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 =22; end % There are a total of 11 entries in each of the rate and state variable arrays. % There are a total of 25 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_CONSTANTS(:,1) = strpad('kappa_R_1a_cGMP in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,2) = strpad('kappa_R_1b_cGMP in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,3) = strpad('kappa_R_2a_cGMP in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,4) = strpad('kappa_R_2b_cGMP in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,5) = strpad('kappa_R_1_sGC in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,6) = strpad('kappa_R_2_sGC in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,7) = strpad('kappa_R_3_sGC in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,8) = strpad('kappa_R_4_sGC in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,9) = strpad('kappa_R_DNO_sGC in component BG_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,10) = strpad('K_GTP in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,11) = strpad('K_E5c in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,12) = strpad('K_cGMP in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,13) = strpad('K_PDE in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,14) = strpad('K_GTP_E5c in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,15) = strpad('K_cGMP_PDE in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,16) = strpad('K_GMP in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,17) = strpad('K_Eb in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,18) = strpad('K_NO in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,19) = strpad('K_E6c in component BG_parameters (per_fmol)'); LEGEND_CONSTANTS(:,20) = strpad('K_NO_product in component BG_parameters (per_fmol)'); LEGEND_VOI = strpad('t in component environment (second)'); LEGEND_CONSTANTS(:,21) = strpad('vol_myo in component environment (pL)'); LEGEND_STATES(:,1) = strpad('q_cGMP in component environment (fmol)'); LEGEND_STATES(:,2) = strpad('q_GTP in component environment (fmol)'); LEGEND_STATES(:,3) = strpad('q_E5c in component environment (fmol)'); LEGEND_STATES(:,4) = strpad('q_PDE in component environment (fmol)'); LEGEND_STATES(:,5) = strpad('q_GTP_E5c in component environment (fmol)'); LEGEND_STATES(:,6) = strpad('q_cGMP_PDE in component environment (fmol)'); LEGEND_STATES(:,7) = strpad('q_GMP in component environment (fmol)'); LEGEND_STATES(:,8) = strpad('q_Eb in component environment (fmol)'); LEGEND_STATES(:,9) = strpad('q_NO in component environment (fmol)'); LEGEND_STATES(:,10) = strpad('q_E6c in component environment (fmol)'); LEGEND_STATES(:,11) = strpad('q_NO_product in component environment (fmol)'); LEGEND_ALGEBRAIC(:,8) = strpad('v_R_1a_cGMP in component cGMP (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,9) = strpad('v_R_1b_cGMP in component cGMP (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,10) = strpad('v_R_2a_cGMP in component cGMP (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,11) = strpad('v_R_2b_cGMP in component cGMP (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,18) = strpad('v_R_1_sGC in component sGC (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,19) = strpad('v_R_2_sGC in component sGC (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,20) = strpad('v_R_3_sGC in component sGC (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,21) = strpad('v_R_4_sGC in component sGC (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,22) = strpad('v_R_DNO_sGC in component sGC (fmol_per_sec)'); LEGEND_CONSTANTS(:,22) = strpad('v_NO_generation in component environment (fmol_per_sec)'); LEGEND_CONSTANTS(:,23) = strpad('R in component constants (J_per_K_per_mol)'); LEGEND_CONSTANTS(:,24) = strpad('T in component constants (kelvin)'); LEGEND_CONSTANTS(:,25) = strpad('F in component constants (C_per_mol)'); LEGEND_ALGEBRAIC(:,1) = strpad('mu_GTP in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,2) = strpad('mu_E5c in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,3) = strpad('mu_cGMP in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,4) = strpad('mu_PDE in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,5) = strpad('mu_GTP_E5c in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,6) = strpad('mu_cGMP_PDE in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,7) = strpad('mu_GMP in component cGMP (J_per_mol)'); LEGEND_ALGEBRAIC(:,12) = strpad('mu_Eb in component sGC (J_per_mol)'); LEGEND_ALGEBRAIC(:,13) = strpad('mu_NO in component sGC (J_per_mol)'); LEGEND_ALGEBRAIC(:,14) = strpad('mu_E6c in component sGC (J_per_mol)'); LEGEND_ALGEBRAIC(:,15) = strpad('mu_E5c in component sGC (J_per_mol)'); LEGEND_ALGEBRAIC(:,16) = strpad('mu_cGMP in component sGC (J_per_mol)'); LEGEND_ALGEBRAIC(:,17) = strpad('mu_NO_product in component sGC (J_per_mol)'); LEGEND_RATES(:,1) = strpad('d/dt q_cGMP in component environment (fmol)'); LEGEND_RATES(:,2) = strpad('d/dt q_GTP in component environment (fmol)'); LEGEND_RATES(:,3) = strpad('d/dt q_E5c in component environment (fmol)'); LEGEND_RATES(:,4) = strpad('d/dt q_PDE in component environment (fmol)'); LEGEND_RATES(:,5) = strpad('d/dt q_GTP_E5c in component environment (fmol)'); LEGEND_RATES(:,6) = strpad('d/dt q_cGMP_PDE in component environment (fmol)'); LEGEND_RATES(:,7) = strpad('d/dt q_GMP in component environment (fmol)'); LEGEND_RATES(:,8) = strpad('d/dt q_Eb in component environment (fmol)'); LEGEND_RATES(:,9) = strpad('d/dt q_NO in component environment (fmol)'); LEGEND_RATES(:,10) = strpad('d/dt q_E6c in component environment (fmol)'); LEGEND_RATES(:,11) = strpad('d/dt q_NO_product in component environment (fmol)'); 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) = 192.663; CONSTANTS(:,2) = 0.00328297; CONSTANTS(:,3) = 56591.2; CONSTANTS(:,4) = 0.0110353; CONSTANTS(:,5) = 3.61127e+06; CONSTANTS(:,6) = 0.00328297; CONSTANTS(:,7) = 4.92446; CONSTANTS(:,8) = 0.0361127; CONSTANTS(:,9) = 0.01; CONSTANTS(:,10) = 17040; CONSTANTS(:,11) = 0.304602; CONSTANTS(:,12) = 1; CONSTANTS(:,13) = 17.6706; CONSTANTS(:,14) = 5190.42; CONSTANTS(:,15) = 35.3412; CONSTANTS(:,16) = 0.0051282; CONSTANTS(:,17) = 0.0276911; CONSTANTS(:,18) = 1; CONSTANTS(:,19) = 30.4602; CONSTANTS(:,20) = 0.1; CONSTANTS(:,21) = 1; STATES(:,1) = 1e-6; STATES(:,2) = 0.0005; STATES(:,3) = 1e-16; STATES(:,4) = 1e-10; STATES(:,5) = 1e-16; STATES(:,6) = 1e-16; STATES(:,7) = 1e-16; STATES(:,8) = 1e-6; STATES(:,9) = 0.00836; STATES(:,10) = 1e-16; STATES(:,11) = 1e-16; CONSTANTS(:,22) = 0.000114; CONSTANTS(:,23) = 8.31; CONSTANTS(:,24) = 310; CONSTANTS(:,25) = 96485; 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(:,1) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,10).*STATES(:,2)); ALGEBRAIC(:,2) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3)); ALGEBRAIC(:,5) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,14).*STATES(:,5)); ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); RATES(:,2) = - ALGEBRAIC(:,8); ALGEBRAIC(:,3) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1)); ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); RATES(:,5) = ALGEBRAIC(:,8) - ALGEBRAIC(:,9); ALGEBRAIC(:,4) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,13).*STATES(:,4)); ALGEBRAIC(:,6) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,15).*STATES(:,6)); ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,7) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,16).*STATES(:,7)); ALGEBRAIC(:,11) = CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); RATES(:,4) = - ALGEBRAIC(:,10)+ALGEBRAIC(:,11); RATES(:,6) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11); RATES(:,7) = ALGEBRAIC(:,11); ALGEBRAIC(:,12) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,17).*STATES(:,8)); ALGEBRAIC(:,13) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,18).*STATES(:,9)); ALGEBRAIC(:,14) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,19).*STATES(:,10)); ALGEBRAIC(:,18) = CONSTANTS(:,5).*(exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,15) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3)); ALGEBRAIC(:,19) = CONSTANTS(:,6).*(exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,15)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,20) = CONSTANTS(:,7).*(exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); RATES(:,10) = (ALGEBRAIC(:,18) - ALGEBRAIC(:,19)) - ALGEBRAIC(:,20); ALGEBRAIC(:,16) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1)); ALGEBRAIC(:,21) = CONSTANTS(:,8).*(exp((ALGEBRAIC(:,15)+ ALGEBRAIC(:,16).*2.00000)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); RATES(:,1) = ((ALGEBRAIC(:,9) - ALGEBRAIC(:,10)) - ALGEBRAIC(:,11)) - 2.00000.*ALGEBRAIC(:,21); RATES(:,3) = ( - ALGEBRAIC(:,8)+ALGEBRAIC(:,9)+ALGEBRAIC(:,19)+ALGEBRAIC(:,20)) - ALGEBRAIC(:,21); RATES(:,8) = - ALGEBRAIC(:,18)+ALGEBRAIC(:,21); ALGEBRAIC(:,17) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,20).*STATES(:,11)); ALGEBRAIC(:,22) = CONSTANTS(:,9).*(exp(ALGEBRAIC(:,13)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); RATES(:,9) = (( - ALGEBRAIC(:,18)+ALGEBRAIC(:,21)) - ALGEBRAIC(:,22))+CONSTANTS(:,22); RATES(:,11) = ALGEBRAIC(:,22); 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(:,1) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,10).*STATES(:,2)); ALGEBRAIC(:,2) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3)); ALGEBRAIC(:,5) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,14).*STATES(:,5)); ALGEBRAIC(:,8) = CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,3) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1)); ALGEBRAIC(:,9) = CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,4) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,13).*STATES(:,4)); ALGEBRAIC(:,6) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,15).*STATES(:,6)); ALGEBRAIC(:,10) = CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,7) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,16).*STATES(:,7)); ALGEBRAIC(:,11) = CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,12) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,17).*STATES(:,8)); ALGEBRAIC(:,13) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,18).*STATES(:,9)); ALGEBRAIC(:,14) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,19).*STATES(:,10)); ALGEBRAIC(:,18) = CONSTANTS(:,5).*(exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,15) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,11).*STATES(:,3)); ALGEBRAIC(:,19) = CONSTANTS(:,6).*(exp(ALGEBRAIC(:,14)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,15)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,20) = CONSTANTS(:,7).*(exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,16) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,12).*STATES(:,1)); ALGEBRAIC(:,21) = CONSTANTS(:,8).*(exp((ALGEBRAIC(:,15)+ ALGEBRAIC(:,16).*2.00000)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,13))./( CONSTANTS(:,23).*CONSTANTS(:,24)))); ALGEBRAIC(:,17) = CONSTANTS(:,23).*CONSTANTS(:,24).*log( CONSTANTS(:,20).*STATES(:,11)); ALGEBRAIC(:,22) = CONSTANTS(:,9).*(exp(ALGEBRAIC(:,13)./( CONSTANTS(:,23).*CONSTANTS(:,24))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,23).*CONSTANTS(:,24)))); 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