7) = strpad('r_G in component r_G (per_second)'); LEGEND_STATES(:,3) = strpad('cAMP in component cAMP (uM)'); LEGEND_ALGEBRAIC(:,3) = strpad('synth in component synth (uM_per_second)'); LEGEND_ALGEBRAIC(:,8) = strpad('degrad in component degrad (uM_per_second)'); LEGEND_STATES(:,4) = strpad('aCaMK in component aCaMK (uM)'); LEGEND_STATES(:,5) = strpad('Ca in component Ca (uM)'); LEGEND_ALGEBRAIC(:,11) = strpad('I_CNG in component I_CNG (nanoampere)'); LEGEND_ALGEBRAIC(:,13) = strpad('J_NCX in component J_NCX (uM_per_second)'); LEGEND_ALGEBRAIC(:,4) = strpad('cc_1 in component cc_1 (uM_per_second)'); LEGEND_STATES(:,6) = strpad('CaCaM in component CaCaM (uM)'); LEGEND_ALGEBRAIC(:,5) = strpad('ck_1 in component ck_1 (uM_per_second)'); LEGEND_STATES(:,7) = strpad('V in component V (millivolt)'); LEGEND_ALGEBRAIC(:,12) = strpad('I_ClCa in component I_ClCa (nanoampere)'); LEGEND_ALGEBRAIC(:,14) = strpad('I_NCX in component I_NCX (nanoampere)'); LEGEND_ALGEBRAIC(:,15) = strpad('I_other in component I_other (nanoampere)'); LEGEND_ALGEBRAIC(:,9) = strpad('inhcng in component inhcng (dimensionless)'); LEGEND_RATES(:,1) = strpad('d/dt bLR in component bLR (dimensionless)'); LEGEND_RATES(:,2) = strpad('d/dt aG in component aG (dimensionless)'); LEGEND_RATES(:,3) = strpad('d/dt cAMP in component cAMP (uM)'); LEGEND_RATES(:,5) = strpad('d/dt Ca in component Ca (uM)'); LEGEND_RATES(:,6) = strpad('d/dt CaCaM in component CaCaM (uM)'); LEGEND_RATES(:,4) = strpad('d/dt aCaMK in component aCaMK (uM)'); LEGEND_RATES(:,7) = strpad('d/dt V in component V (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 = []; CONSTANTS(:,1) = 0.004; CONSTANTS(:,2) = 0.88; CONSTANTS(:,3) = 26; CONSTANTS(:,4) = 13; CONSTANTS(:,5) = 0.9; CONSTANTS(:,6) = 1; CONSTANTS(:,7) = 1; CONSTANTS(:,8) = 1; CONSTANTS(:,9) = 13; CONSTANTS(:,10) = 2; CONSTANTS(:,11) = 6; CONSTANTS(:,12) = 2; CONSTANTS(:,13) = 3; CONSTANTS(:,14) = 1.9; CONSTANTS(:,15) = 5; CONSTANTS(:,16) = 0.06; CONSTANTS(:,17) = 20; CONSTANTS(:,18) = 0.7; CONSTANTS(:,19) = 2; CONSTANTS(:,20) = 1; CONSTANTS(:,21) = 2; CONSTANTS(:,22) = 2; CONSTANTS(:,23) = 2; CONSTANTS(:,24) = 1.5; CONSTANTS(:,25) = 1.3; CONSTANTS(:,26) = 20; CONSTANTS(:,27) = 10; CONSTANTS(:,28) = 5; CONSTANTS(:,29) = 71; CONSTANTS(:,30) = -50; CONSTANTS(:,31) = 0; CONSTANTS(:,32) = -70; CONSTANTS(:,33) = 9.649e4; CONSTANTS(:,34) = 1e-13; CONSTANTS(:,35) = 20; CONSTANTS(:,36) = 0.5; CONSTANTS(:,37) = 1.5; STATES(:,1) = 0; CONSTANTS(:,38) = 1; STATES(:,2) = 0; CONSTANTS(:,39) = 1; STATES(:,3) = 1.35648992164649e-88; STATES(:,4) = 6.60756525051462e-8; STATES(:,5) = 5.09073088043779e-12; STATES(:,6) = 1.86113118246926e-13; STATES(:,7) = -70; CONSTANTS(:,40) = (1.00000e+12./1.00000).*(1.00000./1000.00).*CONSTANTS(:,33).*CONSTANTS(:,34); 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(:,4) = CONSTANTS(:,2).*STATES(:,5); RATES(:,6) = ALGEBRAIC(:,4) - CONSTANTS(:,3).*STATES(:,6); ALGEBRAIC(:,5) = CONSTANTS(:,4).*STATES(:,6); RATES(:,4) = ALGEBRAIC(:,5) - CONSTANTS(:,5).*STATES(:,4); ALGEBRAIC(:,2) = CONSTANTS(:,17).*STATES(:,1); ALGEBRAIC(:,7) = CONSTANTS(:,28).*STATES(:,2); RATES(:,2) = ALGEBRAIC(:,2).