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 3 entries in each of the rate and state variable arrays. % There are a total of 19 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 (hour)'); LEGEND_ALGEBRAIC(:,1) = strpad('Qv in component v (per_second)'); LEGEND_STATES(:,1) = strpad('Vv in component v (mV)'); LEGEND_CONSTANTS(:,1) = strpad('tau_v in component v (second)'); LEGEND_CONSTANTS(:,2) = strpad('v_vm in component v (mV_second)'); LEGEND_CONSTANTS(:,3) = strpad('awake_start in component v (hour)'); LEGEND_CONSTANTS(:,4) = strpad('awake_end in component v (hour)'); LEGEND_ALGEBRAIC(:,2) = strpad('Qm in component m (per_second)'); LEGEND_CONSTANTS(:,5) = strpad('Qmax in component model_parameters (per_second)'); LEGEND_ALGEBRAIC(:,4) = strpad('D in component D (mV)'); LEGEND_CONSTANTS(:,6) = strpad('theta in component model_parameters (mV)'); LEGEND_CONSTANTS(:,7) = strpad('sigma in component model_parameters (mV)'); LEGEND_STATES(:,2) = strpad('Vm in component m (mV)'); LEGEND_CONSTANTS(:,8) = strpad('tau_m in component m (second)'); LEGEND_CONSTANTS(:,9) = strpad('v_mv in component m (mV_second)'); LEGEND_CONSTANTS(:,10) = strpad('A in component m (mV)'); LEGEND_CONSTANTS(:,11) = strpad('awake_start in component m (hour)'); LEGEND_CONSTANTS(:,12) = strpad('awake_end in component m (hour)'); LEGEND_STATES(:,3) = strpad('H in component H (nM)'); LEGEND_CONSTANTS(:,13) = strpad('chi in component H (hour)'); LEGEND_CONSTANTS(:,14) = strpad('mu in component H (nM_second)'); LEGEND_ALGEBRAIC(:,3) = strpad('C in component D (dimensionless)'); LEGEND_CONSTANTS(:,15) = strpad('c0 in component D (dimensionless)'); LEGEND_CONSTANTS(:,19) = strpad('omega in component D (per_hour)'); LEGEND_CONSTANTS(:,16) = strpad('alpha in component D (hour)'); LEGEND_CONSTANTS(:,17) = strpad('v_vc in component D (mV)'); LEGEND_CONSTANTS(:,18) = strpad('v_vh in component D (mV_per_nM)'); LEGEND_RATES(:,1) = strpad('d/dt Vv in component v (mV)'); LEGEND_RATES(:,2) = strpad('d/dt Vm in component m (mV)'); LEGEND_RATES(:,3) = strpad('d/dt H in component H (nM)'); 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) = -12.5; CONSTANTS(:,1) = 10.0; CONSTANTS(:,2) = -2.1; CONSTANTS(:,3) = 167.04; CONSTANTS(:,4) = 240.0; CONSTANTS(:,5) = 100.0; CONSTANTS(:,6) = 10.0; CONSTANTS(:,7) = 3.0; STATES(:,2) = 0.0; CONSTANTS(:,8) = 10.0; CONSTANTS(:,9) = -1.8; CONSTANTS(:,10) = 1.3; CONSTANTS(:,11) = 160.0; CONSTANTS(:,12) = 240.0; STATES(:,3) = 15.0; CONSTANTS(:,13) = 45.0; CONSTANTS(:,14) = 4.4; CONSTANTS(:,15) = 4.5; CONSTANTS(:,16) = 0; CONSTANTS(:,17) = -2.9; CONSTANTS(:,18) = 1.0; CONSTANTS(:,19) = ( 2.00000.* pi)./24.0000; 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(:,5)./(1.00000+exp( - (STATES(:,1) - CONSTANTS(:,6))./CONSTANTS(:,7))); RATES(:,2) = piecewise({VOI>=CONSTANTS(:,11)&VOI<CONSTANTS(:,12), 0.00000 }, ((CONSTANTS(:,10)+ CONSTANTS(:,9).*ALGEBRAIC(:,1)) - STATES(:,2))./(CONSTANTS(:,8)./3600.00)); ALGEBRAIC(:,2) = CONSTANTS(:,5)./(1.00000+exp( - (STATES(:,2) - CONSTANTS(:,6))./CONSTANTS(:,7))); RATES(:,3) = ( CONSTANTS(:,14).*ALGEBRAIC(:,2) - STATES(:,3))./CONSTANTS(:,13); ALGEBRAIC(:,3) = CONSTANTS(:,15)+cos( CONSTANTS(:,19).*(VOI - CONSTANTS(:,16))); ALGEBRAIC(:,4) = CONSTANTS(:,17).*ALGEBRAIC(:,3)+ CONSTANTS(:,18).*STATES(:,3); RATES(:,1) = piecewise({VOI>=CONSTANTS(:,3)&VOI<CONSTANTS(:,4), 0.00000 }, (( CONSTANTS(:,2).*ALGEBRAIC(:,2)+ALGEBRAIC(:,4)) - STATES(:,1))./(CONSTANTS(:,1)./3600.00)); 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(:,5)./(1.00000+exp( - (STATES(:,1) - CONSTANTS(:,6))./CONSTANTS(:,7))); ALGEBRAIC(:,2) = CONSTANTS(:,5)./(1.00000+exp( - (STATES(:,2) - CONSTANTS(:,6))./CONSTANTS(:,7))); ALGEBRAIC(:,3) = CONSTANTS(:,15)+cos( CONSTANTS(:,19).*(VOI - CONSTANTS(:,16))); ALGEBRAIC(:,4) = CONSTANTS(:,17).*ALGEBRAIC(:,3)+ CONSTANTS(:,18).*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