*(CONSTANTS(:,39) - STATES(:,2)) - ALGEBRAIC(:,7); ALGEBRAIC(:,3) = ( STATES(:,2).*CONSTANTS(:,29))./(1.00000+power(STATES(:,4)./CONSTANTS(:,19), CONSTANTS(:,24))); ALGEBRAIC(:,8) = CONSTANTS(:,26).*STATES(:,3); RATES(:,3) = ALGEBRAIC(:,3) - ALGEBRAIC(:,8); ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,36), 0.00000 }, 1.00000); ALGEBRAIC(:,6) = piecewise({VOI<CONSTANTS(:,37), 0.00000 }, 1.00000); ALGEBRAIC(:,10) = CONSTANTS(:,35).*(ALGEBRAIC(:,1) - ALGEBRAIC(:,6)); RATES(:,1) = CONSTANTS(:,16).*ALGEBRAIC(:,10).*(CONSTANTS(:,38) - STATES(:,1)) - CONSTANTS(:,27).*STATES(:,1); ALGEBRAIC(:,9) = 1.00000+( (CONSTANTS(:,15) - 1.00000).*power(STATES(:,6), CONSTANTS(:,25)))./(power(STATES(:,6), CONSTANTS(:,25))+power(CONSTANTS(:,20), CONSTANTS(:,25))); ALGEBRAIC(:,11) = (( CONSTANTS(:,7).*power(STATES(:,3), CONSTANTS(:,21)))./(power(STATES(:,3), CONSTANTS(:,21))+power( ALGEBRAIC(:,9).*CONSTANTS(:,12), CONSTANTS(:,21)))).*(1.00000./1000.00).*(CONSTANTS(:,31) - STATES(:,7)); ALGEBRAIC(:,13) = CONSTANTS(:,10).*STATES(:,5); RATES(:,5) = ( (1000.00./1.00000).*CONSTANTS(:,14).*ALGEBRAIC(:,11) - ALGEBRAIC(:,13)) - (ALGEBRAIC(:,4) - CONSTANTS(:,3).*STATES(:,6)); ALGEBRAIC(:,12) = (( CONSTANTS(:,6).*power(STATES(:,5), CONSTANTS(:,22)))./(power(STATES(:,5), CONSTANTS(:,22))+power(CONSTANTS(:,13), CONSTANTS(:,22)))).*(1.00000./1000.00).*(CONSTANTS(:,30) - STATES(:,7)); ALGEBRAIC(:,14) = (1.00000./1000.00).*CONSTANTS(:,40).*ALGEBRAIC(:,13); ALGEBRAIC(:,15) = CONSTANTS(:,11).*(1.00000./1000.00).*(CONSTANTS(:,32) - STATES(:,7)); RATES(:,7) = (1000.00./1.00000).*(1.00000./CONSTANTS(:,1)).*(ALGEBRAIC(:,11)+ALGEBRAIC(:,12)+ALGEBRAIC(:,14)+ALGEBRAIC(:,15)); 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(:,4) = CONSTANTS(:,2).*STATES(:,5); ALGEBRAIC(:,5) = CONSTANTS(:,4).*STATES(:,6); ALGEBRAIC(:,2) = CONSTANTS(:,17).*STATES(:,1); ALGEBRAIC(:,7) = CONSTANTS(:,28).*STATES(:,2); ALGEBRAIC(:,3) = ( STATES(:,2).*CONSTANTS(:,29))./(1.00000+power(STATES(:,4)./CONSTANTS(:,19), CONSTANTS(:,24))); ALGEBRAIC(:,8) = CONSTANTS(:,26).*STATES(:,3); ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,36), 0.00000 }, 1.00000); ALGEBRAIC(:,6) = piecewise({VOI<CONSTANTS(:,37), 0.00000 }, 1.00000); ALGEBRAIC(:,10) = CONSTANTS(:,35).*(ALGEBRAIC(:,1) - ALGEBRAIC(:,6)); ALGEBRAIC(:,9) = 1.00000+( (CONSTANTS(:,15) - 1.00000).*power(STATES(:,6), CONSTANTS(:,25)))./(power(STATES(:,6), CONSTANTS(:,25))+power(CONSTANTS(:,20), CONSTANTS(:,25))); ALGEBRAIC(:,11) = (( CONSTANTS(:,7).*power(STATES(:,3), CONSTANTS(:,21)))./(power(STATES(:,3), CONSTANTS(:,21))+power( ALGEBRAIC(:,9).*CONSTANTS(:,12), CONSTANTS(:,21)))).*(1.00000./1000.00).*(CONSTANTS(:,31) - STATES(:,7)); ALGEBRAIC(:,13) = CONSTANTS(:,10).*STATES(:,5); ALGEBRAIC(:,12) = (( CONSTANTS(:,6).*power(STATES(:,5), CONSTANTS(:,22)))./(power(STATES(:,5), CONSTANTS(:,22))+power(CONSTANTS(:,13), CONSTANTS(:,22)))).*(1.00000./1000.00).*(CONSTANTS(:,30) - STATES(:,7)); ALGEBRAIC(:,14) = (1.00000./1000.00).*CONSTANTS(:,40).*ALGEBRAIC(:,13); ALGEBRAIC(:,15) = CONSTANTS(:,11).*(1.00000./1000.00).*(CONSTANTS(:,32) - STATES(:,7)); 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